diff options
92 files changed, 6050 insertions, 533 deletions
diff --git a/app-admin/eselect/ChangeLog b/app-admin/eselect/ChangeLog index a6e529631..cd837bfe4 100644 --- a/app-admin/eselect/ChangeLog +++ b/app-admin/eselect/ChangeLog @@ -2,6 +2,16 @@ # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: /var/cvsroot/gentoo-x86/app-admin/eselect/ChangeLog,v 1.179 2011/01/22 21:38:52 ulm Exp $ + 12 Sep 2013; Sébastien Fabbro <bicatali@gentoo.org> eselect-1.3.7-r100.ebuild, + eselect-1.3.8-r100.ebuild: + sync with tree + +*eselect-1.3.8-r100 (02 Sep 2013) + + 02 Sep 2013; Andrew Savchenko <bircoph@gmail.com> +eselect-1.3.8-r100.ebuild, + +files/eselect-1.3.8-alternatives.patch: + Bump to latest eselect. + 18 Jul 2013; Sébastien Fabbro <bicatali@gentoo.org> eselect-1.3.7-r100.ebuild: app-admin/eselect: Re-add emacs and vim flags diff --git a/app-admin/eselect/Manifest b/app-admin/eselect/Manifest index 3c29d5ad5..3d2e95c08 100644 --- a/app-admin/eselect/Manifest +++ b/app-admin/eselect/Manifest @@ -1 +1,2 @@ DIST eselect-1.3.7.tar.xz 166596 SHA256 68b3c9cf3f71633ca81c4d0edd64a77e02dc8d6b9a48641e59f0bf02378a0075 SHA512 909d79d76f144181895853ce132147daeee4ba6caf05bf08963aef147ef2d00be100d6181887d139614f1bebf15f0738ea58e755656b55b7d9d967d399ce72f0 WHIRLPOOL 82d7575e8bbcb2186ef1452e3edb07b7c242c4d14475da0c5867acc70d275e5fb9e166a2b0addb54fb3586eddabcf1eec1e208964db5489e4250bf1f8ad39468 +DIST eselect-1.3.8.tar.xz 168040 SHA256 d0c50bfe0faaddc54fc184f698ee74a6029a21f5155c4670a2bea3ead954c138 SHA512 159bf3ddb05b1966318eaf62d09e454a024f8be7ead2300392abbcbaa54ef748a1c4db1b2f96162994bcab43071396eb96a0b47268f04cb8557f8804818da18e WHIRLPOOL 9c4da0bde2ae2b53e8949d59b13498f55ef2c849dcc8cac503a7d0dda2511311d94dfc7aa27a97432f13aa0b430fec0ab280594dc165bbb40e573dce8c8a74b0 diff --git a/app-admin/eselect/eselect-1.3.7-r100.ebuild b/app-admin/eselect/eselect-1.3.7-r100.ebuild index b03fd64d8..4a8feba43 100644 --- a/app-admin/eselect/eselect-1.3.7-r100.ebuild +++ b/app-admin/eselect/eselect-1.3.7-r100.ebuild @@ -7,7 +7,7 @@ EAPI=5 inherit autotools eutils bash-completion-r1 DESCRIPTION="Gentoo's multi-purpose configuration and management tool" -HOMEPAGE="https://wiki.gentoo.org/wiki/Project:Eselect" +HOMEPAGE="http://wiki.gentoo.org/wiki/Project:Eselect" SRC_URI="mirror://gentoo/${P}.tar.xz" LICENSE="GPL-2+ || ( GPL-2+ CC-BY-SA-2.5 )" diff --git a/app-admin/eselect/eselect-1.3.8-r100.ebuild b/app-admin/eselect/eselect-1.3.8-r100.ebuild new file mode 100644 index 000000000..19efbcad0 --- /dev/null +++ b/app-admin/eselect/eselect-1.3.8-r100.ebuild @@ -0,0 +1,72 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit autotools eutils bash-completion-r1 + +DESCRIPTION="Gentoo's multi-purpose configuration and management tool" +HOMEPAGE="http://wiki.gentoo.org/wiki/Project:Eselect" +SRC_URI="mirror://gentoo/${P}.tar.xz" + +LICENSE="GPL-2+ || ( GPL-2+ CC-BY-SA-2.5 )" +SLOT="0" +KEYWORDS="~alpha ~amd64 ~arm ~hppa ~ia64 ~m68k ~mips ~ppc ~ppc64 ~s390 ~sh ~sparc ~x86 ~ppc-aix ~amd64-fbsd ~sparc-fbsd ~x86-fbsd ~x64-freebsd ~x86-freebsd ~hppa-hpux ~ia64-hpux ~x86-interix ~amd64-linux ~arm-linux ~ia64-linux ~x86-linux ~ppc-macos ~x64-macos ~x86-macos ~m68k-mint ~sparc-solaris ~sparc64-solaris ~x64-solaris ~x86-solaris" +IUSE="doc emacs vim-syntax" + +RDEPEND="sys-apps/sed + || ( + sys-apps/coreutils + sys-freebsd/freebsd-bin + app-misc/realpath + )" +DEPEND="${RDEPEND} + app-arch/xz-utils + doc? ( dev-python/docutils )" +RDEPEND="!app-admin/eselect-news + ${RDEPEND} + sys-apps/file + sys-libs/ncurses" + +PDEPEND="emacs? ( app-emacs/eselect-mode ) + vim-syntax? ( app-vim/eselect-syntax )" + +src_prepare() { + epatch "${FILESDIR}"/${P}-alternatives.patch + AT_M4DIR="." eautoreconf +} + +src_compile() { + emake + use doc && emake html +} + +src_install() { + emake DESTDIR="${D}" install + newbashcomp misc/${PN}.bashcomp ${PN} + dodoc AUTHORS ChangeLog NEWS README TODO doc/*.txt + use doc && dohtml *.html doc/* + + # needed by news module + keepdir /var/lib/gentoo/news + if ! use prefix; then + fowners root:portage /var/lib/gentoo/news + fperms g+w /var/lib/gentoo/news + fi + + # band aid for prefix + if use prefix; then + cd "${ED}"/usr/share/eselect/libs + sed -i "s:ALTERNATIVESDIR_ROOTLESS=\"${EPREFIX}:ALTERNATIVESDIR_ROOTLESS=\":" alternatives.bash || die + fi +} + +pkg_postinst() { + # fowners in src_install doesn't work for the portage group: + # merging changes the group back to root + if ! use prefix; then + chgrp portage "${EROOT}/var/lib/gentoo/news" \ + && chmod g+w "${EROOT}/var/lib/gentoo/news" + fi +} diff --git a/app-admin/eselect/files/eselect-1.3.8-alternatives.patch b/app-admin/eselect/files/eselect-1.3.8-alternatives.patch new file mode 100644 index 000000000..1e3b0ea77 --- /dev/null +++ b/app-admin/eselect/files/eselect-1.3.8-alternatives.patch @@ -0,0 +1,616 @@ +Index: bin/eselect.in +=================================================================== +--- bin/eselect.in (revision 863) ++++ bin/eselect.in (working copy) +@@ -22,10 +22,15 @@ + # Where are modules installed by default? + ESELECT_DEFAULT_MODULES_PATH="${ESELECT_DATA_PATH}/modules" + ++# Where are auto-generated modules placed? (e.g. from alternatives-2.eclass) ++ESELECT_AUTO_GENERATED_MODULES_PATH="${ESELECT_DEFAULT_MODULES_PATH}/auto" ++ + # Look in these places for modules +-ESELECT_MODULES_PATH=( \ +- "${HOME}/.eselect/modules" \ +- "${ESELECT_DEFAULT_MODULES_PATH}" ) ++ESELECT_MODULES_PATH=( ++ "${HOME}/.eselect/modules" ++ "${ESELECT_DEFAULT_MODULES_PATH}" ++ "${ESELECT_AUTO_GENERATED_MODULES_PATH}" ++) + + # Look in this place for libraries + ESELECT_CORE_PATH="${ESELECT_DATA_PATH}/libs" +--- bin/Makefile.am.orig 2013-09-02 14:35:05.328684465 +0400 ++++ bin/Makefile.am 2013-09-02 14:49:50.895842067 +0400 +@@ -4,6 +4,7 @@ + dosed = @SED@ -e 's,\@BASH\@,$(BASH),g' \ + -e 's,\@DATADIR\@,$(datadir),g' \ + -e 's,\@EPREFIX\@,$(EPREFIX),g' \ ++ -e 's,\@LIBEXECDIR\@,$(datadir),g' \ + -e 's,\@VERSION\@,$(VERSION)$(EXTRAVERSION),g' + + % : %.in +Index: libs/Makefile.am +=================================================================== +--- libs/Makefile.am (revision 863) ++++ libs/Makefile.am (working copy) +@@ -1,6 +1,7 @@ + eselectlibsdir = $(datadir)/$(PACKAGE_NAME)/libs/ + + eselectlibs_DATA = \ ++ alternatives.bash \ + config.bash \ + core.bash \ + default.eselect \ +@@ -14,6 +15,7 @@ + tests.bash + + EXTRA_DIST = \ ++ alternatives.bash.in \ + config.bash.in \ + core.bash.in \ + default.eselect.in \ +@@ -30,7 +32,8 @@ + -e 's,\@SED\@,@SED@,g' \ + -e 's,\@PORTAGEQ\@,@PORTAGEQ@,g' \ + -e 's,\@ENV_UPDATE\@,@ENV_UPDATE@,g' \ +- -e 's,\@CANONICALISE\@,@CANONICALISE@,g' ++ -e 's,\@CANONICALISE\@,@CANONICALISE@,g' \ ++ -e 's,\@sysconfdir\@,@sysconfdir@,g' + + %.bash : %.bash.in + @$(dosed) $< > $@ +--- libs/alternatives.bash.in.orig 1970-01-01 01:00:00.000000000 +0100 ++++ libs/alternatives.bash.in 2011-09-06 18:55:43.000000000 +0100 +@@ -0,0 +1,550 @@ ++# Copyright 2008 Mike Kelly ++# Copyright 2009 David Leverton ++# Copyright 2010 Bo Ørsted Andresen ++# 2010: Adapted to eselect Sebastien Fabbro (who doesn't like copyrights) ++# Distributed under the terms of the GNU General Public License v2 ++ ++inherit config output path-manipulation ++ ++ALTERNATIVESDIR_ROOTLESS="@sysconfdir@/env.d/alternatives" ++ALTERNATIVESDIR="${EROOT}${ALTERNATIVESDIR_ROOTLESS}" ++ ++get_current_provider() { ++ local dieprefix="Could not determine current provider for ${ALTERNATIVE}" ++ if [[ -L ${ALTERNATIVESDIR}/${ALTERNATIVE}/_current ]]; then ++ local provider=$(readlink "${ALTERNATIVESDIR}/${ALTERNATIVE}/_current" || die "${dieprefix}: readlink ${symlink} failed") ++ [[ ${provider} == */* ]] && die "${dieprefix}: malformed target for ${symlink}" ++ ++ if [[ -L ${ALTERNATIVESDIR}/${ALTERNATIVE}/${provider} || ++ ( -e ${ALTERNATIVESDIR}/${ALTERNATIVE}/${provider} && ! -d ${ALTERNATIVESDIR}/${ALTERNATIVE}/${provider} ) ]]; then ++ die "${dieprefix}: ${ALTERNATIVESDIR}/${ALTERNATIVE}/${provider} is not a directory" ++ fi ++ ++ echo "${provider}" ++ ++ elif [[ -e ${ALTERNATIVESDIR}/${ALTERNATIVE}/_current ]]; then ++ die "${dieprefix}: ${ALTERNATIVESDIR}/${ALTERNATIVE}/_current is not a symlink" ++ fi ++} ++ ++compare_importance() { ++ local IFS=. ++ local a=( ${1} ) b=( ${2} ) ++ local -i i=0 ++ while (( i<${#a[@]} && i<${#b[@]} )); do ++ if (( a[i]<b[i] )); then ++ return 0 ++ elif (( a[i]>b[i] )); then ++ return 1 ++ fi ++ i+=1 ++ done ++ (( i<${#b[@]} )) ++} ++ ++sort_providers() { ++ local begin=${1:-0} ++ local count=${2:-${#providers[@]}} ++ [[ ${count} -le 1 ]] && return 0 ++ sort_providers ${begin} $((count/2)) ++ sort_providers $((begin+count/2)) $((count-count/2)) ++ local left=( "${providers[@]:begin:count/2}" ) ++ local right=( "${providers[@]:begin+count/2:count-count/2}" ) ++ local -i x i=0 j=0 ++ for (( x=begin; x<begin+count; ++x )); do ++ if (( j>=${#right[@]} )) || { (( i<${#left[@]} )) && compare_importance "${left[i]%%:*}" "${right[j]%%:*}"; }; then ++ providers[x]=${left[i++]} ++ else ++ providers[x]=${right[j++]} ++ fi ++ done ++} ++ ++get_providers() { ++ local p= importance providers=() ++ for p in "${ALTERNATIVESDIR}/${ALTERNATIVE}"/* ; do ++ [[ -d ${p} && ! -L ${p} ]] || continue ++ p=${p##*/} ++ ++ importance=$(< "${ALTERNATIVESDIR}/${ALTERNATIVE}/${p}/_importance") ++ importance=${importance:-0} ++ [[ "${importance}" =~ ^[0123456789]+(\.[0123456789]+)*$ ]] || die "_importance (${importance}) for ${p} is not a dot-separated list of integers" ++ ++ providers+=( "${importance}:${p}" ) ++ done ++ ++ sort_providers ++ for (( p=${#providers[@]}-1 ; p>=0 ; --p )); do ++ echo "${providers[p]#*:}" ++ done ++} ++ ++### show action ### ++describe_show() { ++ echo "Show the current provider in use for ${ALTERNATIVE}" ++} ++ ++do_show() { ++ [[ -z "${ALTERNATIVE}" ]] && die "Need to set ALTERNATIVE in the eselect module" ++ local current="$(get_current_provider)" ++ if [[ -z "${current}" ]] ; then ++ echo "(none)" ++ return 2 ++ fi ++ echo "${current}" ++} ++ ++options_show() { ++ : ++} ++ ++### list action ### ++describe_list() { ++ echo "Lists all available providers for ${ALTERNATIVE}" ++} ++ ++do_list() { ++ [[ -z "${ALTERNATIVE}" ]] && die "Need to set ALTERNATIVE in the eselect module" ++ local n cur= providers=( $(get_providers) ) ++ write_list_start "Available providers for ${ALTERNATIVE}:" ++ ++ cur="$(get_current_provider)" ++ ++ if [[ -n "${providers[@]}" ]] ; then ++ for (( n = 0 ; n < ${#providers[@]} ; ++n )) ; do ++ [[ ${cur} == "${providers[${n}]}" ]] && \ ++ providers[${n}]="${providers[${n}]} $(highlight '*')" ++ done ++ write_numbered_list "${providers[@]}" ++ else ++ write_kv_list_entry "(none found)" "" ++ fi ++} ++ ++options_list() { ++ : ++} ++ ++### files action ### ++describe_files() { ++ echo "Lists symlinks provided by the currently selected provider" ++} ++ ++do_files() { ++ [[ -z "${ALTERNATIVE}" ]] && die "Need to set ALTERNATIVE in the eselect module" ++ ++ local cur="$(get_current_provider)" p= ++ [[ -n "${cur}" ]] || die -q "No selected provider, hence no symlinks provided" ++ local dieprefix="Could not list symlinks provided for ${ALTERNATIVE}" ++ ++ local errors symlink rootsymlink ++ while read -r -d '' symlink; do ++ rootsymlink="${EROOT}${symlink}" ++ rootsymlink=${rootsymlink//+(\/)/\/} ++ echo "${rootsymlink}" ++ if [[ -L ${rootsymlink} ]]; then ++ if [[ ! -e ${rootsymlink} ]]; then ++ write_error_msg "${rootsymlink} is dangling symlink" ++ errors=yes ++ fi ++ elif [[ -d ${rootsymlink} ]]; then ++ write_error_msg "${rootsymlink} is a directory" ++ errors=yes ++ elif [[ -e ${rootsymlink} ]]; then ++ write_error_msg "${rootsymlink} exists but is not a symlink" ++ errors=yes ++ else ++ write_error_msg "${rootsymlink} does not exist" ++ errors=yes ++ fi ++ done <"${ALTERNATIVESDIR}/${ALTERNATIVE}/_current_list" ++} ++ ++options_files() { ++ : ++} ++ ++### set action ### ++ ++describe_set() { ++ echo "Sets a provider for ${ALTERNATIVE}" ++} ++ ++describe_set_parameters() { ++ echo "[ --force ] <provider>" ++} ++ ++describe_set_options() { ++ echo "--force : overwrite or remove existing non-symlink files (but not directories) if necessary" ++ echo "<provider> : the name of the provider to use or the index of the provider preceeded by a dash" ++} ++ ++do_set() { ++ [[ -z "${ALTERNATIVE}" ]] && die "Need to set ALTERNATIVE in the eselect module" ++ ++ local force provider providers ++ if [[ ${1} == --force ]]; then ++ force=yes ++ shift ++ fi ++ ++ if [[ ${1} == -+([[:digit:]]) ]]; then ++ providers=( $(get_providers) ) ++ (( ${1#-} <= ${#providers[@]} )) || die -q "The given provider with index (${1#-}) does not exist" ++ provider=${providers[${1#-}-1]} ++ else ++ provider="${1}" ++ fi ++ [[ -z "${provider}" ]] && die -q "Missing required parameter 'provider'" ++ local dieprefix="Could not set provider ${provider} for alternative ${ALTERNATIVE}" ++ ++ if [[ ! -d ${ALTERNATIVESDIR}/${ALTERNATIVE}/${provider} ]] ; then ++ if is_number ${provider} ; then ++ providers=( $(get_providers) ) ++ [[ -n ${providers[${1#-}-1]} ]] && ++ die -q "The given provider (${provider}) does not exist, did you mean -${provider} (${providers[${1#-}-1]})?" ++ fi ++ die -q "The given provider (${provider}) does not exist" ++ fi ++ ++ local symlink newsymlinks=() oldsymlinks=() ++ ++ while read -r -d '' symlink; do ++ local nicesymlink=${symlink#.} ++ nicesymlink=${nicesymlink//+(\/)/\/} ++ [[ ${nicesymlink} == /* ]] || die "${dieprefix}: bad symlink ${symlink}?" ++ [[ ${nicesymlink} == */ ]] && die "${dieprefix}: bad symlink ${symlink}?" ++ ++ newsymlinks+=( "${nicesymlink}" ) ++ done < <( ++ cd "${ALTERNATIVESDIR}/${ALTERNATIVE}/${provider}" || die "${dieprefix}: cd failed" ++ find . -type l -print0 | LC_ALL=C sort -r -u -z) ++ [[ ${#newsymlinks[@]} -gt 0 ]] || die "${dieprefix}: does not provide any symlinks?" ++ ++ if [[ -f ${ALTERNATIVESDIR}/${ALTERNATIVE}/_current_list ]]; then ++ while read -r -d '' symlink; do ++ local nicesymlink=${symlink//+(\/)/\/} ++ [[ ${nicesymlink} == /* ]] || die "${dieprefix}: old provider ${oldcur} provides bad symlink ${symlink}?" ++ [[ ${nicesymlink} == */ ]] && die "${dieprefix}: old provider ${oldcur} provides bad symlink ${symlink}?" ++ ++ oldsymlinks+=( "${nicesymlink}" ) ++ done < <(LC_ALL=C sort -r -u -z "${ALTERNATIVESDIR}/${ALTERNATIVE}/_current_list") ++ [[ ${#oldsymlinks[@]} -gt 0 ]] || die "${dieprefix}: old provider ${oldcur} does not provide any symlinks?" ++ ++ elif [[ -L ${ALTERNATIVESDIR}/${ALTERNATIVE}/_current_list || -e ${ALTERNATIVESDIR}/${ALTERNATIVE}/_current_list ]]; then ++ die "${dieprefix}: ${ALTERNATIVESDIR}/${ALTERNATIVE}/_current_list is not a file" ++ fi ++ ++ local pass errors= ++ for pass in check perform; do ++ local -i new_i=0 old_i=0 ++ while [[ -n ${newsymlinks[new_i]} || -n ${oldsymlinks[old_i]} ]]; do ++ ++ if ( LC_ALL=C; [[ ${newsymlinks[new_i]} < ${oldsymlinks[old_i]} ]] ); then ++ if [[ ${pass} == check ]]; then ++ if [[ -L ${EROOT}${oldsymlinks[old_i]} ]]; then ++ : ++ elif [[ -d ${EROOT}${oldsymlinks[old_i]} ]]; then ++ write_error_msg "Can't remove ${EROOT}${oldsymlinks[old_i]}: is a directory${force:+ which is a fatal error that cannot be ignored by --force}" ++ errors=yes ++ elif [[ -e ${EROOT}${oldsymlinks[old_i]} ]]; then ++ if [[ -n ${force} ]]; then ++ write_warning_msg "Removing ${EROOT}${oldsymlinks[old_i]} due to --force: is not a symlink" ++ else ++ write_error_msg "Refusing to remove ${EROOT}${oldsymlinks[old_i]}: is not a symlink (use --force to override)" ++ errors=yes ++ fi ++ fi ++ ++ elif [[ ${pass} == perform ]]; then ++ rm -f "${ROOT}${oldsymlinks[old_i]}" || die "${dieprefix}: rm failed" ++ else ++ die "${dieprefix}: unknown \${pass} ${pass}???" ++ fi ++ ++ old_i+=1 ++ ++ else ++ local target=${ALTERNATIVESDIR_ROOTLESS#/}/${ALTERNATIVE}/_current${newsymlinks[new_i]} dir=${newsymlinks[new_i]%/*} ++ while [[ -n ${dir} ]]; do ++ target=../${target} ++ dir=${dir%/*} ++ done ++ ++ if [[ ${pass} == check ]]; then ++ if [[ -L ${EROOT}${newsymlinks[new_i]} ]]; then ++ : ++ elif [[ -d ${EROOT}${newsymlinks[new_i]} ]]; then ++ write_error_msg "Can't overwrite ${EROOT}${newsymlinks[new_i]}: is a directory${force:+ which is a fatal error that cannot be ignored by --force}" ++ errors=yes ++ elif [[ -e ${EROOT}${newsymlinks[new_i]} ]]; then ++ if [[ -n ${force} ]]; then ++ write_warning_msg "Overwriting ${EROOT}${newsymlinks[new_i]} due to --force: is not a symlink" ++ else ++ write_error_msg "Refusing to overwrite ${EROOT}${newsymlinks[new_i]}: is not a symlink (use --force to override)" ++ errors=yes ++ fi ++ fi ++ ++ elif [[ ${pass} == perform ]]; then ++ mkdir -p "${EROOT}${newsymlinks[new_i]%/*}" || die "${dieprefix}: mkdir -p failed" ++ ln -snf "${target#/}" "${EROOT}${newsymlinks[new_i]}" || die "${dieprefix}: ln -snf failed" ++ else ++ die "${dieprefix}: unknown \${pass} ${pass}???" ++ fi ++ ++ [[ ${newsymlinks[new_i]} == ${oldsymlinks[old_i]} ]] && old_i+=1 ++ new_i+=1 ++ fi ++ done ++ ++ [[ -n ${errors} ]] && die "${dieprefix}: see previous errors" ++ done ++ ++ local oldcur="$(get_current_provider)" ++ ln -snf "${provider}" "${ALTERNATIVESDIR}/${ALTERNATIVE}/_current" || die "${dieprefix}: ln -snf failed" ++ ++ : >"${ALTERNATIVESDIR}/${ALTERNATIVE}/_current_list" || die "${dieprefix}: emptying/creating _current_list failed" ++ for symlink in "${newsymlinks[@]}"; do ++ echo -n -e "${symlink}\\0" >>"${ALTERNATIVESDIR}/${ALTERNATIVE}/_current_list" || die "${dieprefix}: appending ${symlink} to _current_list failed" ++ done ++ return 0 ++} ++ ++_options_parameters() { ++ [[ -n ${2} && ${2} != --descriptions ]] && die -q "Unrecognised option ${2}" ++ local describe_func=describe_${1#options_}_options descriptions=${2} opt options oldifs=$IFS ++ if is_function ${describe_func}; then ++ IFS=$'\n' ++ options=( $(${describe_func}) ) ++ IFS=$oldifs ++ for opt in "${options[@]}"; do ++ [[ ${opt} == --* ]] || continue ++ if [[ -n ${descriptions} ]]; then ++ echo "${opt/ : /:}" ++ else ++ echo "${opt%% : *}" ++ fi ++ done ++ fi ++} ++ ++options_set() { ++ _options_parameters $FUNCNAME "$@" ++ get_providers ++} ++ ++### update action ### ++ ++describe_update() { ++ echo "Set a default provider if no valid one currently exists" ++} ++ ++describe_update_parameters() { ++ echo "[--ignore] <provider>" ++} ++ ++describe_update_options() { ++ echo "--ignore : update to any valid provider EXCEPT the specified provider" ++ echo "<provider> : the name of the provider to use" ++} ++ ++do_update() { ++ [[ -z "${ALTERNATIVE}" ]] && die "Need to set ALTERNATIVE in the eselect module" ++ ++ local p cur=$(get_current_provider) providers=( $(get_providers) ) ignore ++ if [[ "--ignore" == ${1} ]] ; then ++ # Try everything except setting the provider to the given ++ # one. So, if it isn't the given one, we end up doing ++ # nothing. Bug #128 ++ shift ++ ignore=${1} ++ fi ++ ++ if [[ ${cur} == ${1} && -z ${ignore} ]]; then ++ # if current provider was just updated, reselect it since it could have changed ++ do_set "${cur}" && return 0 ++ elif [[ -n ${cur} && ${cur} != ${ignore} ]] ; then ++ # verify existing provider's symlinks ++ local p= bad=0 ++ while read -r -d '' p ; do ++ [[ -L "${EROOT}${p}" && -e "${EROOT}${p}" ]] || (( bad++ )) ++ done < "${ALTERNATIVESDIR}/${ALTERNATIVE}/_current_list" ++ ++ [[ "${bad}" -eq 0 ]] && return 0 ++ # fix existing provider if possible ++ has "${cur}" "${providers[@]}" && do_set "${cur}" && return 0 ++ elif has "${1}" "${providers[@]}" && [[ -z ${ignore} ]] ; then ++ # switch to new provider if none was set before or it can't be fixed ++ do_set "${1}" && return 0 ++ fi ++ ++ # if no valid provider has been selected switch to first available, valid ++ # provider, sorted according to importance ++ for p in "${providers[@]}"; do ++ [[ ${ignore} != ${p} ]] && do_set "${p}" && return 0 ++ done ++ ++ # if a provider is set but no providers are available anymore cleanup ++ cur=$(get_current_provider) ++ if [[ -n ${cur} ]]; then ++ do_unset "${cur}" && return 2 ++ fi ++ # if no provider is set and none are available that are not ignored, return 2 for cleanup ++ [[ -z ${providers[@]} || ${providers[@]} == ${ignore} ]] && return 2 ++ ++ # we tried everything to select a valid provider, but failed ++ return 1 ++} ++ ++options_update() { ++ _options_parameters $FUNCNAME "$@" ++ get_providers ++} ++ ++### unset action ### ++ ++describe_unset() { ++ echo "Unset any symlinks created for the current provider for ${ALTERNATIVE}." ++} ++ ++describe_unset_parameters() { ++ echo "[ --force ]" ++} ++ ++describe_unset_options() { ++ echo "--force : remove existing non-symlink files (but not directories) if necessary" ++} ++ ++do_unset() { ++ [[ -z "${ALTERNATIVE}" ]] && die "Need to set ALTERNATIVE in the eselect module" ++ ++ local force= ++ if [[ ${1} == --force ]]; then ++ force=yes ++ shift ++ fi ++ ++ local cur="$(get_current_provider)" p= ++ [[ -n "${cur}" ]] || die -q "Nothing to unset" ++ local dieprefix="Could not unset provider for ${ALTERNATIVE}" ++ ++ local one=false symlink pass errors= ++ for pass in check perform; do ++ while read -r -d '' symlink; do ++ one=true ++ if [[ ${pass} == check ]]; then ++ if [[ -L ${EROOT}${symlink} ]]; then ++ : ++ elif [[ -d ${EROOT}${symlink} ]]; then ++ write_error_msg "Can't remove ${EROOT}${symlink}: is a directory${force:+ which is a fatal error that cannot be ignored by --force}" ++ errors=yes ++ elif [[ -e ${EROOT}${symlink} ]]; then ++ if [[ -n ${force} ]]; then ++ write_warning_msg "Removing ${EROOT}${symlink} due to --force: is not a symlink" ++ else ++ write_error_msg "Refusing to remove ${EROOT}${symlink}: is not a symlink (use --force to override)" ++ errors=yes ++ fi ++ fi ++ ++ elif [[ ${pass} == perform ]]; then ++ rm -f "${EROOT}${symlink}" || die "${dieprefix}: rm failed" ++ else ++ die "${dieprefix}: unknown \${pass} ${pass}???" ++ fi ++ done <"${ALTERNATIVESDIR}/${ALTERNATIVE}/_current_list" ++ ++ [[ -n ${errors} ]] && die "${dieprefix}: see previous errors" ++ done ++ ++ ${one} || die "${dieprefix}: does not provide any symlinks?" ++ ++ rm "${ALTERNATIVESDIR}/${ALTERNATIVE}"/{_current,_current_list} || die "${dieprefix}: rm failed" ++} ++ ++options_unset() { ++ _options_parameters $FUNCNAME "$@" ++ get_current_provider ++} ++ ++### script action ### ++ ++describe_script() { ++ echo "Output an evalable script fragment to set PATH, LD_LIBRARY_PATH and MANPATH to use the specified provider" ++} ++ ++describe_script_parameters() { ++ echo "[--sh | --csh] [<provider>]" ++} ++ ++describe_script_options() { ++ echo "--sh : use Bourne shell syntax (default)" ++ echo "--csh : use C shell syntax" ++ echo "<provider> : the provider to use or the index of the provider preceeded by a dash (if not specified, use the system default)" ++} ++ ++do_script() { ++ [[ -z "${ALTERNATIVE}" ]] && die "Need to set ALTERNATIVE in the eselect module" ++ local syntax=sh provider providers ++ if [[ ${1} == --sh ]]; then ++ shift ++ elif [[ ${1} == --csh ]]; then ++ syntax=csh ++ shift ++ fi ++ ++ if [[ ${1} == -+([[:digit:]]) ]]; then ++ providers=( $(get_providers) ) ++ (( ${1#-} <= ${#providers[@]} )) || die -q "The given provider with index (${1#-}) does not exist" ++ provider=${providers[${1#-}-1]} ++ else ++ provider="${1}" ++ fi ++ [[ -z "${provider}" ]] && die -q "Missing required parameter 'provider'" ++ ++ if [[ ! -d ${ALTERNATIVESDIR}/${ALTERNATIVE}/${provider} ]] ; then ++ if is_number ${provider} ; then ++ providers=( $(get_providers) ) ++ [[ -n ${providers[${1#-}-1]} ]] && ++ die -q "The given provider (${provider}) does not exist, did you mean -${provider} (${providers[${1#-}-1]})?" ++ fi ++ die -q "The given provider (${provider}) does not exist" ++ fi ++ ++ local variables=( PATH LD_LIBRARY_PATH MANPATH ) ++ [[ -n ${!default_*} ]] && local ${!default_*} ++ local default_LD_LIBRARY_PATH=$(grep '^[^#]' "${EROOT}"/etc/ld.so.conf | tr '\n' ':')/lib:/usr/lib ++ local default_MANPATH=$(MANPATH= man -C"${EROOT}"/etc/man.conf -w) ++ ++ local var IFS=: ++ for var in "${variables[@]}"; do ++ local defvar=default_${var} path paths=( ) ++ for path in ${!var}; do ++ [[ ${path} == ${ALTERNATIVESDIR_ROOTLESS}/${ALTERNATIVE}/* ]] && continue ++ [[ -n ${provider} && -d ${ALTERNATIVESDIR}/${ALTERNATIVE}/${provider}/${path#/} ]] && paths+=( "${ALTERNATIVESDIR_ROOTLESS}/${ALTERNATIVE}/${provider}/${path#/}" ) ++ paths+=( "${path}" ) ++ done ++ ++ [[ -n ${provider} ]] && for path in ${!defvar}; do ++ [[ -d ${ALTERNATIVESDIR}/${ALTERNATIVE}/${provider}/${path#/} ]] && paths+=( "${ALTERNATIVESDIR_ROOTLESS}/${ALTERNATIVE}/${provider}/${path#/}" ) ++ done ++ ++ local newval=${paths[*]} ++ if [[ ${newval} != ${!var} ]]; then ++ newval=${newval//\'/\'\\\'\'} ++ if [[ ${syntax} == sh ]]; then ++ echo "${var}='${newval}'; export ${var}" ++ else ++ echo "setenv ${var} '${newval}'" ++ fi ++ fi ++ done ++} ++ ++options_script() { ++ _options_parameters $FUNCNAME "$@" ++ get_providers ++} ++ ++# vim: set ft=eselect sw=4 sts=4 ts=4 et tw=80 : diff --git a/dev-python/pyqtgraph/ChangeLog b/dev-python/pyqtgraph/ChangeLog new file mode 100644 index 000000000..bac3994b6 --- /dev/null +++ b/dev-python/pyqtgraph/ChangeLog @@ -0,0 +1,17 @@ +# ChangeLog for dev-python/pyqtgraph +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 07 Sep 2013; Guillaume Poulin <poulin.guillaume@gmail.com> + pyqtgraph-0.9.7.ebuild: + remove untested keywords + + 07 Sep 2013; Guillaume Poulin <poulin.guillaume@gmail.com> + pyqtgraph-0.9.7.ebuild: + add [${PYTHON_USEDEP}] to depencies to sastify python-r1 + +*pyqtgraph-0.9.7 (07 Sep 2013) + + 07 Sep 2013; Guillaume Poulin <poulin.guillaume@gmail.com> +metadata.xml, + +pyqtgraph-0.9.7.ebuild: + Add dev-python/pyqtgraph diff --git a/dev-python/pyqtgraph/Manifest b/dev-python/pyqtgraph/Manifest new file mode 100644 index 000000000..8e3de3efa --- /dev/null +++ b/dev-python/pyqtgraph/Manifest @@ -0,0 +1 @@ +DIST pyqtgraph-0.9.7.tar.gz 915620 SHA256 0182c649533f91959a5116ac9b919f66eca5c619bdcce1eb5b6f772eeb18a4df SHA512 59d037d290a6274d6f88327e06cf09709e92b32981dcf536a2014b2accb52a2c5284144c6e1f1434a8530f1d89ca37edaaec20bf7495d1de83753d5c6e09eade WHIRLPOOL 2552a6516fde12fe3f8e43a0130bf8a485a06dd0d9f572584d1997a74ba382cc381fd7d51c4f21ea6760b62a373254e08547e5605c877265648f38cae6638b1e diff --git a/dev-python/pyqtgraph/metadata.xml b/dev-python/pyqtgraph/metadata.xml new file mode 100644 index 000000000..b05689e41 --- /dev/null +++ b/dev-python/pyqtgraph/metadata.xml @@ -0,0 +1,14 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci</herd> + <longdescription> + PyQtGraph is a pure-python graphics and GUI library built on + PyQt4/PySide and numpy. It is intended for use in mathematics / + scientific / engineering applications. Despite being written entirely + in python, the library is very fast due to its heavy leverage of numpy + for number crunching and Qt's GraphicsView framework for fast display. + PyQtGraph is distributed under the MIT open-source license. + </longdescription> + <use><flag name="example">Install example of code</flag></use> +</pkgmetadata> diff --git a/dev-python/pyqtgraph/pyqtgraph-0.9.7.ebuild b/dev-python/pyqtgraph/pyqtgraph-0.9.7.ebuild new file mode 100644 index 000000000..b5325d2ad --- /dev/null +++ b/dev-python/pyqtgraph/pyqtgraph-0.9.7.ebuild @@ -0,0 +1,32 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 +PYTHON_COMPAT=( python{2_6,2_7,3_2} ) + +inherit distutils-r1 + +DESCRIPTION="Pure-python graphics and GUI library built on PyQt4/PySide and numpy." +HOMEPAGE="http://www.pyqtgraph.org/" +SRC_URI="http://www.pyqtgraph.org/downloads/${P}.tar.gz" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="opengl example" + +DEPEND="" +RDEPEND="${DEPEND} + dev-python/numpy[${PYTHON_USEDEP}] + sci-libs/scipy[${PYTHON_USEDEP}] + opengl? ( dev-python/pyopengl[${PYTHON_USEDEP}] ) + || ( >=dev-python/PyQt4-4.7.0[${PYTHON_USEDEP}] dev-python/pyside[${PYTHON_USEDEP}] )" + +src_prepare() { + use opengl || rm -r pyqtgraph/opengl + if ! use example; then + sed -i -e '/package_dir/d' setup.py || die "Unable to remove example" + sed -i -e "s/+ \['pyqtgraph\.examples'\]//" setup.py || die "Unable to remove example" + fi +} diff --git a/licenses/CeCILL-2.0 b/licenses/CeCILL-2.0 deleted file mode 100644 index a36324de9..000000000 --- a/licenses/CeCILL-2.0 +++ /dev/null @@ -1,505 +0,0 @@ - - CeCILL FREE SOFTWARE LICENSE AGREEMENT - - - Notice - -This Agreement is a Free Software license agreement that is the result -of discussions between its authors in order to ensure compliance with -the two main principles guiding its drafting: - - * firstly, compliance with the principles governing the distribution - of Free Software: access to source code, broad rights granted to - users, - * secondly, the election of a governing law, French law, with which - it is conformant, both as regards the law of torts and - intellectual property law, and the protection that it offers to - both authors and holders of the economic rights over software. - -The authors of the CeCILL (for Ce[a] C[nrs] I[nria] L[logiciel] L[ibre]) -license are: - -Commissariat l'Energie Atomique - CEA, a public scientific, technical -and industrial establishment, having its principal place of business at -31-33 rue de la Fdration, 75752 Paris cedex 15, France. - -Centre National de la Recherche Scientifique - CNRS, a public scientific -and technological establishment, having its principal place of business -at 3 rue Michel-Ange 75794 Paris cedex 16, France. - -Institut National de Recherche en Informatique et en Automatique - -INRIA, a public scientific and technological establishment, having its -principal place of business at Domaine de Voluceau, Rocquencourt, BP -105, 78153 Le Chesnay cedex, France. - - - Preamble - -The purpose of this Free Software license agreement is to grant users -the right to modify and redistribute the software governed by this -license within the framework of an open source distribution model. - -The exercising of these rights is conditional upon certain obligations -for users so as to preserve this status for all subsequent redistributions. - -In consideration of access to the source code and the rights to copy, -modify and redistribute granted by the license, users are provided only -with a limited warranty and the software's author, the holder of the -economic rights, and the successive licensors only have limited liability. - -In this respect, the risks associated with loading, using, modifying -and/or developing or reproducing the software by the user are brought to -the user's attention, given its Free Software status, which may make it -complicated to use, with the result that its use is reserved for -developers and experienced professionals having in-depth computer -knowledge. 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The Parties agree to -endeavor to seek an amicable solution to any disagreements or disputes -that may arise during the performance of the Agreement. - -13.2 Failing an amicable solution within two (2) months as from their -occurrence, and unless emergency proceedings are necessary, the -disagreements or disputes shall be referred to the Paris Courts having -jurisdiction, by the more diligent Party. - - -Version 2.0 dated 2005-05-21. diff --git a/licenses/STFC b/licenses/STFC new file mode 100644 index 000000000..950d0f9e3 --- /dev/null +++ b/licenses/STFC @@ -0,0 +1,67 @@ +Software licence + +When you complete a registration form for the STFC software and submit it to STFC, your institution (in the registration form and the licence agreement called "the Licensee") is entering into a contract with the Science and Technology Facilities Council ("STFC") on the terms set out in the licence agreement below. + +By submitting the Registration Form to STFC, you are confirming that: + +the institution whose name appears as the Licensee in the Registration Form agrees to the terms of the Licence +you have authority to agree to the terms of the Licence and to enter into a contract with STFC on behalf of that institution; +STFC Software will be used only for Academic Purposes (as defined in the Licence); +the information given on the Registration Form is true; and +you agree to your personal data being used for the purpose of managing your institution's licence of the STFC Software, including contacting you to tell you about changes to and error corrections for that software and generally about the software. +Please read the terms of the Licence carefully. If you do not agree to them, you should not submit the registration form. + +A contract between the Licensee and STFC will come into existence when you click on the SUBMIT button at the end of the Registration Form. + +STFC is an executive Non-Departmental Public Body established as a Research Council by Royal Charter under the Science and Technology Act 1965. Its address is Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot OX11 0QX and its VAT number is GB 618 3673 25. + +If you wish to contact STFC about the Licence or the STFC Software, please e-mail Linda Baines. + +Licence + +STFC grants any person who obtains a copy of this software (the Software), free of charge, the non-exclusive, worldwide right to use, copy, modify, distribute and sub-license the use of the Software on the terms and clauses appearing below: + +Any use of the Software is for academic purposes only and any sub-licensees may only use the Software for academic purposes. Academic purposes means fundamental or basic research or academic teaching, including any fundamental research that is funded by any public or charitable body, but not any purpose that generates revenue (as opposed to grant income) for any person. Any research that is wholly or partially sponsored by any profit-making organisation, or that is carried out for the benefit of any profit-making organisation, is not an academic purpose. + +The STFC copyright notice and any other notice placed by STFC on the Software must be reproduced on every copy of the Software, and on every Derived Work. A Derived Work means any modification of, or enhancement or improvement to, any of the Software, and any software or other work developed or derived from any of the Software. + +The following software is supplied to the Licensee on the terms of the licence set out below and as indicated on this website from time to time: + +Third party softwareLicence + + Sun Java Cryptography Extension (JCE)Binary Code License Agreement + Sun Java Cryptography Extension + + Java Commodity Grid (CoG) toolkitCommon Public License Version 0.5 + The Apache Software License, Version 1.1 + + The Legion of the Bouncy Castle Crypto APIs for JavaThe Legion Of The Bouncy Castle Crypto APIs for Java + + + + In any published work produced by the user and which includes results achieved by using the Software, the user shall acknowledge that the Software was used in producing the information contained in such publication. + + STFC gives no warranty and makes no representation in relation to the Software. The Licensee and anyone to whom the Licensee makes the Software or any Derived Work available, use the Software at their own risk. + + All warranties, clauses, terms, undertakings and obligations on the part of STFC, implied by statute, common law, custom, trade usage, course of dealing or in any other way are excluded to the fullest extent permitted by law. + + Subject to condition 8, STFC will not be liable for: + + any loss of profits, loss of revenue, loss or corruption of data, loss of contracts or opportunity, loss of savings or third party claims (in each case whether direct or indirect); + any indirect loss or damage arising out of or in connection with the Software; + any direct loss or damage arising out of, or in connection with, the Software + + in each case, whether that loss arises as a result of STFC'ss negligence, or in any other way, even if STFC has been advised of the possibility of that loss arising, or if it was within STFC's contemplation. + + None of these clauses limits or excludes STFC's liability for death or personal injury caused by its negligence or for any fraud, or for any sort of liability that, by law, cannot be limited or excluded. + + These clauses set out the entire agreement relating to the Software. The licensee acknowledges that it has not relied on any warranty, representation, statement, agreement or undertaking given by STFC, and waives any claim in respect of any of the same. + + The rights granted above will cease immediately on any breach of these clauses and the licensee will destroy all copies of the Software and any Derived Work in its control or possession. Clauses 5, 6, 7, 8, 9, 10, and 11 will survive termination and continue indefinitely. + + The licence and these clauses are governed by, and are to be construed in accordance with, English law. The English Courts will have exclusive jurisdiction to deal with any dispute which has arisen or may arise out of or in connection with the Software, the rights granted and these clauses, except that STFC may bring proceedings for an injunction in any jurisdiction. + + If the whole or any part of these clauses are void or unenforceable in any jurisdiction, the other provisions, and the rest of the void or unenforceable provision, will continue in force in that jurisdiction, and the validity and enforceability of that provision in any other jurisdiction will not be affected. + + © 2013 Science and Technology Facilities Council - All Rights Reserved. + diff --git a/media-gfx/librecad/ChangeLog b/media-gfx/librecad/ChangeLog index be52d5aad..3b1ab260f 100644 --- a/media-gfx/librecad/ChangeLog +++ b/media-gfx/librecad/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header$ + 3 Sept 2013: Dongxu Li <dongxuli2011@gmail.com> +librecad-2.0.0_rc2.ebuild: + Version bump 2.0.0_rc2 + 17 Jun 2013; Sébastien Fabbro <bicatali@gentoo.org> -files/1.0.0_rc2-gcc4.6.patch, -files/librecad-1.0.0_rc2-version.patch, -librecad-1.0.2.ebuild, -librecad-2.0.0_beta5.ebuild, diff --git a/media-gfx/librecad/Manifest b/media-gfx/librecad/Manifest index d74adebb1..a903ee806 100644 --- a/media-gfx/librecad/Manifest +++ b/media-gfx/librecad/Manifest @@ -1,2 +1,3 @@ DIST librecad-1.0.3.tar.gz 4578450 SHA256 8c2f5a7e55a4ae41a9bd47e2e7981577c740edd526e1f305cd6cbf581d053f30 SHA512 5a8e6e612bc954f3af0dfc26d1fc19938c80e216ac252fb65a38a13651c6e2313d593a3ee834ecc98bbd72a4dfd28ef1c39dd9ed6a6f9140d28b765edb59bee9 WHIRLPOOL d8157af2021bba2cee626d023125045455a2fe5f453ae065c9660be61f4c0d687a1c72957d1af1aa640cfde3815625bb7d0899dc5541fcb82bfe0eea4cfad6c6 DIST librecad-2.0.0_rc1.zip 16210997 SHA256 9a5345463c19b64cf5f4e4f308460988a60ce4c8c8d311b08d16805fbec68f90 SHA512 b97eaf81050cfe06a7910ac3a7c64d7906dec3159ac3e5f24f92bd74e60d86c67b661b65fd6c258996043e8c4ae09b1d8d5cb92aea28b313eca10e54149abde1 WHIRLPOOL 768244e63bf34bfff259712fd1c5e9aee872eda496106bc8e33ab5f4c3f1c8c0131167984d55bf5d6e82d9af0e2cdb5e01a5d125f19749369679dfbf7bd60f5f +DIST librecad-2.0.0_rc2.zip 16315454 SHA256 65c65a1f9200b9428be3033837513b6dba5b5405a43c32255d7bf27e3b3ecdfd SHA512 50c562389104373893ed695c3ed6366019136fc9d3ce137080fa1813bc671c36e82f2628e1c458479d8925a8f6e2af6934055c3354f65b9a8bb7c9cae18fc2b3 WHIRLPOOL 3f9a4c258da479276a48379b1a37ad8ec5bed2f3857b0c93af5a4d02613c18c95386008e0dfd0b18c7d2087f3086fbd43ce195e7f32ae07ab1909479b4d0e53a diff --git a/media-gfx/librecad/librecad-2.0.0_rc2.ebuild b/media-gfx/librecad/librecad-2.0.0_rc2.ebuild new file mode 100644 index 000000000..7017bccb8 --- /dev/null +++ b/media-gfx/librecad/librecad-2.0.0_rc2.ebuild @@ -0,0 +1,45 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit qt4-r2 eutils flag-o-matic + +DESCRIPTION="Generic 2D CAD program" +HOMEPAGE="http://www.librecad.org/" +SRC_URI="https://github.com/LibreCAD/LibreCAD/archive/${PV/_/}.zip -> ${P}.zip" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="debug doc 3d" + +DEPEND=" + dev-qt/qtgui:4 + dev-qt/qthelp:4 + dev-qt/qtsvg:4 + dev-libs/boost + dev-cpp/muParser + media-libs/freetype + " +RDEPEND="${DEPEND}" + +src_unpack() { + unpack ${A} + mv * ${P} +} + +src_prepare() { + # currently RS_VECTOR3D causes an internal compiler error on GCC-4.8 + use 3d || sed -i -e '/RS_VECTOR2D/ s/^#//' librecad/src/src.pro +} + +src_install() { + dobin unix/librecad + insinto /usr/share/${PN} + doins -r unix/resources/* + use doc && dohtml -r support/doc/* + doicon librecad/res/main/${PN}.png + make_desktop_entry ${PN} LibreCAD ${PN} Graphics +} diff --git a/profiles/package.mask b/profiles/package.mask index 230760bc6..b7e5303ff 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -32,6 +32,7 @@ # Live ebuilds go here # keep this on top +>=sci-libs/fftw-9999 >=media-gfx/brlcad-9999 >=dev-lang/path64-9999 >=dev-lang/julia-9999 diff --git a/sci-biology/amos/ChangeLog b/sci-biology/amos/ChangeLog index f121b1666..22c5625b3 100644 --- a/sci-biology/amos/ChangeLog +++ b/sci-biology/amos/ChangeLog @@ -2,6 +2,15 @@ # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*amos-3.1.0-r1 (11 Sep 2013) + + 11 Sep 2013; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + +amos-3.1.0-r1.ebuild, +files/amos-3.1.0-gcc-4.7.patch, + +files/amos-3.1.0-goBambus2.py-indent-and-cleanup.patch: + Fix indentation error and remove unused import of string module (there could + be more cleanup as suggested by pychecker). Credits to + http://sourceforge.net/p/amos/support-requests/1/ + 19 Mar 2013; Justin Lecher <jlec@gentoo.org> amos-9999.ebuild: Bump to latest git HEAD, fixes qt problems, #348031 @@ -10,4 +19,3 @@ 22 May 2012; Justin Lecher <jlec@gentoo.org> amos-9999.ebuild: Bump to EAPI=4, remove unnecessary bits - diff --git a/sci-biology/amos/Manifest b/sci-biology/amos/Manifest new file mode 100644 index 000000000..27ad50ff2 --- /dev/null +++ b/sci-biology/amos/Manifest @@ -0,0 +1 @@ +DIST amos-3.1.0.tar.gz 2094268 SHA256 2d9f50e39186ad3dde3d3b28cc265e8d632430657f40fc3978ce34ab1b3db43b SHA512 7a416b9a0438b47425355383b709491a58f38c8d834df29e43c942170e710c6ea7e3bc8c509a58421b1340ad6eece9ea2da357ce5cd1d41ce08375676ee30491 WHIRLPOOL df9b547fcc0b7bf0149641fd8df9e4558f61bb6c17ded0facfeecde25d3a6307b40414e7cb8b2f021fa8cc192ee956672c26e0fc287981f4733a393739e80b61 diff --git a/sci-biology/amos/amos-3.1.0-r1.ebuild b/sci-biology/amos/amos-3.1.0-r1.ebuild new file mode 100644 index 000000000..f1e0470b8 --- /dev/null +++ b/sci-biology/amos/amos-3.1.0-r1.ebuild @@ -0,0 +1,30 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/amos/amos-3.1.0.ebuild,v 1.8 2013/03/19 07:41:20 jlec Exp $ + +EAPI=4 + +inherit eutils + +DESCRIPTION="A Modular, Open-Source whole genome assembler" +HOMEPAGE="http://amos.sourceforge.net/" +SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz" + +LICENSE="Artistic" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="qt4" + +DEPEND="qt4? ( dev-qt/qtcore:4 )" +RDEPEND="${DEPEND} + dev-perl/DBI + dev-perl/Statistics-Descriptive + sci-biology/mummer" + +MAKEOPTS+=" -j1" + +src_prepare() { + epatch \ + "${FILESDIR}"/${P}-gcc-4.7.patch \ + "${FILESDIR}"/${P}-goBambus2.py-indent-and-cleanup.patch +} diff --git a/sci-biology/amos/files/amos-3.1.0-gcc-4.7.patch b/sci-biology/amos/files/amos-3.1.0-gcc-4.7.patch new file mode 100644 index 000000000..de2a41184 --- /dev/null +++ b/sci-biology/amos/files/amos-3.1.0-gcc-4.7.patch @@ -0,0 +1,15 @@ + src/Align/find-tandem.cc | 1 + + 1 files changed, 1 insertions(+), 0 deletions(-) + +diff --git a/src/Align/find-tandem.cc b/src/Align/find-tandem.cc +index ddf1cab..a29e21e 100644 +--- a/src/Align/find-tandem.cc ++++ b/src/Align/find-tandem.cc +@@ -7,6 +7,7 @@ + #include <vector> + #include <ctime> + #include <sys/time.h> ++#include <unistd.h> + using namespace std; + + const int OFFSET_TABLE_SIZE = 100; diff --git a/sci-biology/amos/files/amos-3.1.0-goBambus2.py-indent-and-cleanup.patch b/sci-biology/amos/files/amos-3.1.0-goBambus2.py-indent-and-cleanup.patch new file mode 100644 index 000000000..97a8f59d0 --- /dev/null +++ b/sci-biology/amos/files/amos-3.1.0-goBambus2.py-indent-and-cleanup.patch @@ -0,0 +1,25 @@ +--- amos-3.1.0/src/Pipeline/goBambus2.py.orig 2013-09-11 01:05:29.850090457 +0200 ++++ amos-3.1.0/src/Pipeline/goBambus2.py 2013-09-11 01:07:03.250090701 +0200 +@@ -1,7 +1,7 @@ + #pipeline script for assembly + Bambus 2 + #contributed by Todd J Treangen + +-import string, sys, os, subprocess#, spincursor ++import sys, os, subprocess#, spincursor + + RED = "\033[0;31m" + GREEN = "\033[0;32m" +@@ -360,7 +360,7 @@ + print "\t\t%s...failed%s"%(RED,NONE) + sys.exit(1) + +- p = subprocess.Popen(AMOSDIR+"OutputResults -b %s -prefix %s %s"%(amosbank, prefix+".scaff.linear"), shell=True, stdin=subprocess.PIPE, stdout=vtext, stderr=logfile) ++ p = subprocess.Popen(AMOSDIR+"OutputResults -b %s -prefix %s %s"%(amosbank, prefix+".scaff.linear"), shell=True, stdin=subprocess.PIPE, stdout=vtext, stderr=logfile) + + if xopt_dict["verbose"] == 1: + print "10) running OutputResults" +@@ -388,4 +388,3 @@ + else: + print "\t\t%s...failed%s"%(RED,NONE) + sys.exit(1) +-) diff --git a/sci-biology/biopython/ChangeLog b/sci-biology/biopython/ChangeLog new file mode 100644 index 000000000..0f1dbf120 --- /dev/null +++ b/sci-biology/biopython/ChangeLog @@ -0,0 +1,10 @@ +# ChangeLog for sci-biology/biopython +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*biopython-1.62 (11 Sep 2013) + + 11 Sep 2013; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + +biopython-1.62.ebuild, +metadata.xml: + biopython-1.62.ebuild Manifest metadata.xml + diff --git a/sci-biology/biopython/biopython-1.62.ebuild b/sci-biology/biopython/biopython-1.62.ebuild new file mode 100644 index 000000000..9413e775b --- /dev/null +++ b/sci-biology/biopython/biopython-1.62.ebuild @@ -0,0 +1,49 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/biopython/biopython-1.61.ebuild,v 1.3 2013/07/02 12:47:34 jlec Exp $ + +EAPI=5 + +PYTHON_COMPAT=( python{2_5,2_6,2_7,3_3} ) + +inherit distutils-r1 + +DESCRIPTION="Python modules for computational molecular biology" +HOMEPAGE="http://www.biopython.org/ http://pypi.python.org/pypi/biopython/" +SRC_URI="http://biopython.org/DIST/biopython-1.62.tar.gz" + +LICENSE="HPND" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux" +IUSE="mysql postgres" + +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RDEPEND="${PYTHON_DEPS} + dev-python/matplotlib[${PYTHON_USEDEP}] + dev-python/networkx[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/pygraphviz[${PYTHON_USEDEP}] + dev-python/reportlab[${PYTHON_USEDEP}] + media-gfx/pydot[${PYTHON_USEDEP}] + mysql? ( dev-python/mysql-python[${PYTHON_USEDEP}] ) + postgres? ( dev-python/psycopg[${PYTHON_USEDEP}] )" +DEPEND="${RDEPEND} + sys-devel/flex" + +DOCS=( CONTRIB DEPRECATED NEWS README ) +S="${WORKDIR}/biopython-1.62" + +python_test() { + cd Tests + ${PYTHON} run_tests.py +} + +python_install_all() { + distutils-r1_python_install_all + + insinto /usr/share/doc/${PF} + doins -r Doc/* + insinto /usr/share/${PN} + cp -r --preserve=mode Scripts Tests "${ED}"/usr/share/${PN} || die +} diff --git a/sci-biology/biopython/metadata.xml b/sci-biology/biopython/metadata.xml new file mode 100644 index 000000000..f17a827e3 --- /dev/null +++ b/sci-biology/biopython/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata> diff --git a/sci-biology/emboss/ChangeLog b/sci-biology/emboss/ChangeLog index ebe48966e..76a5b350a 100644 --- a/sci-biology/emboss/ChangeLog +++ b/sci-biology/emboss/ChangeLog @@ -1,7 +1,25 @@ # ChangeLog for sci-biology/emboss -# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/ChangeLog,v 1.61 2011/03/09 16:29:05 jlec Exp $ +*emboss-6.3.1_p4-r2 (11 Sep 2013) +*emboss-6.5.7 (11 Sep 2013) +*emboss-6.6.0 (11 Sep 2013) + + 11 Sep 2013; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + +emboss-6.3.1_p4-r2.ebuild, +emboss-6.5.7.ebuild, +emboss-6.6.0.ebuild, + +files/ax_lib_mysql.m4, +files/emboss-6.3.1_p4-r2_Makefile.patch, + +files/emboss-6.3.1_p4-r2_compilations-paths.patch, + +files/emboss-6.3.1_p4-r2_libtool.patch, + +files/emboss-6.3.1_p4-r2_plcol.patch, -emboss-6.3.1_p4-r1.ebuild, + -files/emboss-6.3.1_p4-r1_plcol.patch: + Partial success on removal of all crazy libraries and includes from CFLAGS and + LDFLAGS used throught EMBOSS sources. While compile commandline are now clean + still libtool is passed with LDFLAGS carrying over the many X11 and graphics + libraries. Seems the source is ltmain.sh which uses on the linker lines but + editing m4/libtool.m4 is not the right way to do it. Same applies to ltmain.sh + in top-level directory. Any volunteers? Bug #394425 + 19 Jul 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +files/emboss-6.3.1_p4-r1_plcol.patch, emboss-6.3.1_p4-r1.ebuild: added plcol patch with increased diff line count, bug #391669; same patch diff --git a/sci-biology/emboss/Manifest b/sci-biology/emboss/Manifest index 6b505c551..df13d6994 100644 --- a/sci-biology/emboss/Manifest +++ b/sci-biology/emboss/Manifest @@ -1,3 +1,5 @@ DIST EMBOSS-6.3.1.tar.gz 23572243 SHA256 4f3290600a970c2a23a7e47f884d1fc8156ec40538f7191a6e83e23680d27a8d SHA512 16f69feb693c36855733bf443e763c41de515324f87ac8c8bbad7d389b408ae0226bece39d7b6037fb279a6a140bb4137c0a7f553da0b3b8630a17bbe9e10e44 WHIRLPOOL 52eb01b1cd825ae978a1df3b7f4214c8c91f677639a67e0a5d0783daf63396a48edec206bcab0a0d21deb1acae56920f07329d67c0a0be6d4026859c2acdcb84 -DIST emboss-6.3.1_p4-r1.patch.bz2 9429 SHA256 4ceb304032f9e0d1977afae43055975ff51c186f1707749476da8b0bfb8b3619 SHA512 91ba840adba573e3790d8291e0babc3f4b54f70eecbfbeaa888f12f8659cd6071773046226bbad6d18426207a9af16b3cce8c27a182028fccf642295786e234b WHIRLPOOL 1836ba8b4998beaa3e8f5afab3d7454eed072c4562fa3e1153df37ca8d9321f94bc3785ec535cd183bdc13dca25dd7dcfc7f5b2f173b88917fa879e6e9a61c1d +DIST EMBOSS-6.5.7.tar.gz 99290173 SHA256 18b8d5d3eeb18fdee97f799f5b1fb4c10a4a5ed5b97d1f85f42110f64cfa556f SHA512 6a865e6a879a0449334fb8b400925e67a2b043165d561c56c8e5f7032263267cd2e1efa8fcc98851fac1e04f6c821672237cfa797e3a7fa42decae3e5ef9755d WHIRLPOOL df83bda991f9192572656922b2a552fb1556babaa465d09318f2113620737f3474dfbcc969978e6d1511729c4a3f91e86be9d8920d5e00df0ed37379f53dca42 +DIST EMBOSS-6.6.0.tar.gz 117962028 SHA256 7184a763d39ad96bb598bfd531628a34aa53e474db9e7cac4416c2a40ab10c6e SHA512 2d28a03381f7dc98d205aa50202fbbac02ad218fc775d86579d310296be124403623484b1907154d915f15cd32a9f8cf16ecfaa6c4a28b362e24dc8e6380b75a WHIRLPOOL 25241e865b1ad4e5459f84a2b0def7cd00a6e2904db714838dfe0533e01f8373cfdd4c78df225f9d2a77ead4cb9998791bd19f46b32e220810ad950fa288b9fe +DIST emboss-6.3.1_p4-r2.patch.bz2 9429 SHA256 4ceb304032f9e0d1977afae43055975ff51c186f1707749476da8b0bfb8b3619 SHA512 91ba840adba573e3790d8291e0babc3f4b54f70eecbfbeaa888f12f8659cd6071773046226bbad6d18426207a9af16b3cce8c27a182028fccf642295786e234b WHIRLPOOL 1836ba8b4998beaa3e8f5afab3d7454eed072c4562fa3e1153df37ca8d9321f94bc3785ec535cd183bdc13dca25dd7dcfc7f5b2f173b88917fa879e6e9a61c1d DIST emboss-6.3.1_p4-upstream.patch.gz 4070 SHA256 61d1b62e3148541d496103711db6526ba76488a0899af2c98264b03bf8d6e24c SHA512 4653dc754df1ea8e7123b67749db4e25d5b0125f41ceee368c724dc46bc9f0fa32a16bce4c24b9264c04c7ce2a3b527b0c7f7179e962c7c2aff2d5c7256c9c7e WHIRLPOOL cea18119bcee441a0f1169b0fbc027a5d3657f4cb977d02700ef1caf78308272de4b08f7f0d496b75d1179e16077e3352c9b66ca032714e5b8b2bbd470440f86 diff --git a/sci-biology/emboss/emboss-6.3.1_p4-r2.ebuild b/sci-biology/emboss/emboss-6.3.1_p4-r2.ebuild new file mode 100644 index 000000000..dd7737a44 --- /dev/null +++ b/sci-biology/emboss/emboss-6.3.1_p4-r2.ebuild @@ -0,0 +1,88 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/emboss-6.3.1_p4.ebuild,v 1.2 2011/03/09 16:29:05 jlec Exp $ + +EAPI="4" + +inherit emboss eutils + +EBO_PATCH="4" +EBOV=${PV/_p*} + +DESCRIPTION="The European Molecular Biology Open Software Suite - A sequence analysis package" +SRC_URI=" + ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-${EBOV}.tar.gz + http://dev.gentoo.org/~jlec/distfiles/${PF}.patch.bz2" +##[[ -n ${EBO_PATCH} ]] && SRC_URI+=" ftp://${PN}.open-bio.org/pub/EMBOSS/fixes/patches/patch-1-${EBO_PATCH}.gz -> ${P}-upstream.patch.gz" +[[ -n ${EBO_PATCH} ]] && SRC_URI+=" http://pkgs.fedoraproject.org/lookaside/pkgs/EMBOSS/patch-1-4.gz/7a42594c5eda4adc6457f33e4ab0d8f2/patch-1-${EBO_PATCH}.gz -> ${P}-upstream.patch.gz" + +KEYWORDS="~amd64 ~ppc ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~ppc-macos" +IUSE+=" minimal" + +RDEPEND+=" !sys-devel/cons" +PDEPEND+=" + !minimal? ( + sci-biology/aaindex + sci-biology/cutg + sci-biology/prints + sci-biology/prosite + sci-biology/rebase + sci-biology/transfac + )" + +S="${WORKDIR}"/EMBOSS-${EBOV} + +EBO_EXTRA_ECONF="--includedir=${EPREFIX}/usr/include/emboss" + +DOCS+=" FAQ THANKS" + +src_prepare() { + [[ -n ${EBO_PATCH} ]] && epatch "${WORKDIR}"/${P}-upstream.patch + epatch "${WORKDIR}"/${PF}.patch + epatch "${FILESDIR}/${PF}"_plcol.patch + epatch "${FILESDIR}/${PF}"_compilations-paths.patch + # cp "${FILESDIR}"/ax_lib_mysql.m4 "${S}"/m4/mysql.m4 + emboss_src_prepare + autoreconf -vfi + epatch "${FILESDIR}/${PF}"_libtool.patch +} + +src_compile() { + epatch "${FILESDIR}/${PF}"_Makefile.patch +} + +src_install() { + default + + sed -e "s:EPREFIX:${EPREFIX}:g" "${FILESDIR}"/${PN}-README.Gentoo-2 > README.Gentoo && \ + dodoc README.Gentoo + + # Install env file for setting libplplot and acd files path. + cat <<- EOF > 22emboss + # ACD files location + EMBOSS_ACDROOT="${EPREFIX}/usr/share/EMBOSS/acd" + EMBOSS_DATA="${EPREFIX}/usr/share/EMBOSS/data" + EOF + doenvd 22emboss + + # Clashes #330507, resolved upstream + mv "${ED}"/usr/bin/{digest,pepdigest} || die + + # Remove useless dummy files from the image. + find "${ED}"/usr/share/EMBOSS -name dummyfile -delete || die "Failed to remove dummy files." + + # Move the provided codon files to a different directory. This will avoid + # user confusion and file collisions on case-insensitive file systems (see + # bug #115446). This change is documented in "README.Gentoo". + mv "${ED}"/usr/share/EMBOSS/data/CODONS{,.orig} || \ + die "Failed to move CODON directory." + + # Move the provided restriction enzyme prototypes file to a different name. + # This avoids file collisions with versions of rebase that install their + # own enzyme prototypes file (see bug #118832). + mv "${ED}"/usr/share/EMBOSS/data/embossre.equ{,.orig} || \ + die "Failed to move enzyme equivalence file." + + # fix /usr/share/doc/emboss-6.3.1_p4-r1/html to point to /usr/share/doc/emboss-6.3.1_p4-r1/programs/html + # instead of /usr/share/EMBOSS/doc/html (which does not exist) +} diff --git a/sci-biology/emboss/emboss-6.5.7.ebuild b/sci-biology/emboss/emboss-6.5.7.ebuild new file mode 100644 index 000000000..48be3bff3 --- /dev/null +++ b/sci-biology/emboss/emboss-6.5.7.ebuild @@ -0,0 +1,79 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/emboss-6.3.1_p4.ebuild,v 1.2 2011/03/09 16:29:05 jlec Exp $ + +EAPI="4" + +inherit emboss eutils + +EBO_PATCH="4" +EBOV=${PV/_p*} + +DESCRIPTION="The European Molecular Biology Open Software Suite - A sequence analysis package" +SRC_URI=" + ftp://emboss.open-bio.org/pub/EMBOSS/old/6.5.0/EMBOSS-${EBOV}.tar.gz" +# ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-6.6.0.tar.gz +# ftp://emboss.open-bio.org/pub/EMBOSS/old/6.5.0/EMBOSS-6.5.7.tar.gz + +##[[ -n ${EBO_PATCH} ]] && SRC_URI+=" ftp://${PN}.open-bio.org/pub/EMBOSS/fixes/patches/patch-1-${EBO_PATCH}.gz -> ${P}-upstream.patch.gz" +#[[ -n ${EBO_PATCH} ]] && SRC_URI+=" http://pkgs.fedoraproject.org/lookaside/pkgs/EMBOSS/patch-1-4.gz/7a42594c5eda4adc6457f33e4ab0d8f2/patch-1-${EBO_PATCH}.gz -> ${P}-upstream.patch.gz" + +KEYWORDS="~amd64 ~ppc ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~ppc-macos" +IUSE+=" minimal" + +RDEPEND+=" !sys-devel/cons" +PDEPEND+=" + !minimal? ( + sci-biology/aaindex + sci-biology/cutg + sci-biology/prints + sci-biology/prosite + sci-biology/rebase + sci-biology/transfac + )" + +S="${WORKDIR}"/EMBOSS-${EBOV} + +EBO_EXTRA_ECONF="--includedir=${EPREFIX}/usr/include/emboss" + +DOCS+=" FAQ THANKS" + +src_prepare() { + [[ -n ${EBO_PATCH} ]] && epatch "${WORKDIR}"/${P}-upstream.patch + epatch "${WORKDIR}"/${PF}.patch + epatch "${FILESDIR}/${PF}_plcol.patch" + emboss_src_prepare +} + +src_install() { + default + + sed -e "s:EPREFIX:${EPREFIX}:g" "${FILESDIR}"/${PN}-README.Gentoo-2 > README.Gentoo && \ + dodoc README.Gentoo + + # Install env file for setting libplplot and acd files path. + cat <<- EOF > 22emboss + # ACD files location + EMBOSS_ACDROOT="${EPREFIX}/usr/share/EMBOSS/acd" + EMBOSS_DATA="${EPREFIX}/usr/share/EMBOSS/data" + EOF + doenvd 22emboss + + # Clashes #330507, resolved upstream + mv "${ED}"/usr/bin/{digest,pepdigest} || die + + # Remove useless dummy files from the image. + find "${ED}"/usr/share/EMBOSS -name dummyfile -delete || die "Failed to remove dummy files." + + # Move the provided codon files to a different directory. This will avoid + # user confusion and file collisions on case-insensitive file systems (see + # bug #115446). This change is documented in "README.Gentoo". + mv "${ED}"/usr/share/EMBOSS/data/CODONS{,.orig} || \ + die "Failed to move CODON directory." + + # Move the provided restriction enzyme prototypes file to a different name. + # This avoids file collisions with versions of rebase that install their + # own enzyme prototypes file (see bug #118832). + mv "${ED}"/usr/share/EMBOSS/data/embossre.equ{,.orig} || \ + die "Failed to move enzyme equivalence file." +} diff --git a/sci-biology/emboss/emboss-6.3.1_p4-r1.ebuild b/sci-biology/emboss/emboss-6.6.0.ebuild index 5f02bb9db..4ab735390 100644 --- a/sci-biology/emboss/emboss-6.3.1_p4-r1.ebuild +++ b/sci-biology/emboss/emboss-6.6.0.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2012 Gentoo Foundation +# Copyright 1999-2013 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/emboss-6.3.1_p4.ebuild,v 1.2 2011/03/09 16:29:05 jlec Exp $ @@ -11,10 +11,12 @@ EBOV=${PV/_p*} DESCRIPTION="The European Molecular Biology Open Software Suite - A sequence analysis package" SRC_URI=" - ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-${EBOV}.tar.gz - http://dev.gentoo.org/~jlec/distfiles/${PF}.patch.bz2" + ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-${PV}.tar.gz" +# ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-6.6.0.tar.gz +# ftp://emboss.open-bio.org/pub/EMBOSS/old/6.5.0/EMBOSS-6.5.7.tar.gz + ##[[ -n ${EBO_PATCH} ]] && SRC_URI+=" ftp://${PN}.open-bio.org/pub/EMBOSS/fixes/patches/patch-1-${EBO_PATCH}.gz -> ${P}-upstream.patch.gz" -[[ -n ${EBO_PATCH} ]] && SRC_URI+=" http://pkgs.fedoraproject.org/lookaside/pkgs/EMBOSS/patch-1-4.gz/7a42594c5eda4adc6457f33e4ab0d8f2/patch-1-${EBO_PATCH}.gz -> ${P}-upstream.patch.gz" +#[[ -n ${EBO_PATCH} ]] && SRC_URI+=" http://pkgs.fedoraproject.org/lookaside/pkgs/EMBOSS/patch-1-4.gz/7a42594c5eda4adc6457f33e4ab0d8f2/patch-1-${EBO_PATCH}.gz -> ${P}-upstream.patch.gz" KEYWORDS="~amd64 ~ppc ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~ppc-macos" IUSE+=" minimal" diff --git a/sci-biology/emboss/files/ax_lib_mysql.m4 b/sci-biology/emboss/files/ax_lib_mysql.m4 new file mode 100644 index 000000000..e27d755db --- /dev/null +++ b/sci-biology/emboss/files/ax_lib_mysql.m4 @@ -0,0 +1,147 @@ +# =========================================================================== +# http://www.gnu.org/software/autoconf-archive/ax_lib_mysql.html +# =========================================================================== +# +# SYNOPSIS +# +# AX_LIB_MYSQL([MINIMUM-VERSION]) +# +# DESCRIPTION +# +# This macro provides tests of availability of MySQL client library of +# particular version or newer. +# +# AX_LIB_MYSQL macro takes only one argument which is optional. If there +# is no required version passed, then macro does not run version test. +# +# The --with-mysql option takes one of three possible values: +# +# no - do not check for MySQL client library +# +# yes - do check for MySQL library in standard locations (mysql_config +# should be in the PATH) +# +# path - complete path to mysql_config utility, use this option if +# mysql_config can't be found in the PATH +# +# This macro calls: +# +# AC_SUBST(MYSQL_CFLAGS) +# AC_SUBST(MYSQL_LDFLAGS) +# AC_SUBST(MYSQL_VERSION) +# +# And sets: +# +# HAVE_MYSQL +# +# LICENSE +# +# Copyright (c) 2008 Mateusz Loskot <mateusz@loskot.net> +# +# Copying and distribution of this file, with or without modification, are +# permitted in any medium without royalty provided the copyright notice +# and this notice are preserved. This file is offered as-is, without any +# warranty. + +#serial 12 + +AC_DEFUN([AX_LIB_MYSQL], +[ + AC_ARG_WITH([mysql], + AS_HELP_STRING([--with-mysql=@<:@ARG@:>@], + [use MySQL client library @<:@default=yes@:>@, optionally specify path to mysql_config] + ), + [ + if test "$withval" = "no"; then + want_mysql="no" + elif test "$withval" = "yes"; then + want_mysql="yes" + else + want_mysql="yes" + MYSQL_CONFIG="$withval" + fi + ], + [want_mysql="yes"] + ) + AC_ARG_VAR([MYSQL_CONFIG], [Full path to mysql_config program]) + + MYSQL_CFLAGS="" + MYSQL_LDFLAGS="" + MYSQL_VERSION="" + + dnl + dnl Check MySQL libraries + dnl + + if test "$want_mysql" = "yes"; then + + if test -z "$MYSQL_CONFIG" ; then + AC_PATH_PROGS([MYSQL_CONFIG], [mysql_config mysql_config5], [no]) + fi + + if test "$MYSQL_CONFIG" != "no"; then + MYSQL_CFLAGS="`$MYSQL_CONFIG --cflags`" + MYSQL_LDFLAGS="`$MYSQL_CONFIG --libs`" + + MYSQL_VERSION=`$MYSQL_CONFIG --version` + + found_mysql="yes" + else + found_mysql="no" + fi + fi + + dnl + dnl Check if required version of MySQL is available + dnl + + + mysql_version_req=ifelse([$1], [], [], [$1]) + + if test "$found_mysql" = "yes" -a -n "$mysql_version_req"; then + + AC_MSG_CHECKING([if MySQL version is >= $mysql_version_req]) + + dnl Decompose required version string of MySQL + dnl and calculate its number representation + mysql_version_req_major=`expr $mysql_version_req : '\([[0-9]]*\)'` + mysql_version_req_minor=`expr $mysql_version_req : '[[0-9]]*\.\([[0-9]]*\)'` + mysql_version_req_micro=`expr $mysql_version_req : '[[0-9]]*\.[[0-9]]*\.\([[0-9]]*\)'` + if test "x$mysql_version_req_micro" = "x"; then + mysql_version_req_micro="0" + fi + + mysql_version_req_number=`expr $mysql_version_req_major \* 1000000 \ + \+ $mysql_version_req_minor \* 1000 \ + \+ $mysql_version_req_micro` + + dnl Decompose version string of installed MySQL + dnl and calculate its number representation + mysql_version_major=`expr $MYSQL_VERSION : '\([[0-9]]*\)'` + mysql_version_minor=`expr $MYSQL_VERSION : '[[0-9]]*\.\([[0-9]]*\)'` + mysql_version_micro=`expr $MYSQL_VERSION : '[[0-9]]*\.[[0-9]]*\.\([[0-9]]*\)'` + if test "x$mysql_version_micro" = "x"; then + mysql_version_micro="0" + fi + + mysql_version_number=`expr $mysql_version_major \* 1000000 \ + \+ $mysql_version_minor \* 1000 \ + \+ $mysql_version_micro` + + mysql_version_check=`expr $mysql_version_number \>\= $mysql_version_req_number` + if test "$mysql_version_check" = "1"; then + AC_MSG_RESULT([yes]) + else + AC_MSG_RESULT([no]) + fi + fi + + if test "$found_mysql" = "yes" ; then + AC_DEFINE([HAVE_MYSQL], [1], + [Define to 1 if MySQL libraries are available]) + fi + + AC_SUBST([MYSQL_VERSION]) + AC_SUBST([MYSQL_CFLAGS]) + AC_SUBST([MYSQL_LDFLAGS]) +]) diff --git a/sci-biology/emboss/files/emboss-6.3.1_p4-r2_Makefile.patch b/sci-biology/emboss/files/emboss-6.3.1_p4-r2_Makefile.patch new file mode 100644 index 000000000..419369ea3 --- /dev/null +++ b/sci-biology/emboss/files/emboss-6.3.1_p4-r2_Makefile.patch @@ -0,0 +1,47 @@ +--- EMBOSS-6.3.1/nucleus/Makefile 2013-09-11 14:50:25.140219756 +0200 ++++ nucleus/Makefile 2013-09-11 14:52:00.920220006 +0200 +@@ -165,7 +165,7 @@ + ESYSTEMLIBS = + EXEEXT = + FGREP = /bin/grep -F +-GD_LIBS = -ljpeg -lfontconfig -lfreetype -lz -lm -lgd ++GD_LIBS = + GREP = /bin/grep + HAVE_MEMMOVE = + HAVE_STRERROR = +@@ -180,7 +180,7 @@ + LD = /usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64 + LDFLAGS = -Wl,--as-needed + LIBOBJS = +-LIBS = -L/usr/lib64/mysql -lmysqlclient -lpthread -lz -lm -lrt -lssl -lcrypto -ldl -lm -lhpdf -lpng16 -L/usr/lib64 -lz -ljpeg -lfontconfig -lfreetype -lz -lm -lgd ++LIBS = + LIBTOOL = $(SHELL) $(top_builddir)/libtool + LIPO = + LN_S = ln -s +@@ -219,7 +219,7 @@ + # zap the crap + PLPLOT_CFLAGS = + PLPLOT_CPPFLAGS = +-PLPLOT_LIBS = -lplplotd -lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lcairo -lSM -lICE -lX11 -lXext -lgd -lpng -lz -ljpeg -lfreetype -lSM -lICE -lX11 -lXext -lpthread -lLASi -lpangoft2-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lfreetype -lfontconfig -lhpdf -lm -lcsirocsa -lnistcd -lqsastime -lfreetype ++PLPLOT_LIBS = + PNG_CFLAGS = -I/usr/include/libpng16 + PNG_LIBS = -lpng16 + POSIX_MALLOC_THRESHOLD = -DPOSIX_MALLOC_THRESHOLD=10 +@@ -336,7 +336,7 @@ + VERS_INF = -version-info 6:3:0 + LINKFLAGS = $(VERS_INF) + #LINKFLAGS = $(VERS_INF) $(CYGWIN_LDFLAGS) $(CYGWIN_LIBS) +-libnucleus_la_LDFLAGS = $(LINKFLAGS) ++libnucleus_la_LDFLAGS = $(LDFLAGS) + libnucleus_la_LIBADD = -L../ajax/core -L../ajax/graphics -L../ajax/acd -lajax -lajaxg -lacd + all: all-am + +@@ -407,7 +407,7 @@ + rm -f $${locs}; \ + } + libnucleus.la: $(libnucleus_la_OBJECTS) $(libnucleus_la_DEPENDENCIES) $(EXTRA_libnucleus_la_DEPENDENCIES) +- $(libnucleus_la_LINK) -rpath $(libdir) $(libnucleus_la_OBJECTS) $(libnucleus_la_LIBADD) $(LIBS) ++ $(libnucleus_la_LINK) -rpath $(libdir) $(libnucleus_la_OBJECTS) $(LIBS) + + mostlyclean-compile: + -rm -f *.$(OBJEXT) diff --git a/sci-biology/emboss/files/emboss-6.3.1_p4-r2_compilations-paths.patch b/sci-biology/emboss/files/emboss-6.3.1_p4-r2_compilations-paths.patch new file mode 100644 index 000000000..8f87ef9fa --- /dev/null +++ b/sci-biology/emboss/files/emboss-6.3.1_p4-r2_compilations-paths.patch @@ -0,0 +1,315 @@ +--- EMBOSS-6.3.1/configure.in 2013-09-11 03:55:15.510117066 +0200 ++++ configure.in 2013-09-11 03:48:10.410115955 +0200 +@@ -449,7 +447,8 @@ + if test "`uname -a | grep Darwin`"; then + OSXX=`sw_vers -productVersion | sed 's/\(10\.[[0-9]]*\).*/\1/'` + if test ${OSXX} '>' '10.4'; then +- CFLAGS="$CFLAGS -I/usr/X11/include -L/usr/X11/lib" ++ CPPFLAGS="$CPPFLAGS -I/usr/X11/include" ++ LDFLAGS="$LDFLAGS -L/usr/X11/lib" + fi + fi + fi +@@ -461,7 +460,7 @@ + AM_CONDITIONAL(ESYSTEMLIBS, test "$have_systemlibs" = "yes") + AC_SUBST(ESYSTEMLIBS) + AC_SUBST(DEFINE_USE_SYSTEM_PCRE) +-AC_SUBST(PLPLOT_CFLAGS) ++AC_SUBST(PLPLOT_CPPFLAGS) + AC_SUBST(PLPLOT_LIBS) + + +--- EMBOSS-6.3.1/ajax/graphics/Makefile.am 2013-09-11 03:27:30.110112715 +0200 ++++ ajax/graphics/Makefile.am 2013-09-11 03:58:50.860117628 +0200 +@@ -19,7 +19,7 @@ + + + INCLUDES = \ +-$(EXTRA_INCLUDES) -I$(top_srcdir)/ajax/core ++$(EXTRA_INCLUDES) -I$(top_srcdir)/ajax/core -I$(top_srcdir)/plplot + + AJAXGSRC = ajgraph.c ajhist.c + +--- EMBOSS-6.3.1/ajax/acd/Makefile.am 2013-09-11 03:27:30.110112715 +0200 ++++ ajax/acd/Makefile.am 2013-09-11 03:59:10.310117679 +0200 +@@ -24,7 +24,8 @@ + -I$(top_srcdir)/ajax/core \ + -I$(top_srcdir)/ajax/graphics \ + -I$(top_srcdir)/ajax/ensembl \ +--I$(top_srcdir)/ajax/ajaxdb ++-I$(top_srcdir)/ajax/ajaxdb \ ++-I$(top_srcdir)/plplot + + ACDSRC = ajacd.c + +--- EMBOSS-6.3.1/nucleus/Makefile.am 2013-09-11 03:27:30.110112715 +0200 ++++ nucleus/Makefile.am 2013-09-11 03:59:28.630117727 +0200 +@@ -32,7 +32,7 @@ + $(EXTRA_INCLUDES) \ + -I$(top_srcdir)/ajax/core -I$(top_srcdir)/ajax/graphics \ + -I$(top_srcdir)/ajax/ensembl -I$(top_srcdir)/ajax/ajaxdb \ +- -I$(top_srcdir)/ajax/acd ++ -I$(top_srcdir)/ajax/acd -I$(top_srcdir)/plplot + + NUCLSRC = embaln.c embcom.c embcons.c embdata.c embdbi.c embdmx.c \ + embdomain.c embest.c embexit.c embgroup.c embiep.c embindex.c \ +--- EMBOSS-6.3.1/emboss/Makefile.am 2013-09-11 03:27:30.110112715 +0200 ++++ emboss/Makefile.am 2013-09-11 03:59:46.340117773 +0200 +@@ -89,7 +89,7 @@ + $(EXTRA_INCLUDES) \ + -I$(top_srcdir)/ajax/core -I$(top_srcdir)/ajax/graphics \ + -I$(top_srcdir)/ajax/ensembl -I$(top_srcdir)/ajax/ajaxdb \ +- -I$(top_srcdir)/ajax/acd ++ -I$(top_srcdir)/ajax/acd -I$(top_srcdir)/plplot + + + aaindexextract_SOURCES = aaindexextract.c +--- EMBOSS-6.3.1/Makefile.am 2013-09-11 04:19:01.770120791 +0200 ++++ Makefile.am 2013-09-11 04:19:18.460120835 +0200 +@@ -13,8 +13,8 @@ + JEMBOSS_DIR = jemboss + endif + +-SUBDIRS = $(EXTRA_DIRS) ajax nucleus emboss test doc $(JEMBOSS_DIR) +-DIST_SUBDIRS = $(EXTRA_DIRS) ajax nucleus emboss test doc $(JEMBOSS_DIR) ++SUBDIRS = $(EXTRA_DIRS) plplot ajax nucleus emboss test doc $(JEMBOSS_DIR) ++DIST_SUBDIRS = $(EXTRA_DIRS) plplot ajax nucleus emboss test doc $(JEMBOSS_DIR) + + # AJAX_FIXED_ROOT = \"`pwd`/emboss/acd\" + +--- EMBOSS-6.3.1/plplot/Makefile.am 2013-09-11 09:34:44.620170277 +0200 ++++ plplot/Makefile.am 2013-09-11 09:35:35.820170411 +0200 +@@ -10,26 +10,27 @@ + if AMPNG + + if AMPDF +-TESTPDF_CFLAGS = -Wl,-G -lhpdf ++TESTPDF_LIBS = -Wl,-G -lhpdf + else +-TESTPDF_CFLAGS = -Wl,-G ++TESTPDF_LIBS = -Wl,-G + endif + +-TESTPNG_CFLAGS = $(TESTPDF_CFLAGS) -lgd -lpng -lz -lX11 -lm ++TESTPNG_LIBS = $(TESTPDF_LIBS) -lgd -lpng -lz -lX11 -lm + else +-TESTPNG_CFLAGS = $(TESTPDF_CFLAGS) -lX11 ++TESTPNG_LIBS = $(TESTPDF_LIBS) -lX11 + endif + endif + endif + +-AM_CFLAGS = $(TESTPNG_CFLAGS) ++AM_LIBS = $(TESTPNG_LIBS) + + if ISCYGWIN + CYGWIN_LDFLAGS = -no-undefined -Wl,--add-stdcall-alias -Wl,--export-all-symbols -Wl,--enable-auto-import + CYGWIN_LIBS = -lX11 -lgd -lpng -lz + endif + +-INCLUDES = $(X_CFLAGS) -I$(srcdir)/ -I/usr/include/gd -DPREFIX=\"$(prefix)\" -DBUILD_DIR=\"$(srcdir)\" -DDRV_DIR=\"$(srcdir)\" -DEMBOSS_TOP=\"$(EMBOSS_TOP)\" ++INCLUDES = -I$(srcdir)/ -I/usr/include/gd -DPREFIX=\"$(prefix)\" -DBUILD_DIR=\"$(srcdir)\" -DDRV_DIR=\"$(srcdir)\" -DEMBOSS_TOP=\"$(EMBOSS_TOP)\" ++LIBS = $(AM_LIBS) + + PLPLOTSRC = pdfutils.c plargs.c plbox.c plcont.c plcore.c \ + plctrl.c plcvt.c pldtik.c plfill.c plhist.c plline.c plmap.c \ +--- EMBOSS-6.3.1/m4/pngdriver.m4 2013-09-11 10:39:07.680180369 +0200 ++++ m4/pngdriver.m4 2013-09-11 10:44:16.000181174 +0200 +@@ -63,7 +63,8 @@ + if test "`uname`" = "SunOS"; then + AC_CHECK_LIB(iconv, libiconv_close, ICCHECK=1, ICCHECK=0, -L${ALT_HOME}/lib -liconv) + if test $ICCHECK = "1" ; then +- LDFLAGS="${LDFLAGS} -L${ALT_HOME}/lib -liconv" ++ LDFLAGS="${LDFLAGS} -L${ALT_HOME}/lib" ++ LIBS="${LIBS} -liconv" + fi + LDFLAGS="$LDFLAGS -R$ALT_HOME/lib" + fi +--- EMBOSS-6.3.1/m4/java.m4 2013-09-11 10:39:03.490180358 +0200 ++++ m4/java.m4 2013-09-11 10:46:08.240181467 +0200 +@@ -180,7 +180,7 @@ + + if test "$withval" = "yes" ; then + CFLAGS="$CFLAGS -D_REENTRANT" +- LDFLAGS="$LDFLAGS -lpthread" ++ LDFLAGS="$LDFLAGS" + LIBS="$LIBS -lpthread" + fi + +@@ -192,38 +192,38 @@ + + if test "$withval" = "linux" ; then + CFLAGS="$CFLAGS -D_REENTRANT" +- LDFLAGS="$LDFLAGS -lpthread" ++ LDFLAGS="$LDFLAGS" + LIBS="$LIBS -lpthread" + fi + + if test "$withval" = "solaris" ; then + CFLAGS="$CFLAGS -D_POSIX_C_SOURCE=199506L" +- LDFLAGS="$LDFLAGS -lpthread" ++ LDFLAGS="$LDFLAGS" + LIBS="$LIBS -lpthread" + fi + if test "$withval" = "macos" ; then + CFLAGS="$CFLAGS" +- LDFLAGS="$LDFLAGS -lpthread" ++ LDFLAGS="$LDFLAGS" + LIBS="$LIBS -lpthread" + fi + if test "$withval" = "hpux" ; then + CFLAGS="$CFLAGS -Ae +z -DNATIVE -D_POSIX_C_SOURCE=199506L" +- LDFLAGS="$LDFLAGS -lpthread" ++ LDFLAGS="$LDFLAGS" + LIBS="$LIBS -lpthread" + fi + if test "$withval" = "irix" ; then + CFLAGS="$CFLAGS" +- LDFLAGS="$LDFLAGS -lpthread" ++ LDFLAGS="$LDFLAGS" + LIBS="$LIBS -lpthread" + fi + if test "$withval" = "aix" ; then + CFLAGS="$CFLAGS -D_REENTRANT" +- LDFLAGS="$LDFLAGS -lpthread" ++ LDFLAGS="$LDFLAGS" + LIBS="$LIBS -lpthread" + fi + if test "$withval" = "osf" ; then + CFLAGS="$CFLAGS -D_REENTRANT -D_OSF_SOURCE" +- LDFLAGS="$LDFLAGS -lpthread" ++ LDFLAGS="$LDFLAGS" + LIBS="$LIBS -lpthread" + fi + else +--- EMBOSS-6.3.1/m4/mysql.m4 2013-09-11 11:03:07.160184129 +0200 ++++ m4/mysql.m4 2013-09-11 11:04:39.440184370 +0200 +@@ -85,7 +85,6 @@ + AC_MSG_CHECKING([for MySQL libraries]) + + dnl MYSQL_CFLAGS="`$MYSQL_CONFIG --cflags`" +- MYSQL_CFLAGS="`$MYSQL_CONFIG --include`" + MYSQL_LIBS="`$MYSQL_CONFIG --libs`" + + MYSQL_VERSION=`$MYSQL_CONFIG --version` +--- EMBOSS-6.3.1/m4/mysql.m4 2013-09-11 11:38:09.330189621 +0200 ++++ m4/mysql.m4 2013-09-11 11:41:02.170190072 +0200 +@@ -170,6 +170,4 @@ + fi + + AC_SUBST([MYSQL_VERSION]) +- AC_SUBST([MYSQL_CFLAGS]) +- AC_SUBST([MYSQL_LIBS]) + ]) +--- EMBOSS-6.3.1/configure.in 2013-09-11 12:23:17.330196695 +0200 ++++ configure.in 2013-09-11 12:23:21.480196706 +0200 +@@ -8,6 +8,8 @@ + AC_INIT(ajax/core/ajmath.c) + AM_INIT_AUTOMAKE([EMBOSS],[6.3.1]) + ++AC_CONFIG_MACRO_DIR([m4]) ++ + # Make sure CFLAGS is defined to stop LT_INIT adding -g + CFLAGS="$CFLAGS " + +--- EMBOSS-6.3.1/nucleus/Makefile.am 2013-09-11 12:33:14.260198254 +0200 ++++ nucleus/Makefile.am 2013-09-11 12:33:16.650198260 +0200 +@@ -58,4 +58,4 @@ + endif + + libnucleus_la_LDFLAGS = $(LINKFLAGS) +-libnucleus_la_LIBADD = ../ajax/core/libajax.la ../ajax/graphics/libajaxg.la ../ajax/acd/libacd.la ++libnucleus_la_LIBADD = -L../ajax/core -L../ajax/graphics -L../ajax/acd -lajax -lajaxg -lacd +--- EMBOSS-6.3.1/ajax/ensembl/Makefile.am 2013-09-11 12:41:06.340199487 +0200 ++++ ajax/ensembl/Makefile.am 2013-09-11 12:41:40.460199577 +0200 +@@ -56,5 +56,5 @@ + LINKFLAGS = $(VERS_INF) + endif + +-libensembl_la_LDFLAGS = $(LINKFLAGS) +-libensembl_la_LIBADD = ../core/libajax.la ++libensembl_la_LDFLAGS = $(LINKFLAGS) -L../core ++libensembl_la_LIBADD = -lajax +--- EMBOSS-6.3.1/ajax/graphics/Makefile.am 2013-09-11 12:42:17.730199674 +0200 ++++ ajax/graphics/Makefile.am 2013-09-11 12:42:47.000199750 +0200 +@@ -35,5 +35,5 @@ + LINKFLAGS = $(VERS_INF) + endif + +-libajaxg_la_LDFLAGS = $(LINKFLAGS) +-libajaxg_la_LIBADD = ../core/libajax.la $(EXTRA_LIBS) ++libajaxg_la_LDFLAGS = $(LINKFLAGS) -L../core/ ++libajaxg_la_LIBADD = -lajax $(EXTRA_LIBS) +--- EMBOSS-6.3.1/ajax/acd/Makefile.am 2013-09-11 12:43:11.660199815 +0200 ++++ ajax/acd/Makefile.am 2013-09-11 12:44:01.520199945 +0200 +@@ -41,5 +41,5 @@ + LINKFLAGS = $(VERS_INF) + endif + +-libacd_la_LDFLAGS = $(LINKFLAGS) +-libacd_la_LIBADD = ../core/libajax.la ../graphics/libajaxg.la ../ajaxdb/libajaxdb.la ++libacd_la_LDFLAGS = $(LINKFLAGS) -L../core -L../graphics -L../ajaxdb ++libacd_la_LIBADD = -lajax -lajaxg -lajaxdb +--- EMBOSS-6.3.1/ajax/ajaxdb/Makefile.am 2013-09-11 12:44:10.980199970 +0200 ++++ ajax/ajaxdb/Makefile.am 2013-09-11 12:44:40.040200046 +0200 +@@ -37,5 +37,5 @@ + LINKFLAGS = $(VERS_INF) + endif + +-libajaxdb_la_LDFLAGS = $(LINKFLAGS) +-libajaxdb_la_LIBADD = ../core/libajax.la ../ensembl/libensembl.la ++libajaxdb_la_LDFLAGS = $(LINKFLAGS) -L../core -L../ensembl ++libajaxdb_la_LIBADD = -lajax -lensembl +--- EMBOSS-6.3.1/configure.in 2013-09-11 13:24:39.720206315 +0200 ++++ configure.in 2013-09-11 13:24:58.610206364 +0200 +@@ -319,10 +319,8 @@ + AX_LIB_MYSQL + AX_LIB_POSTGRESQL + +-CFLAGS="$CFLAGS $MYSQL_CFLAGS" + LIBS="${MYSQL_LIBS} ${LIBS}" + +-CFLAGS="$POSTGRESQL_CFLAGS $CFLAGS" + LIBS="$POSTGRESQL_LIBS $LIBS" + + +--- EMBOSS-6.3.1/ajax/core/Makefile.am 2013-09-11 13:47:36.790209912 +0200 ++++ ajax/core/Makefile.am 2013-09-11 13:47:40.550209922 +0200 +@@ -65,5 +65,5 @@ + LINKFLAGS = $(VERS_INF) + endif + +-libajax_la_LDFLAGS = $(LINKFLAGS) ++libajax_la_LDFLAGS = + libajax_la_LIBADD = $(EXTRA_LIBS) $(POSTGRESQL_LIBS) $(MYSQL_LIBS) +--- EMBOSS-6.3.1/nucleus/Makefile.am 2013-09-11 14:03:21.960212381 +0200 ++++ nucleus/Makefile.am 2013-09-11 14:03:58.910212478 +0200 +@@ -22,11 +22,14 @@ + EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib \ + -I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre + else +-EXTRA_INCLUDES = $(PLPLOT_CFLAGS) ++EXTRA_INCLUDES = + endif + endif + + ++# zap the crap ++PLPLOT_CFLAGS = ++ + INCLUDES = $(X_CFLAGS) -I$(srcdir)/ \ + -I$(top_srcdir)/ajax \ + $(EXTRA_INCLUDES) \ +--- EMBOSS-6.3.1/emboss/Makefile.am 2013-09-11 14:23:50.570215591 +0200 ++++ emboss/Makefile.am 2013-09-11 14:24:24.950215680 +0200 +@@ -328,9 +328,7 @@ + + LDADD = ../nucleus/libnucleus.la ../ajax/acd/libacd.la \ + ../ajax/ajaxdb/libajaxdb.la ../ajax/ensembl/libensembl.la \ +- ../ajax/graphics/libajaxg.la ../ajax/core/libajax.la \ +- $(EXTRA_LDS) \ +- $(XLIB) ++ ../ajax/graphics/libajaxg.la ../ajax/core/libajax.la + + pkgdata_DATA = emboss.default.template + pkgdatadir=$(prefix)/share/$(PACKAGE) diff --git a/sci-biology/emboss/files/emboss-6.3.1_p4-r2_libtool.patch b/sci-biology/emboss/files/emboss-6.3.1_p4-r2_libtool.patch new file mode 100644 index 000000000..ad358e174 --- /dev/null +++ b/sci-biology/emboss/files/emboss-6.3.1_p4-r2_libtool.patch @@ -0,0 +1,18 @@ +--- EMBOSS-6.3.1/m4/libtool.m4 2013-09-11 12:03:45.180193633 +0200 ++++ m4/libtool.m4 2013-09-11 12:04:19.280193722 +0200 +@@ -4768,13 +4768,13 @@ + *Sun\ F*) # Sun Fortran 8.3 + tmp_sharedflag='-G' ;; + esac +- _LT_TAGVAR(archive_cmds, $1)='$CC '"$tmp_sharedflag""$tmp_addflag"' $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib' ++ _LT_TAGVAR(archive_cmds, $1)='$CC '"$tmp_sharedflag""$tmp_addflag"' $libobjs $deplibs ${wl}-soname $wl$soname -Wl,--as-needed -o $lib' + + if test "x$supports_anon_versioning" = xyes; then + _LT_TAGVAR(archive_expsym_cmds, $1)='echo "{ global:" > $output_objdir/$libname.ver~ + cat $export_symbols | sed -e "s/\(.*\)/\1;/" >> $output_objdir/$libname.ver~ + echo "local: *; };" >> $output_objdir/$libname.ver~ +- $CC '"$tmp_sharedflag""$tmp_addflag"' $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-version-script ${wl}$output_objdir/$libname.ver -o $lib' ++ $CC '"$tmp_sharedflag""$tmp_addflag"' $libobjs $deplibs ${wl}-soname $wl$soname ${wl}-version-script ${wl}$output_objdir/$libname.ver -Wl,--as-needed -o $lib' + fi + + case $cc_basename in diff --git a/sci-biology/emboss/files/emboss-6.3.1_p4-r1_plcol.patch b/sci-biology/emboss/files/emboss-6.3.1_p4-r2_plcol.patch index 0f5e592b7..0f5e592b7 100644 --- a/sci-biology/emboss/files/emboss-6.3.1_p4-r1_plcol.patch +++ b/sci-biology/emboss/files/emboss-6.3.1_p4-r2_plcol.patch diff --git a/sci-biology/ncbi-tools++/ChangeLog b/sci-biology/ncbi-tools++/ChangeLog index 270521cab..3da37d966 100644 --- a/sci-biology/ncbi-tools++/ChangeLog +++ b/sci-biology/ncbi-tools++/ChangeLog @@ -2,6 +2,87 @@ # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 14 Sep 2013; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + ncbi-tools++-9.0.0-r1.ebuild: + Support at least when user passes USE="gnutls -ssl -openssl" but what we + really want is to prefer gnutls over openssl if both are available on the + system. + + 14 Sep 2013; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + ncbi-tools++-9.0.0-r1.ebuild, + +files/ncbi-tools++-9.0.0-remove-LZO-definition-upstream.patch: + Add upstream ncbi-tools++-9.0.0-remove-LZO-definition-upstream.patch with + line + offset changes. + + 13 Sep 2013; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + ncbi-tools++-9.0.0-r1.ebuild, ncbi-tools++-12.0.0.ebuild, + +files/ncbi-tools++-9.0.0-fix-svn-URL-upstream.patch, + +files/ncbi-tools++-12.0.0-fix-svn-URL-upstream.patch: + Fix URL to point to a public SVN repository (an upstream patch from email + list): + + Date: Sun, 28 Jul 2013 22:05:34 -0400 + CC: <cpp@ncbi.nlm.nih.gov> + Subject: Re: [C++] new project startup example needed + + 13 Sep 2013; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + ncbi-tools++-12.0.0.ebuild, + files/ncbi-tools++-9.0.0-fix-creaders-linking.patch, + +files/ncbi-tools++-12.0.0-fix-FreeTDS-upstream.patch, + files/ncbi-tools++-12.0.0-fix-creaders-linking.patch: + Added an upstream patch from: + + Date: Wed, 28 Aug 2013 10:50:29 -0400 + List cpp <cpp@ncbi.nlm.nih.gov> + Subject: Re: [C++] error building ncbi toolkit v.12.0.0 + + Fixed line offsets in the ncbi-tools++-12.0.0-fix-creaders-linking.patch + file. + + Fixed file path in ncbi-tools++-9.0.0-fix-creaders-linking.patch header. + + The patches copied blindly from ncbi-tools++-9.0.0-r1 under 12.0.0 need to be + adjusted still to have correct line numbers. They do NOT apply cleanly at the + moment. + + 13 Sep 2013; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + ncbi-tools++-9.0.0-r1.ebuild, ncbi-tools++-12.0.0.ebuild, + files/ncbi-tools++-9.0.0-as-needed.patch, + +files/ncbi-tools++-9.0.0-fix-undef-reference-to-GenBankReaders_Register_Id1. + patch, files/ncbi-tools++-12.0.0-as-needed.patch: + files/ncbi-tools++-12.0.0-as-needed.patch + files/ncbi-tools++-9.0.0-as-needed.patch + + Remove redundant connect per message from Aaron Ucko <ucko@ncbi.nlm.nih.gov>: + + > +DLL_LIB = xncbi xutil seqset connect xconnect xnetblast + Then simply remove connect, which is redundant with xconnect. (connect + consists of code shared with NCBI's C Toolkit; xconnect adds a C++ + layer.) + + + 13 Sep 2013; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + ncbi-tools++-12.0.0.ebuild, + +files/ncbi-tools++-12.0.0-fix-creaders-linking.patch: + No, the fix-creaders-linking is needed for 12.0.0 as well. + +*ncbi-tools++-12.0.0 (13 Sep 2013) + + 13 Sep 2013; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + +ncbi-tools++-12.0.0.ebuild, +files/ncbi-tools++-12.0.0-as-needed.patch, + +files/ncbi-tools++-12.0.0-conf-opts.patch: + Latest release which needs so far only the two Gentoo patches. Would + be better to drop ${PV} from their filename to avoid their duplication + I think. + + 13 Sep 2013; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + ncbi-tools++-9.0.0-r1.ebuild, + +files/ncbi-tools++-9.0.0-fix-creaders-linking.patch: + add glew to dependencies inferrred via mesa + fix lib/libxobjread.so: undefined reference to 'AlignmentFileFree' message by + upstream patch + 12 Jun 2013; Justin Lecher <jlec@gentoo.org> ncbi-tools++-9.0.0-r1.ebuild: Drop empty line diff --git a/sci-biology/ncbi-tools++/Manifest b/sci-biology/ncbi-tools++/Manifest index 48b9d939a..88fdd5a5e 100644 --- a/sci-biology/ncbi-tools++/Manifest +++ b/sci-biology/ncbi-tools++/Manifest @@ -1 +1,2 @@ +DIST ncbi_cxx--12_0_0.tar.gz 37925914 SHA256 432d5c72cc02dad263f1b2f1ab875e04e60b1ded0c5537ed54e8095b50554d20 SHA512 1a79f2d95960efde6263289814102499460ec235dad36337dd398d668665e44015e06e40fd0e66a8fb16f526d326949adcaadcb667debeba5d8570b1a92e30ed WHIRLPOOL 16f0b6de7e0d898bca7a2a46a64a4aa0795f99673d4715a21cca2dc5aa728143b56f02ad9c108543195a8f86f4267777d2be9428dcf52f5495083a63961ad867 DIST ncbi_cxx--9_0_0.tar.gz 33815259 SHA256 f561eb6de12dc7a1e3325d6fc1f76ca097099a31116fb407fa52e54174757fc7 SHA512 b8ce298d4e180915c86ea94cd0cba44cabe8ae1173525a7af3038736572427b4cb25191c6b8ad0fcde14c2677a03fbc675ab22dc64d496dd4a21d70b978c2fab WHIRLPOOL 1c5569c5fc73f67850eb6b35eece0e719a97fee5368f43cca9733b6d2a308dc0c66d2814da15e7b64a400ab7df130ab77e9fc6f3412778cc7c003684a1f6b594 diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-as-needed.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-as-needed.patch new file mode 100644 index 000000000..821380023 --- /dev/null +++ b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-as-needed.patch @@ -0,0 +1,1864 @@ + src/algo/align/contig_assembly/Makefile.xalgocontig_assembly.lib | 2 ++ + src/algo/align/ngalign/Makefile.xngalign.lib | 2 ++ + src/algo/align/nw/Makefile.xalgoalignnw.lib | 2 ++ + src/algo/align/prosplign/Makefile.prosplign.lib | 2 ++ + src/algo/align/splign/Makefile.xalgoalignsplign.lib | 2 ++ + src/algo/blast/api/Makefile.xblast.lib | 2 +- + src/algo/blast/blastinput/Makefile.blastinput.lib | 2 +- + src/algo/blast/core/Makefile.blast.lib | 2 ++ + src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib | 2 ++ + src/algo/blast/dbindex_search/Makefile.xalgoblastdbindex_search.lib | 2 ++ + src/algo/blast/format/Makefile.xblastformat.lib | 2 +- + src/algo/blast/gumbel_params/Makefile.gumbelparams.lib | 1 + + src/algo/cobalt/Makefile.cobalt.lib | 2 ++ + src/algo/dustmask/Makefile.xalgodustmask.lib | 1 + + src/algo/gnomon/Makefile.gnomon.lib | 2 +- + src/algo/ms/formats/pepxml/Makefile.pepXML.lib | 2 ++ + src/algo/ms/omssa/Makefile.xomssa.lib | 2 ++ + src/algo/phy_tree/Makefile.xalgophytree.lib | 2 +- + src/algo/phy_tree/phytree_format/Makefile.phytreeformat.lib | 2 ++ + src/algo/segmask/Makefile.xalgosegmask.lib | 1 + + src/algo/seqqa/Makefile.xalgoseqqa.lib | 2 ++ + src/algo/sequence/Makefile.xalgoseq.lib | 2 ++ + src/algo/structure/bma_refine/Makefile.xbma_refiner.lib | 3 +++ + src/algo/structure/cd_utils/Makefile.xcd_utils.lib | 2 +- + src/algo/structure/struct_dp/Makefile.xstruct_dp.lib | 2 ++ + src/algo/structure/struct_util/Makefile.xstruct_util.lib | 2 ++ + src/algo/structure/threader/Makefile.xstruct_thread.lib | 2 ++ + src/algo/text/Makefile.xalgotext.lib | 2 ++ + src/algo/volume_merge/Makefile.xalgovmerge.lib | 2 ++ + src/algo/winmask/Makefile.xalgowinmask.lib | 2 ++ + src/cgi/Makefile.cgi.lib | 2 ++ + src/cgi/Makefile.fcgi.lib | 2 ++ + src/connect/Makefile.connssl.lib | 2 ++ + src/connect/Makefile.xconnect.lib | 4 ++++ + src/connect/Makefile.xthrserv.lib | 2 +- + src/connect/Makefile.xxconnect.lib | 2 ++ + src/connect/services/Makefile.ncbi_xcache_netcache.lib | 2 +- + src/connect/services/Makefile.xconnserv.lib | 2 +- + src/connect/test/Makefile.conntest.lib | 2 ++ + src/corelib/Makefile.test_boost.lib | 2 ++ + src/corelib/Makefile.test_mt.lib | 2 ++ + src/corelib/test/Makefile.pbacktest.lib | 2 ++ + src/db/bdb/Makefile.bdb.lib | 4 ++++ + src/db/bdb/Makefile.ncbi_xcache_bdb.lib | 2 +- + src/db/sqlite/Makefile.sqlitewrapp.lib | 3 +++ + src/dbapi/Makefile.dbapi.lib | 5 +++++ + src/dbapi/driver/Makefile.dbapi_driver.lib | 2 ++ + src/dbapi/driver/samples/Makefile.dbapi_sample_base.lib | 2 ++ + src/dbapi/lang_bind/python/Makefile.python_ncbi_dbapi.lib | 2 +- + src/dbapi/simple/Makefile.sdbapi.lib | 1 + + src/html/Makefile.html.lib | 2 ++ + src/misc/cgi_redirect/Makefile.cgi_redirect.lib | 2 ++ + src/misc/grid_cgi/Makefile.xgridcgi.lib | 2 ++ + src/objects/access/Makefile.access.lib | 1 + + src/objects/biblio/Makefile.biblio.lib | 2 ++ + src/objects/biotree/Makefile.biotree.lib | 2 ++ + src/objects/blast/Makefile.blast.lib | 2 ++ + src/objects/blast/Makefile.xnetblastcli.lib | 2 ++ + src/objects/blastdb/Makefile.blastdb.lib | 2 ++ + src/objects/blastxml/Makefile.blastxml.lib | 2 ++ + src/objects/cdd/Makefile.cdd.lib | 2 ++ + src/objects/cn3d/Makefile.cn3d.lib | 2 ++ + src/objects/docsum/Makefile.docsum.lib | 2 ++ + src/objects/entrez2/Makefile.entrez2.lib | 2 ++ + src/objects/entrez2/Makefile.entrez2cli.lib | 2 ++ + src/objects/entrezgene/Makefile.entrezgene.lib | 2 ++ + src/objects/featdef/Makefile.featdef.lib | 2 ++ + src/objects/gbseq/Makefile.gbseq.lib | 2 ++ + src/objects/general/Makefile.general.lib | 2 ++ + src/objects/genomecoll/Makefile.genome_collection.lib | 2 ++ + src/objects/homologene/Makefile.homologene.lib | 2 ++ + src/objects/id1/Makefile.id1.lib | 2 ++ + src/objects/id1/Makefile.id1cli.lib | 2 ++ + src/objects/id2/Makefile.id2.lib | 2 ++ + src/objects/id2/Makefile.id2cli.lib | 2 ++ + src/objects/insdseq/Makefile.insdseq.lib | 2 ++ + src/objects/macro/Makefile.macro.lib | 2 ++ + src/objects/medlars/Makefile.medlars.lib | 2 ++ + src/objects/medline/Makefile.medline.lib | 2 ++ + src/objects/mim/Makefile.mim.lib | 2 ++ + src/objects/mla/Makefile.mla.lib | 2 ++ + src/objects/mla/Makefile.mlacli.lib | 2 ++ + src/objects/mmdb/Makefile.mmdb.lib | 2 ++ + src/objects/ncbimime/Makefile.ncbimime.lib | 2 ++ + src/objects/objprt/Makefile.objprt.lib | 2 ++ + src/objects/omssa/Makefile.omssa.lib | 2 ++ + src/objects/pcassay/Makefile.pcassay.lib | 2 ++ + src/objects/pcsubstance/Makefile.pcsubstance.lib | 2 ++ + src/objects/proj/Makefile.proj.lib | 2 ++ + src/objects/pub/Makefile.pub.lib | 2 ++ + src/objects/pubmed/Makefile.pubmed.lib | 2 ++ + src/objects/remap/Makefile.remap.lib | 2 ++ + src/objects/remap/Makefile.remapcli.lib | 2 ++ + src/objects/scoremat/Makefile.scoremat.lib | 2 ++ + src/objects/seq/Makefile.seq.lib | 2 ++ + src/objects/seqcode/Makefile.seqcode.lib | 2 ++ + src/objects/seqedit/Makefile.seqedit.lib | 1 + + src/objects/seqset/Makefile.seqset.lib | 1 + + src/objects/seqsplit/Makefile.seqsplit.lib | 2 ++ + src/objects/seqtest/Makefile.seqtest.lib | 2 ++ + src/objects/submit/Makefile.submit.lib | 1 + + src/objects/taxon1/Makefile.taxon1.lib | 2 ++ + src/objects/taxon3/Makefile.taxon3.lib | 2 ++ + src/objects/tinyseq/Makefile.tinyseq.lib | 2 ++ + src/objects/valerr/Makefile.valerr.lib | 2 ++ + src/objects/valid/Makefile.valid.lib | 2 ++ + src/objects/variation/Makefile.variation.lib | 1 + + src/objmgr/split/Makefile.id2_split.lib | 2 +- + src/objmgr/util/Makefile.util.lib | 1 + + src/objtools/align/Makefile.xalntool.lib | 2 ++ + src/objtools/align_format/Makefile.align_format.lib | 2 ++ + src/objtools/alnmgr/Makefile.alnmgr.lib | 1 + + src/objtools/blast/blastdb_format/Makefile.blastdb_format.lib | 2 ++ + src/objtools/blast/gene_info_reader/Makefile.gene_info.lib | 2 ++ + src/objtools/blast/gene_info_writer/Makefile.gene_info_writer.lib | 2 ++ + src/objtools/blast/seqdb_reader/Makefile.seqdb.lib | 2 ++ + src/objtools/blast/seqdb_writer/Makefile.writedb.lib | 2 ++ + src/objtools/blast/services/Makefile.blast_services.lib | 1 + + src/objtools/cddalignview/Makefile.cddalignview.lib | 2 ++ + src/objtools/cleanup/Makefile.cleanup.lib | 2 +- + src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib | 3 +++ + .../data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib | 2 ++ + src/objtools/data_loaders/cdd/Makefile.ncbi_xloader_cdd.lib | 2 ++ + src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib | 2 +- + src/objtools/data_loaders/genbank/id2/Makefile.ncbi_xreader_id2.lib | 2 ++ + src/objtools/data_loaders/patcher/Makefile.ncbi_xloader_patcher.lib | 2 ++ + src/objtools/data_loaders/trace/Makefile.xloader_trace.lib | 2 ++ + src/objtools/edit/Makefile.edit.lib | 2 ++ + src/objtools/eutils/api/Makefile.eutils.lib | 2 ++ + src/objtools/eutils/egquery/Makefile.egquery.lib | 2 ++ + src/objtools/eutils/ehistory/Makefile.ehistory.lib | 2 ++ + src/objtools/eutils/einfo/Makefile.einfo.lib | 2 ++ + src/objtools/eutils/elink/Makefile.elink.lib | 2 ++ + src/objtools/eutils/epost/Makefile.epost.lib | 2 ++ + src/objtools/eutils/esearch/Makefile.esearch.lib | 2 ++ + src/objtools/eutils/espell/Makefile.espell.lib | 2 ++ + src/objtools/eutils/esummary/Makefile.esummary.lib | 2 ++ + src/objtools/eutils/linkout/Makefile.linkout.lib | 2 ++ + src/objtools/eutils/uilist/Makefile.uilist.lib | 2 ++ + src/objtools/format/Makefile.xformat.lib | 2 ++ + src/objtools/lds/Makefile.lds.lib | 2 +- + src/objtools/manip/Makefile.xobjmanip.lib | 2 ++ + src/objtools/readers/Makefile.xobjread.lib | 3 +-- + src/objtools/readers/Makefile.xobjreadex.lib | 2 +- + src/objtools/seqmasks_io/Makefile.seqmasks_io.lib | 2 +- + src/objtools/simple/Makefile.xobjsimple.lib | 1 + + src/objtools/snputil/Makefile.snputil.lib | 2 ++ + src/objtools/validator/Makefile.validator.lib | 2 ++ + src/objtools/writers/Makefile.xobjwrite.lib | 1 + + src/sample/app/asn/Makefile.sample_asn.lib | 2 ++ + src/sample/app/soap/Makefile.soap_dataobj.lib | 2 ++ + src/sample/lib/asn_lib/Makefile.asn_sample_lib.lib | 2 ++ + src/sample/lib/basic/Makefile.basic_sample_lib.lib | 2 ++ + src/sample/lib/dtd/Makefile.dtd_sample_lib.lib | 2 ++ + src/sample/lib/xsd/Makefile.xsd_sample_lib.lib | 2 ++ + src/serial/Makefile.serial.lib | 2 ++ + src/serial/soap/Makefile.soap.lib | 2 ++ + src/serial/soap/Makefile.soap_server.lib | 2 ++ + src/serial/test/Makefile.we_cpp.lib | 1 + + src/sra/data_loaders/bam/Makefile.ncbi_xloader_bam.lib | 2 +- + src/sra/sdk/libs/align/Makefile.align-writer.lib | 2 +- + src/util/Makefile.util.lib | 2 ++ + src/util/compress/api/Makefile.compress.lib | 2 +- + src/util/qparse/Makefile.xqueryparse.lib | 2 ++ + src/util/regexp/Makefile.regexp.lib | 2 ++ + src/util/sequtil/Makefile.sequtil.lib | 2 ++ + src/util/xregexp/Makefile.xregexp.lib | 2 +- + 167 files changed, 307 insertions(+), 23 deletions(-) + +diff --git a/src/algo/align/contig_assembly/Makefile.xalgocontig_assembly.lib b/src/algo/align/contig_assembly/Makefile.xalgocontig_assembly.lib +index c8851d8..35ae629 100644 +--- a/src/algo/align/contig_assembly/Makefile.xalgocontig_assembly.lib ++++ b/src/algo/align/contig_assembly/Makefile.xalgocontig_assembly.lib +@@ -10,3 +10,5 @@ LIB = xalgocontig_assembly + + CXXFLAGS = $(FAST_CXXFLAGS) + LDFLAGS = $(FAST_LDFLAGS) ++ ++DLL_LIB = align_format blastinput dbapi_driver seq xalgoalignnw xalgodustmask xalnmgr xblast xncbi xobjmgr xobjutil xser # axf +diff --git a/src/algo/align/ngalign/Makefile.xngalign.lib b/src/algo/align/ngalign/Makefile.xngalign.lib +index d163f7c..ade88ce 100644 +--- a/src/algo/align/ngalign/Makefile.xngalign.lib ++++ b/src/algo/align/ngalign/Makefile.xngalign.lib +@@ -15,3 +15,5 @@ LIB = xngalign + + CXXFLAGS = $(FAST_CXXFLAGS) -I./. + LDFLAGS = $(FAST_LDFLAGS) ++ ++DLL_LIB = seq xalgoalignutil xncbi blastinput xalgoalignnw align_format xcgi ncbi_xloader_genbank ncbi_xreader ncbi_xreader_id2 +diff --git a/src/algo/align/nw/Makefile.xalgoalignnw.lib b/src/algo/align/nw/Makefile.xalgoalignnw.lib +index acc1ddf..acba81c 100644 +--- a/src/algo/align/nw/Makefile.xalgoalignnw.lib ++++ b/src/algo/align/nw/Makefile.xalgoalignnw.lib +@@ -15,3 +15,5 @@ CXXFLAGS = $(FAST_CXXFLAGS) + LDFLAGS = $(FAST_LDFLAGS) + + WATCHERS = kiryutin ++ ++DLL_LIB = access align_format dbapi_driver general seq writedb xncbi xser # axf +diff --git a/src/algo/align/prosplign/Makefile.prosplign.lib b/src/algo/align/prosplign/Makefile.prosplign.lib +index 248ee37..73143ad 100644 +--- a/src/algo/align/prosplign/Makefile.prosplign.lib ++++ b/src/algo/align/prosplign/Makefile.prosplign.lib +@@ -10,3 +10,5 @@ LIB = prosplign + + CXXFLAGS = $(FAST_CXXFLAGS) + LDFLAGS = $(FAST_LDFLAGS) ++ ++DLL_LIB = align_format blastinput dbapi_driver general igblast seq xalgoalignutil xalnmgr xncbi xobjmgr xobjutil xser # axf +diff --git a/src/algo/align/splign/Makefile.xalgoalignsplign.lib b/src/algo/align/splign/Makefile.xalgoalignsplign.lib +index d67680b..3d56789 100644 +--- a/src/algo/align/splign/Makefile.xalgoalignsplign.lib ++++ b/src/algo/align/splign/Makefile.xalgoalignsplign.lib +@@ -10,3 +10,5 @@ LIB = xalgoalignsplign + + CXXFLAGS = $(FAST_CXXFLAGS) + LDFLAGS = $(FAST_LDFLAGS) ++ ++DLL_LIB = access align_format blastinput dbapi_driver gene_info general seq seqdb xalgoalignnw xalgoalignutil xalgoseq xblast xncbi xobjmgr xobjutil xser xutil # axf prosplign +diff --git a/src/algo/blast/api/Makefile.xblast.lib b/src/algo/blast/api/Makefile.xblast.lib +index 073973b..c6a4c2c 100644 +--- a/src/algo/blast/api/Makefile.xblast.lib ++++ b/src/algo/blast/api/Makefile.xblast.lib +@@ -78,7 +78,7 @@ SRC = $(SRC_C:%=.core_%) $(SRC_CXX) + + LIB = xblast + +-DLL_LIB = xalgodustmask xobjutil $(OBJMGR_LIBS) ++DLL_LIB = xalgodustmask xobjutil $(OBJMGR_LIBS) seqdb xnetblast xnetblastcli xalgoblastdbindex xalgowinmask tables composition_adjustment xobjread + + CFLAGS = $(FAST_CFLAGS) + # Strict gcc flags +diff --git a/src/algo/blast/blastinput/Makefile.blastinput.lib b/src/algo/blast/blastinput/Makefile.blastinput.lib +index bfb315c..2cd809a 100644 +--- a/src/algo/blast/blastinput/Makefile.blastinput.lib ++++ b/src/algo/blast/blastinput/Makefile.blastinput.lib +@@ -24,7 +24,7 @@ SRC = $(SRC_CXX) + + LIB = blastinput + +-DLL_LIB = xblast $(OBJMGR_LIBS) ++DLL_LIB = seqdb ncbi_xloader_blastdb ncbi_xloader_blastdb_rmt align_format xalnmgr xblast xcgi xobjread xobjutil ncbi_xloader_genbank ncbi_xreader ncbi_xreader_id2 xalnmgr xcgi + + # should be redundant, given the above :-/ + ASN_DEP = seqset xnetblast +diff --git a/src/algo/blast/core/Makefile.blast.lib b/src/algo/blast/core/Makefile.blast.lib +index 8e889a7..1326aee 100644 +--- a/src/algo/blast/core/Makefile.blast.lib ++++ b/src/algo/blast/core/Makefile.blast.lib +@@ -23,3 +23,5 @@ LDFLAGS = $(FAST_LDFLAGS) + + + WATCHERS = coulouri maning madden camacho ++ ++DLL_LIB = xutil +diff --git a/src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib b/src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib +index fcfb9f9..0e762b4 100644 +--- a/src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib ++++ b/src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib +@@ -14,3 +14,5 @@ LDFLAGS = $(FAST_LDFLAGS) + ASN_DEP = seqset + + WATCHERS = morgulis ++ ++DLL_LIB = dbapi_driver seq seqdb seqset xncbi xobjmgr xobjread xobjutil xser xutil # axf +diff --git a/src/algo/blast/dbindex_search/Makefile.xalgoblastdbindex_search.lib b/src/algo/blast/dbindex_search/Makefile.xalgoblastdbindex_search.lib +index e64f111..475f4a1 100644 +--- a/src/algo/blast/dbindex_search/Makefile.xalgoblastdbindex_search.lib ++++ b/src/algo/blast/dbindex_search/Makefile.xalgoblastdbindex_search.lib +@@ -10,3 +10,5 @@ LDFLAGS = $(FAST_LDFLAGS) + ASN_DEP = seqset + + WATCHERS = morgulis ++ ++DLL_LIB = dbapi_driver xncbi xobjmgr # axf +diff --git a/src/algo/blast/format/Makefile.xblastformat.lib b/src/algo/blast/format/Makefile.xblastformat.lib +index f7da067..9920332 100644 +--- a/src/algo/blast/format/Makefile.xblastformat.lib ++++ b/src/algo/blast/format/Makefile.xblastformat.lib +@@ -7,6 +7,6 @@ SRC = blastfmtutil blastxml_format blast_format data4xmlformat build_archive vec + + CPPFLAGS = $(ORIG_CPPFLAGS) + +-DLL_LIB = blastxml xhtml xcgi ++DLL_LIB = blastxml xhtml xcgi align_format general scoremat seq seqdb xalnmgr xblast xnetblast xobjmgr xobjutil blast_services ncbi_xloader_genbank xcgi # cobalt + + WATCHERS = jianye zaretska madden camacho fongah2 +diff --git a/src/algo/blast/gumbel_params/Makefile.gumbelparams.lib b/src/algo/blast/gumbel_params/Makefile.gumbelparams.lib +index 316d4fa..844de85 100644 +--- a/src/algo/blast/gumbel_params/Makefile.gumbelparams.lib ++++ b/src/algo/blast/gumbel_params/Makefile.gumbelparams.lib +@@ -11,3 +11,4 @@ LDFLAGS = $(FAST_LDFLAGS) + + WATCHERS = boratyng madden camacho + ++DLL_LIB = dbapi_driver xncbi xutil # axf +diff --git a/src/algo/cobalt/Makefile.cobalt.lib b/src/algo/cobalt/Makefile.cobalt.lib +index e618f67..b406cc5 100644 +--- a/src/algo/cobalt/Makefile.cobalt.lib ++++ b/src/algo/cobalt/Makefile.cobalt.lib +@@ -14,3 +14,5 @@ ASN_DEP = seq seqset biotree xnetblast blastdb + + CXXFLAGS = $(FAST_CXXFLAGS) + LDFLAGS = $(FAST_LDFLAGS) ++ ++DLL_LIB = align_format dbapi_driver general igblast seq seqdb seqset xalgoalignnw xalgophytree xblast xncbi xnetblast xobjmgr xobjutil xser fastme # axf +diff --git a/src/algo/dustmask/Makefile.xalgodustmask.lib b/src/algo/dustmask/Makefile.xalgodustmask.lib +index 84e2568..3632356 100644 +--- a/src/algo/dustmask/Makefile.xalgodustmask.lib ++++ b/src/algo/dustmask/Makefile.xalgodustmask.lib +@@ -11,3 +11,4 @@ SRC = symdust + CXXFLAGS = $(FAST_CXXFLAGS) + LDFLAGS = $(FAST_LDFLAGS) + ++DLL_LIB = dbapi_driver seq xncbi xobjmgr # axf +diff --git a/src/algo/gnomon/Makefile.gnomon.lib b/src/algo/gnomon/Makefile.gnomon.lib +index af363c0..3235647 100644 +--- a/src/algo/gnomon/Makefile.gnomon.lib ++++ b/src/algo/gnomon/Makefile.gnomon.lib +@@ -6,7 +6,7 @@ SRC = $(ASN:%=%__) $(ASN:%=%___) \ + gnomon_engine gnomon_objmgr score gnomon_model parse hmm gnomon_seq asn1 chainer id_handler \ + annot select_alignments_alt + LIB = xalgognomon +-DLL_LIB = xobjutil $(SOBJMGR_LIBS) ++DLL_LIB = xobjutil $(SOBJMGR_LIBS) xalgoseq + + CXXFLAGS = $(FAST_CXXFLAGS) + LDFLAGS = $(FAST_LDFLAGS) +diff --git a/src/algo/ms/formats/pepxml/Makefile.pepXML.lib b/src/algo/ms/formats/pepxml/Makefile.pepXML.lib +index 686dd70..98f57b2 100644 +--- a/src/algo/ms/formats/pepxml/Makefile.pepXML.lib ++++ b/src/algo/ms/formats/pepxml/Makefile.pepXML.lib +@@ -2,3 +2,5 @@ WATCHERS = lewisg slottad + + LIB = pepXML + SRC = pepXML__ pepXML___ ++ ++DLL_LIB = access align_format dbapi_driver xncbi xser # axf +diff --git a/src/algo/ms/omssa/Makefile.xomssa.lib b/src/algo/ms/omssa/Makefile.xomssa.lib +index 872b92e..78261eb 100644 +--- a/src/algo/ms/omssa/Makefile.xomssa.lib ++++ b/src/algo/ms/omssa/Makefile.xomssa.lib +@@ -19,3 +19,5 @@ LIB = xomssa + CFLAGS = $(FAST_CFLAGS) + CXXFLAGS = $(FAST_CXXFLAGS) + LDFLAGS = $(FAST_LDFLAGS) ++ ++DLL_LIB = xutil omssa pepXML xcompress xconnect seqdb xblast xregexp +diff --git a/src/algo/phy_tree/Makefile.xalgophytree.lib b/src/algo/phy_tree/Makefile.xalgophytree.lib +index 5964ef4..8163366 100644 +--- a/src/algo/phy_tree/Makefile.xalgophytree.lib ++++ b/src/algo/phy_tree/Makefile.xalgophytree.lib +@@ -6,7 +6,7 @@ ASN_DEP = biotree + + SRC = bio_tree phy_node dist_methods lex.newick newick.tab tree_to_dist_mat phytree_calc + LIB = xalgophytree +-DLL_LIB = biotree ++DLL_LIB = biotree seq xalnmgr xobjutil # fastme + + # The -I flag is necessary because filenames in #line directives throw + # off some compilers (GCC 2.95 at least). :-/ +diff --git a/src/algo/phy_tree/phytree_format/Makefile.phytreeformat.lib b/src/algo/phy_tree/phytree_format/Makefile.phytreeformat.lib +index 15d7440..fab9207 100644 +--- a/src/algo/phy_tree/phytree_format/Makefile.phytreeformat.lib ++++ b/src/algo/phy_tree/phytree_format/Makefile.phytreeformat.lib +@@ -10,3 +10,5 @@ CPPFLAGS = $(ORIG_CPPFLAGS) + ASN_DEP = biotree seqset taxon1 + + WATCHERS = boratyng ++ ++DLL_LIB = access align_format biotree dbapi_driver fastme gene_info seq taxon1 xalgophytree xncbi xobjmgr xobjutil xser # axf +diff --git a/src/algo/segmask/Makefile.xalgosegmask.lib b/src/algo/segmask/Makefile.xalgosegmask.lib +index bd011c1..97281ec 100644 +--- a/src/algo/segmask/Makefile.xalgosegmask.lib ++++ b/src/algo/segmask/Makefile.xalgosegmask.lib +@@ -11,3 +11,4 @@ SRC = segmask + CXXFLAGS = $(FAST_CXXFLAGS) + LDFLAGS = $(FAST_LDFLAGS) + ++DLL_LIB = align_format xobjmgr +diff --git a/src/algo/seqqa/Makefile.xalgoseqqa.lib b/src/algo/seqqa/Makefile.xalgoseqqa.lib +index b1bea47..a0e5b1b 100644 +--- a/src/algo/seqqa/Makefile.xalgoseqqa.lib ++++ b/src/algo/seqqa/Makefile.xalgoseqqa.lib +@@ -12,3 +12,5 @@ LIB = xalgoseqqa + CXXFLAGS = $(FAST_CXXFLAGS) + LDFLAGS = $(FAST_LDFLAGS) + CPPFLAGS = $(ORIG_CPPFLAGS) $(PCRE_INCLUDE) ++ ++DLL_LIB = access align_format dbapi_driver entrez2cli gene_info general seq seqtest xalgognomon xalgoseq xalnmgr xncbi xobjmgr xobjutil xser # axf +diff --git a/src/algo/sequence/Makefile.xalgoseq.lib b/src/algo/sequence/Makefile.xalgoseq.lib +index 51f4cd7..724e939 100644 +--- a/src/algo/sequence/Makefile.xalgoseq.lib ++++ b/src/algo/sequence/Makefile.xalgoseq.lib +@@ -13,3 +13,5 @@ LDFLAGS = $(FAST_LDFLAGS) + CPPFLAGS = $(ORIG_CPPFLAGS) $(PCRE_INCLUDE) + + WATCHERS = dicuccio ++ ++DLL_LIB = taxon1 xalnmgr xregexp align_format seqset xobjmgr xobjutil +diff --git a/src/algo/structure/bma_refine/Makefile.xbma_refiner.lib b/src/algo/structure/bma_refine/Makefile.xbma_refiner.lib +index 5562f82..68d3a87 100644 +--- a/src/algo/structure/bma_refine/Makefile.xbma_refiner.lib ++++ b/src/algo/structure/bma_refine/Makefile.xbma_refiner.lib +@@ -24,3 +24,6 @@ SRC = RowSelector \ + RefinerTrial \ + RefinerEngine \ + Interface ++ ++DLL_LIB = blastinput cdd ncbi_xcache_bdb xcd_utils xncbi xser xutil ++ +diff --git a/src/algo/structure/cd_utils/Makefile.xcd_utils.lib b/src/algo/structure/cd_utils/Makefile.xcd_utils.lib +index eda71f8..8d3a96a 100644 +--- a/src/algo/structure/cd_utils/Makefile.xcd_utils.lib ++++ b/src/algo/structure/cd_utils/Makefile.xcd_utils.lib +@@ -68,6 +68,6 @@ SRC = \ + cuTaxTree \ + cuUtils + +-DLL_LIB = xobjread ++DLL_LIB = xobjread blastdb blast_services cdd entrez2cli id1cli mmdb ncbimime scoremat taxon1 xblast xobjmgr xregexp + + CPPFLAGS = $(ORIG_CPPFLAGS) +diff --git a/src/algo/structure/struct_dp/Makefile.xstruct_dp.lib b/src/algo/structure/struct_dp/Makefile.xstruct_dp.lib +index 676a8dd..3d3e4c9 100644 +--- a/src/algo/structure/struct_dp/Makefile.xstruct_dp.lib ++++ b/src/algo/structure/struct_dp/Makefile.xstruct_dp.lib +@@ -9,3 +9,5 @@ WATCHERS = thiessen + SRC = block_align + + LIB = xstruct_dp ++ ++DLL_LIB = xncbi +diff --git a/src/algo/structure/struct_util/Makefile.xstruct_util.lib b/src/algo/structure/struct_util/Makefile.xstruct_util.lib +index 5a38c7d..35d7077 100644 +--- a/src/algo/structure/struct_util/Makefile.xstruct_util.lib ++++ b/src/algo/structure/struct_util/Makefile.xstruct_util.lib +@@ -17,3 +17,5 @@ SRC = aaa_dummy_pch \ + su_block_multiple_alignment \ + su_pssm \ + su_sequence_set ++ ++DLL_LIB = seqset seq xncbi scoremat xstruct_dp xblast +diff --git a/src/algo/structure/threader/Makefile.xstruct_thread.lib b/src/algo/structure/threader/Makefile.xstruct_thread.lib +index c06a2c0..9f1ff25 100644 +--- a/src/algo/structure/threader/Makefile.xstruct_thread.lib ++++ b/src/algo/structure/threader/Makefile.xstruct_thread.lib +@@ -10,3 +10,5 @@ SRC = thrdalgs thrdatd thrdbwfi thrdcpal thrdcpll thrdcprl \ + thrdttbi thrdzsc + + LIB = xstruct_thread ++ ++DLL_LIB = xutil +diff --git a/src/algo/text/Makefile.xalgotext.lib b/src/algo/text/Makefile.xalgotext.lib +index 81ba0e6..f25073e 100644 +--- a/src/algo/text/Makefile.xalgotext.lib ++++ b/src/algo/text/Makefile.xalgotext.lib +@@ -10,3 +10,5 @@ CXXFLAGS = $(FAST_CXXFLAGS) + LDFLAGS = $(FAST_LDFLAGS) + + ASN_DEP = general ++ ++DLL_LIB = align_format blastinput ncbi_xcache_bdb xcompress xncbi xutil # axf +diff --git a/src/algo/volume_merge/Makefile.xalgovmerge.lib b/src/algo/volume_merge/Makefile.xalgovmerge.lib +index 499861a..3ffb80b 100644 +--- a/src/algo/volume_merge/Makefile.xalgovmerge.lib ++++ b/src/algo/volume_merge/Makefile.xalgovmerge.lib +@@ -10,3 +10,5 @@ SRC = volume_merge + CXXFLAGS = $(FAST_CXXFLAGS) + LDFLAGS = $(FAST_LDFLAGS) + ++ ++DLL_LIB = xncbi +diff --git a/src/algo/winmask/Makefile.xalgowinmask.lib b/src/algo/winmask/Makefile.xalgowinmask.lib +index afaf676..ad2c1fe 100644 +--- a/src/algo/winmask/Makefile.xalgowinmask.lib ++++ b/src/algo/winmask/Makefile.xalgowinmask.lib +@@ -21,3 +21,5 @@ SRC = seq_masker seq_masker_score_mean seq_masker_score_mean_glob \ + CXXFLAGS = $(FAST_CXXFLAGS) + LDFLAGS = $(FAST_LDFLAGS) + ++DLL_LIB = seqmasks_io xobjread xobjutil ++ +diff --git a/src/cgi/Makefile.cgi.lib b/src/cgi/Makefile.cgi.lib +index a990390..edf40aa 100644 +--- a/src/cgi/Makefile.cgi.lib ++++ b/src/cgi/Makefile.cgi.lib +@@ -11,3 +11,5 @@ LIB = xcgi + CPPFLAGS = $(ORIG_CPPFLAGS) $(FASTCGI_INCLUDE) + + WATCHERS = vakatov ++ ++DLL_LIB = xncbi xutil +diff --git a/src/cgi/Makefile.fcgi.lib b/src/cgi/Makefile.fcgi.lib +index 2569b41..6b85780 100644 +--- a/src/cgi/Makefile.fcgi.lib ++++ b/src/cgi/Makefile.fcgi.lib +@@ -12,3 +12,5 @@ LIB = xfcgi + CPPFLAGS = $(ORIG_CPPFLAGS) $(FASTCGI_INCLUDE) -DNCBI_XFCGI_EXPORTS + + WATCHERS = vakatov ++ ++DLL_LIB = xncbi xutil +diff --git a/src/connect/Makefile.connssl.lib b/src/connect/Makefile.connssl.lib +index b400ca2..8756320 100644 +--- a/src/connect/Makefile.connssl.lib ++++ b/src/connect/Makefile.connssl.lib +@@ -8,3 +8,5 @@ CPPFLAGS = $(GNUTLS_INCLUDE) $(ORIG_CPPFLAGS) + LIBS = $(GNUTLS_LIBS) $(ORIG_LIBS) + + WATCHERS = lavr ++ ++DLL_LIB = connect +diff --git a/src/connect/Makefile.xconnect.lib b/src/connect/Makefile.xconnect.lib +index 473bb0b..88dae10 100644 +--- a/src/connect/Makefile.xconnect.lib ++++ b/src/connect/Makefile.xconnect.lib +@@ -11,9 +11,13 @@ include $(srcdir)/Makefile.xxconnect.lib + SRC = $(SRC_C) $(SRC_CXX) + UNIX_SRC = $(LOCAL_LBSM) + ++DLL_LIB = xncbi ++ + LIB = xconnect + PROJ_TAG = core + + LIBS = $(NETWORK_LIBS) $(ORIG_LIBS) + + WATCHERS = lavr ++ ++DLL_LIB = xncbi xutil +diff --git a/src/connect/Makefile.xthrserv.lib b/src/connect/Makefile.xthrserv.lib +index 1e5b857..0833a78 100644 +--- a/src/connect/Makefile.xthrserv.lib ++++ b/src/connect/Makefile.xthrserv.lib +@@ -4,6 +4,6 @@ SRC = threaded_server server server_monitor connection_pool + LIB = xthrserv + PROJ_TAG = core + LIBS = $(NETWORK_LIBS) +-DLL_LIB = xutil xconnect ++DLL_LIB = xncbi xutil xconnect + + WATCHERS = ivanovp +diff --git a/src/connect/Makefile.xxconnect.lib b/src/connect/Makefile.xxconnect.lib +index d7ba751..8e27819 100644 +--- a/src/connect/Makefile.xxconnect.lib ++++ b/src/connect/Makefile.xxconnect.lib +@@ -16,3 +16,5 @@ PROJ_TAG = core + LIBS = $(NETWORK_LIBS) $(ORIG_LIBS) + + WATCHERS = lavr ++ ++DLL_LIB = xncbi xutil connect +diff --git a/src/connect/services/Makefile.ncbi_xcache_netcache.lib b/src/connect/services/Makefile.ncbi_xcache_netcache.lib +index 606f4f1..e6cfdac 100644 +--- a/src/connect/services/Makefile.ncbi_xcache_netcache.lib ++++ b/src/connect/services/Makefile.ncbi_xcache_netcache.lib +@@ -6,7 +6,7 @@ SRC = neticache_client + LIB = ncbi_xcache_netcache + + LIB_OR_DLL = both +-DLL_LIB = xconnserv xconnect xutil ++DLL_LIB = xconnserv xconnect xutil xncbi + + CPPFLAGS = $(ORIG_CPPFLAGS) + LIBS = $(ORIG_LIBS) +diff --git a/src/connect/services/Makefile.xconnserv.lib b/src/connect/services/Makefile.xconnserv.lib +index 4b8f21f..04fcbf8 100644 +--- a/src/connect/services/Makefile.xconnserv.lib ++++ b/src/connect/services/Makefile.xconnserv.lib +@@ -15,6 +15,6 @@ LIB = xconnserv + PROJ_TAG = core + LIBS = $(NETWORK_LIBS) + +-DLL_LIB = xthrserv xconnect xutil ++DLL_LIB = xthrserv xconnect xutil xncbi + + WATCHERS = kazimird +diff --git a/src/connect/test/Makefile.conntest.lib b/src/connect/test/Makefile.conntest.lib +index 58a2fa5..3d9876c 100644 +--- a/src/connect/test/Makefile.conntest.lib ++++ b/src/connect/test/Makefile.conntest.lib +@@ -4,3 +4,5 @@ SRC = ncbi_conntest + LIB = xconntest + + WATCHERS = lavr ++ ++DLL_LIB = xncbi xutil connect +diff --git a/src/corelib/Makefile.test_boost.lib b/src/corelib/Makefile.test_boost.lib +index e8fa174..f90441d 100644 +--- a/src/corelib/Makefile.test_boost.lib ++++ b/src/corelib/Makefile.test_boost.lib +@@ -9,3 +9,5 @@ REQUIRES = Boost.Test.Included + + WATCHERS = ivanovp + PROJ_TAG = test ++ ++DLL_LIB = xncbi +diff --git a/src/corelib/Makefile.test_mt.lib b/src/corelib/Makefile.test_mt.lib +index 6153eab..f64c3a2 100644 +--- a/src/corelib/Makefile.test_mt.lib ++++ b/src/corelib/Makefile.test_mt.lib +@@ -8,3 +8,5 @@ LIB = test_mt + USE_PCH = no + WATCHERS = grichenk + PROJ_TAG = test ++ ++DLL_LIB = xncbi +diff --git a/src/corelib/test/Makefile.pbacktest.lib b/src/corelib/test/Makefile.pbacktest.lib +index da0c616..c4c62ab 100644 +--- a/src/corelib/test/Makefile.pbacktest.lib ++++ b/src/corelib/test/Makefile.pbacktest.lib +@@ -4,3 +4,5 @@ SRC = pbacktest + LIB = xpbacktest + + WATCHERS = lavr ++ ++DLL_LIB = xncbi +diff --git a/src/db/bdb/Makefile.bdb.lib b/src/db/bdb/Makefile.bdb.lib +index 3729707..cd2827c 100644 +--- a/src/db/bdb/Makefile.bdb.lib ++++ b/src/db/bdb/Makefile.bdb.lib +@@ -14,3 +14,7 @@ LIB = bdb + CPPFLAGS = $(ORIG_CPPFLAGS) $(BERKELEYDB_INCLUDE) + + WATCHERS = kuznets ++ ++DLL_LIB = xncbi xutil ++LIBS = $(BERKELEYDB_LIBS) ++ +diff --git a/src/db/bdb/Makefile.ncbi_xcache_bdb.lib b/src/db/bdb/Makefile.ncbi_xcache_bdb.lib +index 7e97a26..8f54efc 100644 +--- a/src/db/bdb/Makefile.ncbi_xcache_bdb.lib ++++ b/src/db/bdb/Makefile.ncbi_xcache_bdb.lib +@@ -8,7 +8,7 @@ SRC = bdb_blobcache + LIB = ncbi_xcache_bdb + + LIB_OR_DLL = both +-DLL_LIB = bdb xutil ++DLL_LIB = bdb xutil xncbi + + CPPFLAGS = $(ORIG_CPPFLAGS) $(BERKELEYDB_INCLUDE) + LIBS = $(BERKELEYDB_LIBS) $(ORIG_LIBS) +diff --git a/src/db/sqlite/Makefile.sqlitewrapp.lib b/src/db/sqlite/Makefile.sqlitewrapp.lib +index cecfd16..c01668b 100644 +--- a/src/db/sqlite/Makefile.sqlitewrapp.lib ++++ b/src/db/sqlite/Makefile.sqlitewrapp.lib +@@ -8,3 +8,6 @@ CPPFLAGS= $(ORIG_CPPFLAGS) $(SQLITE3_INCLUDE) + REQUIRES = SQLITE3 + + WATCHERS = ivanovp ++ ++DLL_LIB = xncbi xutil ++LIBS = $(SQLITE3_LIBS) +diff --git a/src/dbapi/Makefile.dbapi.lib b/src/dbapi/Makefile.dbapi.lib +index 6e3ad4c..e3d6a49 100644 +--- a/src/dbapi/Makefile.dbapi.lib ++++ b/src/dbapi/Makefile.dbapi.lib +@@ -10,3 +10,8 @@ LIB = dbapi + CPPFLAGS = $(ORIG_CPPFLAGS) $(SYBASE_INCLUDE) + + WATCHERS = ivanovp ++ ++#ASN_DEP = driver dbapi_driver ++ ++DLL_LIB = xncbi xutil # dbapi_driver$(DLL) ++LIBS = $(PYTHON_LIBS) +diff --git a/src/dbapi/driver/Makefile.dbapi_driver.lib b/src/dbapi/driver/Makefile.dbapi_driver.lib +index dfeac5a..bc113ed 100644 +--- a/src/dbapi/driver/Makefile.dbapi_driver.lib ++++ b/src/dbapi/driver/Makefile.dbapi_driver.lib +@@ -22,3 +22,5 @@ CXXFLAGS_darwin = -fno-inline + CXXFLAGS = $(ORIG_CXXFLAGS) $(CXXFLAGS_$(OSTYPE)) + + WATCHERS = ivanovp ++ ++DLL_LIB = xncbi xutil +diff --git a/src/dbapi/driver/samples/Makefile.dbapi_sample_base.lib b/src/dbapi/driver/samples/Makefile.dbapi_sample_base.lib +index 941ccd6..f1f872c 100644 +--- a/src/dbapi/driver/samples/Makefile.dbapi_sample_base.lib ++++ b/src/dbapi/driver/samples/Makefile.dbapi_sample_base.lib +@@ -6,3 +6,5 @@ LIB = dbapi_sample_base + CPPFLAGS = $(ORIG_CPPFLAGS) $(SYBASE_INCLUDE) + + WATCHERS = ivanovp ++ ++DLL_LIB = xncbi xutil dbapi_driver +diff --git a/src/dbapi/lang_bind/python/Makefile.python_ncbi_dbapi.lib b/src/dbapi/lang_bind/python/Makefile.python_ncbi_dbapi.lib +index ebe08c4..86ecda6 100644 +--- a/src/dbapi/lang_bind/python/Makefile.python_ncbi_dbapi.lib ++++ b/src/dbapi/lang_bind/python/Makefile.python_ncbi_dbapi.lib +@@ -11,7 +11,7 @@ LIB_OR_DLL = dll + + # Dependencies for shared library + DLL_LIB = dbapi dbapi_driver$(DLL) $(XCONNEXT) xconnect xutil xncbi +-LIBS = $(RUNPATH_ORIGIN)/python_ncbi_dbapi/$(NCBI_PACKAGE_VERSION) $(ORIG_LIBS) ++LIBS = $(RUNPATH_ORIGIN)/python_ncbi_dbapi/$(NCBI_PACKAGE_VERSION) $(ORIG_LIBS) $(PYTHON_LIBS) + # Drop other flags to build with full dependencies under ICC. + DLL_LDFLAGS = $(DLL_UNDEF_FLAGS) + +diff --git a/src/dbapi/simple/Makefile.sdbapi.lib b/src/dbapi/simple/Makefile.sdbapi.lib +index 603fd1e..0d06323 100644 +--- a/src/dbapi/simple/Makefile.sdbapi.lib ++++ b/src/dbapi/simple/Makefile.sdbapi.lib +@@ -5,3 +5,4 @@ LIB = sdbapi + + WATCHERS = ivanovp + ++DLL_LIB = xncbi xutil dbapi_driver ncbi_xdbapi_ftds xconnect xser bdb xconnserv +diff --git a/src/html/Makefile.html.lib b/src/html/Makefile.html.lib +index a57c1e3..0005299 100644 +--- a/src/html/Makefile.html.lib ++++ b/src/html/Makefile.html.lib +@@ -8,3 +8,5 @@ SRC = node html htmlhelper page pager selection components \ + LIB = xhtml + + WATCHERS = ivanov ++ ++DLL_LIB = xncbi xutil +diff --git a/src/misc/cgi_redirect/Makefile.cgi_redirect.lib b/src/misc/cgi_redirect/Makefile.cgi_redirect.lib +index 6d7a4af..332e5d0 100644 +--- a/src/misc/cgi_redirect/Makefile.cgi_redirect.lib ++++ b/src/misc/cgi_redirect/Makefile.cgi_redirect.lib +@@ -7,3 +7,5 @@ SRC = redirect + LIB = xcgi_redirect + + WATCHERS = ivanov ++ ++DLL_LIB = axf dbapi_driver xcgi xhtml xncbi +diff --git a/src/misc/grid_cgi/Makefile.xgridcgi.lib b/src/misc/grid_cgi/Makefile.xgridcgi.lib +index c9ef138..8e25cbe 100644 +--- a/src/misc/grid_cgi/Makefile.xgridcgi.lib ++++ b/src/misc/grid_cgi/Makefile.xgridcgi.lib +@@ -9,3 +9,5 @@ LIB = xgridcgi + CPPFLAGS = $(ORIG_CPPFLAGS) $(FASTCGI_INCLUDE) + + WATCHERS = vakatov ++ ++DLL_LIB = xncbi xcgi xconnserv xhtml +diff --git a/src/objects/access/Makefile.access.lib b/src/objects/access/Makefile.access.lib +index 11421d9..e7900a1 100644 +--- a/src/objects/access/Makefile.access.lib ++++ b/src/objects/access/Makefile.access.lib +@@ -1,2 +1,3 @@ + LIB = access + SRC = access__ access___ ++DLL_LIB = xncbi xser +diff --git a/src/objects/biblio/Makefile.biblio.lib b/src/objects/biblio/Makefile.biblio.lib +index 2c7d491..cb54ba6 100644 +--- a/src/objects/biblio/Makefile.biblio.lib ++++ b/src/objects/biblio/Makefile.biblio.lib +@@ -1,2 +1,4 @@ + LIB = biblio + SRC = biblio__ biblio___ citation_base ++ ++DLL_LIB = general xser xncbi xutil +diff --git a/src/objects/biotree/Makefile.biotree.lib b/src/objects/biotree/Makefile.biotree.lib +index 8019285..2c689ae 100644 +--- a/src/objects/biotree/Makefile.biotree.lib ++++ b/src/objects/biotree/Makefile.biotree.lib +@@ -1,3 +1,5 @@ + ASN_DEP = seq seqset + LIB = biotree + SRC = biotree__ biotree___ ++ ++DLL_LIB = xncbi xser +diff --git a/src/objects/blast/Makefile.blast.lib b/src/objects/blast/Makefile.blast.lib +index 0dd0fa3..d50f29f 100644 +--- a/src/objects/blast/Makefile.blast.lib ++++ b/src/objects/blast/Makefile.blast.lib +@@ -2,3 +2,5 @@ LIB = xnetblast + SRC = blast__ blast___ names + + WATCHERS = camacho ++ ++DLL_LIB = xncbi xutil xser seq seqset scoremat +diff --git a/src/objects/blast/Makefile.xnetblastcli.lib b/src/objects/blast/Makefile.xnetblastcli.lib +index 96325c4..5a72805 100644 +--- a/src/objects/blast/Makefile.xnetblastcli.lib ++++ b/src/objects/blast/Makefile.xnetblastcli.lib +@@ -2,3 +2,5 @@ ASN_DEP = xnetblast + + LIB = xnetblastcli + SRC = blastclient blastclient_ ++ ++DLL_LIB = xncbi xutil seqset xconnect xnetblast +diff --git a/src/objects/blastdb/Makefile.blastdb.lib b/src/objects/blastdb/Makefile.blastdb.lib +index be2c0d1..2884db2 100644 +--- a/src/objects/blastdb/Makefile.blastdb.lib ++++ b/src/objects/blastdb/Makefile.blastdb.lib +@@ -1,2 +1,4 @@ + LIB = blastdb + SRC = blastdb__ blastdb___ ++ ++DLL_LIB = xncbi xser seq +diff --git a/src/objects/blastxml/Makefile.blastxml.lib b/src/objects/blastxml/Makefile.blastxml.lib +index d18eb78..f90501d 100644 +--- a/src/objects/blastxml/Makefile.blastxml.lib ++++ b/src/objects/blastxml/Makefile.blastxml.lib +@@ -1,2 +1,4 @@ + LIB = blastxml + SRC = blastxml__ blastxml___ ++ ++DLL_LIB = xser +diff --git a/src/objects/cdd/Makefile.cdd.lib b/src/objects/cdd/Makefile.cdd.lib +index 978cae9..24b726c 100644 +--- a/src/objects/cdd/Makefile.cdd.lib ++++ b/src/objects/cdd/Makefile.cdd.lib +@@ -1,2 +1,4 @@ + LIB = cdd + SRC = cdd__ cdd___ ++ ++DLL_LIB = mmdb xser scoremat cn3d +diff --git a/src/objects/cn3d/Makefile.cn3d.lib b/src/objects/cn3d/Makefile.cn3d.lib +index 1af5d1d..ecd31b2 100644 +--- a/src/objects/cn3d/Makefile.cn3d.lib ++++ b/src/objects/cn3d/Makefile.cn3d.lib +@@ -1,3 +1,5 @@ + ASN_DEP = mmdb + LIB = cn3d + SRC = cn3d__ cn3d___ ++ ++DLL_LIB = mmdb xser +diff --git a/src/objects/docsum/Makefile.docsum.lib b/src/objects/docsum/Makefile.docsum.lib +index 0e68886..0bc8a1c 100644 +--- a/src/objects/docsum/Makefile.docsum.lib ++++ b/src/objects/docsum/Makefile.docsum.lib +@@ -1,2 +1,4 @@ + LIB = docsum + SRC = docsum__ docsum___ ++ ++DLL_LIB = xser +diff --git a/src/objects/entrez2/Makefile.entrez2.lib b/src/objects/entrez2/Makefile.entrez2.lib +index 4507f72..4c47ad3 100644 +--- a/src/objects/entrez2/Makefile.entrez2.lib ++++ b/src/objects/entrez2/Makefile.entrez2.lib +@@ -2,3 +2,5 @@ WATCHERS = lavr + + LIB = entrez2 + SRC = entrez2__ entrez2___ ++ ++DLL_LIB = xser +diff --git a/src/objects/entrez2/Makefile.entrez2cli.lib b/src/objects/entrez2/Makefile.entrez2cli.lib +index 42a4649..2fdcc6f 100644 +--- a/src/objects/entrez2/Makefile.entrez2cli.lib ++++ b/src/objects/entrez2/Makefile.entrez2cli.lib +@@ -4,3 +4,5 @@ ASN_DEP = entrez2 + + LIB = entrez2cli + SRC = entrez2_client entrez2_client_ ++ ++DLL_LIB = xncbi xconnect entrez2 +diff --git a/src/objects/entrezgene/Makefile.entrezgene.lib b/src/objects/entrezgene/Makefile.entrezgene.lib +index a1bd4f4..27319c3 100644 +--- a/src/objects/entrezgene/Makefile.entrezgene.lib ++++ b/src/objects/entrezgene/Makefile.entrezgene.lib +@@ -1,2 +1,4 @@ + LIB = entrezgene + SRC = entrezgene__ entrezgene___ ++ ++DLL_LIB = xser seq +diff --git a/src/objects/featdef/Makefile.featdef.lib b/src/objects/featdef/Makefile.featdef.lib +index 51c7c8d..e603711 100644 +--- a/src/objects/featdef/Makefile.featdef.lib ++++ b/src/objects/featdef/Makefile.featdef.lib +@@ -1,2 +1,4 @@ + LIB = featdef + SRC = featdef__ featdef___ ++ ++DLL_LIB = xser +diff --git a/src/objects/gbseq/Makefile.gbseq.lib b/src/objects/gbseq/Makefile.gbseq.lib +index 9dabdeb..4b27881 100644 +--- a/src/objects/gbseq/Makefile.gbseq.lib ++++ b/src/objects/gbseq/Makefile.gbseq.lib +@@ -1,2 +1,4 @@ + LIB = gbseq + SRC = gbseq__ gbseq___ ++ ++DLL_LIB = xser +diff --git a/src/objects/general/Makefile.general.lib b/src/objects/general/Makefile.general.lib +index 951304f..3be083d 100644 +--- a/src/objects/general/Makefile.general.lib ++++ b/src/objects/general/Makefile.general.lib +@@ -1,2 +1,4 @@ + LIB = general + SRC = general__ general___ uoconv ++ ++DLL_LIB = xser xncbi xutil +diff --git a/src/objects/genomecoll/Makefile.genome_collection.lib b/src/objects/genomecoll/Makefile.genome_collection.lib +index f039af6..f6b41a7 100644 +--- a/src/objects/genomecoll/Makefile.genome_collection.lib ++++ b/src/objects/genomecoll/Makefile.genome_collection.lib +@@ -4,3 +4,5 @@ LIB = genome_collection + SRC = genome_collection__ genome_collection___ + + WATCHERS = dicuccio ++ ++DLL_LIB = xser seq +diff --git a/src/objects/homologene/Makefile.homologene.lib b/src/objects/homologene/Makefile.homologene.lib +index 15d13ad..d44b2e3 100644 +--- a/src/objects/homologene/Makefile.homologene.lib ++++ b/src/objects/homologene/Makefile.homologene.lib +@@ -4,3 +4,5 @@ + + LIB = homologene + SRC = homologene__ homologene___ ++ ++DLL_LIB = xser seq +diff --git a/src/objects/id1/Makefile.id1.lib b/src/objects/id1/Makefile.id1.lib +index d60c728..bf98427 100644 +--- a/src/objects/id1/Makefile.id1.lib ++++ b/src/objects/id1/Makefile.id1.lib +@@ -4,3 +4,5 @@ LIB = id1 + SRC = id1__ id1___ + + WATCHERS = vasilche ++ ++DLL_LIB = xser seqset +diff --git a/src/objects/id1/Makefile.id1cli.lib b/src/objects/id1/Makefile.id1cli.lib +index e87ea83..745c5cb 100644 +--- a/src/objects/id1/Makefile.id1cli.lib ++++ b/src/objects/id1/Makefile.id1cli.lib +@@ -4,3 +4,5 @@ LIB = id1cli + SRC = id1_client id1_client_ + + WATCHERS = vasilche ++ ++DLL_LIB = id1 xconnect +diff --git a/src/objects/id2/Makefile.id2.lib b/src/objects/id2/Makefile.id2.lib +index 09d8b36..1e74a58 100644 +--- a/src/objects/id2/Makefile.id2.lib ++++ b/src/objects/id2/Makefile.id2.lib +@@ -2,3 +2,5 @@ LIB = id2 + SRC = id2__ id2___ + + WATCHERS = vasilche ++ ++DLL_LIB = xser seq seqsplit +diff --git a/src/objects/id2/Makefile.id2cli.lib b/src/objects/id2/Makefile.id2cli.lib +index 5d41f23..ccec62a 100644 +--- a/src/objects/id2/Makefile.id2cli.lib ++++ b/src/objects/id2/Makefile.id2cli.lib +@@ -4,3 +4,5 @@ LIB = id2cli + SRC = id2_client id2_client_ + + WATCHERS = vasilche ++ ++DLL_LIB = id2 xconnect +diff --git a/src/objects/insdseq/Makefile.insdseq.lib b/src/objects/insdseq/Makefile.insdseq.lib +index fa729b7..5754057 100644 +--- a/src/objects/insdseq/Makefile.insdseq.lib ++++ b/src/objects/insdseq/Makefile.insdseq.lib +@@ -1,2 +1,4 @@ + LIB = insdseq + SRC = insdseq__ insdseq___ ++ ++DLL_LIB = xser +diff --git a/src/objects/macro/Makefile.macro.lib b/src/objects/macro/Makefile.macro.lib +index 3a0a7c0..25a3b73 100644 +--- a/src/objects/macro/Makefile.macro.lib ++++ b/src/objects/macro/Makefile.macro.lib +@@ -2,3 +2,5 @@ + + LIB = macro + SRC = macro__ macro___ ++ ++DLL_LIB = xser +diff --git a/src/objects/medlars/Makefile.medlars.lib b/src/objects/medlars/Makefile.medlars.lib +index 3a6d0cd..5c8e00e 100644 +--- a/src/objects/medlars/Makefile.medlars.lib ++++ b/src/objects/medlars/Makefile.medlars.lib +@@ -1,2 +1,4 @@ + LIB = medlars + SRC = medlars__ medlars___ ++ ++DLL_LIB = xser biblio +diff --git a/src/objects/medline/Makefile.medline.lib b/src/objects/medline/Makefile.medline.lib +index ea28066..eb42aa4 100644 +--- a/src/objects/medline/Makefile.medline.lib ++++ b/src/objects/medline/Makefile.medline.lib +@@ -1,2 +1,4 @@ + LIB = medline + SRC = medline__ medline___ ++ ++DLL_LIB = general biblio +diff --git a/src/objects/mim/Makefile.mim.lib b/src/objects/mim/Makefile.mim.lib +index c2cd50e..2fed8f4 100644 +--- a/src/objects/mim/Makefile.mim.lib ++++ b/src/objects/mim/Makefile.mim.lib +@@ -1,2 +1,4 @@ + LIB = mim + SRC = mim__ mim___ ++ ++DLL_LIB = xser +diff --git a/src/objects/mla/Makefile.mla.lib b/src/objects/mla/Makefile.mla.lib +index a748f68..5b5523a 100644 +--- a/src/objects/mla/Makefile.mla.lib ++++ b/src/objects/mla/Makefile.mla.lib +@@ -1,2 +1,4 @@ + LIB = mla + SRC = mla__ mla___ ++ ++DLL_LIB = xser medline pubmed pub medlars +diff --git a/src/objects/mla/Makefile.mlacli.lib b/src/objects/mla/Makefile.mlacli.lib +index 48af427..4cee3ac 100644 +--- a/src/objects/mla/Makefile.mlacli.lib ++++ b/src/objects/mla/Makefile.mlacli.lib +@@ -2,3 +2,5 @@ ASN_DEP = mla + + LIB = mlacli + SRC = mla_client mla_client_ ++ ++DLL_LIB = xncbi xconnect mla +diff --git a/src/objects/mmdb/Makefile.mmdb.lib b/src/objects/mmdb/Makefile.mmdb.lib +index 6fc8e25..5c6c100 100644 +--- a/src/objects/mmdb/Makefile.mmdb.lib ++++ b/src/objects/mmdb/Makefile.mmdb.lib +@@ -8,3 +8,5 @@ CPPFLAGS = -I$(srcdir) -I$(top_srcdir)/src/objects/mmdb $(ORIG_CPPFLAGS) + + LIB = mmdb + SRC = $(ASN:%=%__) $(ASN:%=%___) ++ ++DLL_LIB = xser pub seq +diff --git a/src/objects/ncbimime/Makefile.ncbimime.lib b/src/objects/ncbimime/Makefile.ncbimime.lib +index 93cafdf..1360ade 100644 +--- a/src/objects/ncbimime/Makefile.ncbimime.lib ++++ b/src/objects/ncbimime/Makefile.ncbimime.lib +@@ -1,2 +1,4 @@ + LIB = ncbimime + SRC = ncbimime__ ncbimime___ ++ ++DLL_LIB = mmdb cn3d seqset cdd +diff --git a/src/objects/objprt/Makefile.objprt.lib b/src/objects/objprt/Makefile.objprt.lib +index 40d6b09..c00e6d2 100644 +--- a/src/objects/objprt/Makefile.objprt.lib ++++ b/src/objects/objprt/Makefile.objprt.lib +@@ -1,2 +1,4 @@ + LIB = objprt + SRC = objprt__ objprt___ ++ ++DLL_LIB = xser +diff --git a/src/objects/omssa/Makefile.omssa.lib b/src/objects/omssa/Makefile.omssa.lib +index b79617f..e1d4a9e 100644 +--- a/src/objects/omssa/Makefile.omssa.lib ++++ b/src/objects/omssa/Makefile.omssa.lib +@@ -2,3 +2,5 @@ APP_DEP = seq + + LIB = omssa + SRC = omssa__ omssa___ ++ ++DLL_LIB = seq +diff --git a/src/objects/pcassay/Makefile.pcassay.lib b/src/objects/pcassay/Makefile.pcassay.lib +index 1086865..587adb5 100644 +--- a/src/objects/pcassay/Makefile.pcassay.lib ++++ b/src/objects/pcassay/Makefile.pcassay.lib +@@ -1,2 +1,4 @@ + LIB = pcassay + SRC = pcassay__ pcassay___ ++ ++DLL_LIB = xser pcsubstance seq +diff --git a/src/objects/pcsubstance/Makefile.pcsubstance.lib b/src/objects/pcsubstance/Makefile.pcsubstance.lib +index b36802e..c3f6a39 100644 +--- a/src/objects/pcsubstance/Makefile.pcsubstance.lib ++++ b/src/objects/pcsubstance/Makefile.pcsubstance.lib +@@ -1,2 +1,4 @@ + LIB = pcsubstance + SRC = pcsubstance__ pcsubstance___ ++ ++DLL_LIB = xser general pub +diff --git a/src/objects/proj/Makefile.proj.lib b/src/objects/proj/Makefile.proj.lib +index c5bb3d3..fbde99a 100644 +--- a/src/objects/proj/Makefile.proj.lib ++++ b/src/objects/proj/Makefile.proj.lib +@@ -1,2 +1,4 @@ + LIB = proj + SRC = proj__ proj___ ++ ++DLL_LIB = xser pubmed seqset +diff --git a/src/objects/pub/Makefile.pub.lib b/src/objects/pub/Makefile.pub.lib +index 78c12e1..9baa08d 100644 +--- a/src/objects/pub/Makefile.pub.lib ++++ b/src/objects/pub/Makefile.pub.lib +@@ -1,2 +1,4 @@ + LIB = pub + SRC = pub__ pub___ ++ ++DLL_LIB = medline biblio +diff --git a/src/objects/pubmed/Makefile.pubmed.lib b/src/objects/pubmed/Makefile.pubmed.lib +index 8b8d553..46e3125 100644 +--- a/src/objects/pubmed/Makefile.pubmed.lib ++++ b/src/objects/pubmed/Makefile.pubmed.lib +@@ -1,2 +1,4 @@ + LIB = pubmed + SRC = pubmed__ pubmed___ ++ ++DLL_LIB = xser medline +diff --git a/src/objects/remap/Makefile.remap.lib b/src/objects/remap/Makefile.remap.lib +index 9a35d90..1256648 100644 +--- a/src/objects/remap/Makefile.remap.lib ++++ b/src/objects/remap/Makefile.remap.lib +@@ -1,2 +1,4 @@ + LIB = remap + SRC = remap__ remap___ ++ ++DLL_LIB = xser seq +diff --git a/src/objects/remap/Makefile.remapcli.lib b/src/objects/remap/Makefile.remapcli.lib +index e45f34f..2751bf9 100644 +--- a/src/objects/remap/Makefile.remapcli.lib ++++ b/src/objects/remap/Makefile.remapcli.lib +@@ -4,3 +4,5 @@ ASN_DEP = remap + + LIB = remapcli + SRC = remap_client remap_client_ ++ ++DLL_LIB = xncbi xconnect remap +diff --git a/src/objects/scoremat/Makefile.scoremat.lib b/src/objects/scoremat/Makefile.scoremat.lib +index 62e01f5..93bb071 100644 +--- a/src/objects/scoremat/Makefile.scoremat.lib ++++ b/src/objects/scoremat/Makefile.scoremat.lib +@@ -1,2 +1,4 @@ + LIB = scoremat + SRC = scoremat__ scoremat___ ++ ++DLL_LIB = seqset seq +diff --git a/src/objects/seq/Makefile.seq.lib b/src/objects/seq/Makefile.seq.lib +index 1b5edc5..30ef316 100644 +--- a/src/objects/seq/Makefile.seq.lib ++++ b/src/objects/seq/Makefile.seq.lib +@@ -13,3 +13,5 @@ SRC = $(ASN:%=%__) $(ASN:%=%___) seqport_util \ + seq_loc_from_string seq_loc_reverse_complementer + + WATCHERS = vasilche grichenk ++ ++DLL_LIB = general seqcode pub sequtil biblio xser xncbi xutil +diff --git a/src/objects/seqcode/Makefile.seqcode.lib b/src/objects/seqcode/Makefile.seqcode.lib +index dc9d60e..dabd95b 100644 +--- a/src/objects/seqcode/Makefile.seqcode.lib ++++ b/src/objects/seqcode/Makefile.seqcode.lib +@@ -1,2 +1,4 @@ + LIB = seqcode + SRC = seqcode__ seqcode___ ++ ++DLL_LIB = xncbi xser +diff --git a/src/objects/seqedit/Makefile.seqedit.lib b/src/objects/seqedit/Makefile.seqedit.lib +index 283a9b7..520b0bb 100644 +--- a/src/objects/seqedit/Makefile.seqedit.lib ++++ b/src/objects/seqedit/Makefile.seqedit.lib +@@ -1,3 +1,4 @@ + LIB = seqedit + SRC = seqedit__ seqedit___ + ++DLL_LIB = xser seq seqset +diff --git a/src/objects/seqset/Makefile.seqset.lib b/src/objects/seqset/Makefile.seqset.lib +index 87f16d0..febce67 100644 +--- a/src/objects/seqset/Makefile.seqset.lib ++++ b/src/objects/seqset/Makefile.seqset.lib +@@ -1,2 +1,3 @@ + LIB = seqset + SRC = seqset__ seqset___ gb_release_file ++DLL_LIB = xser seq +diff --git a/src/objects/seqsplit/Makefile.seqsplit.lib b/src/objects/seqsplit/Makefile.seqsplit.lib +index 87ae869..1743321 100644 +--- a/src/objects/seqsplit/Makefile.seqsplit.lib ++++ b/src/objects/seqsplit/Makefile.seqsplit.lib +@@ -2,3 +2,5 @@ LIB = seqsplit + SRC = seqsplit__ seqsplit___ + + WATCHERS = vasilche ++ ++DLL_LIB = xser seq seqset +diff --git a/src/objects/seqtest/Makefile.seqtest.lib b/src/objects/seqtest/Makefile.seqtest.lib +index 609a12c..e3d1e4b 100644 +--- a/src/objects/seqtest/Makefile.seqtest.lib ++++ b/src/objects/seqtest/Makefile.seqtest.lib +@@ -4,3 +4,5 @@ ASN = seqtest + + LIB = seqtest + SRC = $(ASN:%=%__) $(ASN:%=%___) ++ ++DLL_LIB = xser seq +diff --git a/src/objects/submit/Makefile.submit.lib b/src/objects/submit/Makefile.submit.lib +index 74798f8..c74707c 100644 +--- a/src/objects/submit/Makefile.submit.lib ++++ b/src/objects/submit/Makefile.submit.lib +@@ -1,2 +1,3 @@ + LIB = submit + SRC = submit__ submit___ ++DLL_LIB = xser xncbi seq biblio seqset +diff --git a/src/objects/taxon1/Makefile.taxon1.lib b/src/objects/taxon1/Makefile.taxon1.lib +index 61658ab..f46db75 100644 +--- a/src/objects/taxon1/Makefile.taxon1.lib ++++ b/src/objects/taxon1/Makefile.taxon1.lib +@@ -3,3 +3,5 @@ LIB = taxon1 + SRC = taxon1__ taxon1___ taxon1 cache utils ctreecont + + WATCHERS = domrach ++ ++DLL_LIB = xser seq xconnect +diff --git a/src/objects/taxon3/Makefile.taxon3.lib b/src/objects/taxon3/Makefile.taxon3.lib +index 7e4c93d..00be2c0 100644 +--- a/src/objects/taxon3/Makefile.taxon3.lib ++++ b/src/objects/taxon3/Makefile.taxon3.lib +@@ -4,3 +4,5 @@ LIB = taxon3 + SRC = taxon3__ taxon3___ taxon3 + + WATCHERS = bollin ++ ++DLL_LIB = connect xser xconnect seq +diff --git a/src/objects/tinyseq/Makefile.tinyseq.lib b/src/objects/tinyseq/Makefile.tinyseq.lib +index 1c7ccf3..e1954cc 100644 +--- a/src/objects/tinyseq/Makefile.tinyseq.lib ++++ b/src/objects/tinyseq/Makefile.tinyseq.lib +@@ -1,2 +1,4 @@ + LIB = tinyseq + SRC = tinyseq__ tinyseq___ ++ ++DLL_LIB = xser +diff --git a/src/objects/valerr/Makefile.valerr.lib b/src/objects/valerr/Makefile.valerr.lib +index b202355..9699bb2 100644 +--- a/src/objects/valerr/Makefile.valerr.lib ++++ b/src/objects/valerr/Makefile.valerr.lib +@@ -2,3 +2,5 @@ LIB = valerr + SRC = valerr__ valerr___ + + ASN_DEP = seqset ++ ++DLL_LIB = xser +diff --git a/src/objects/valid/Makefile.valid.lib b/src/objects/valid/Makefile.valid.lib +index 86a00a0..64226d6 100644 +--- a/src/objects/valid/Makefile.valid.lib ++++ b/src/objects/valid/Makefile.valid.lib +@@ -1,3 +1,5 @@ + # $Id: Makefile.valid.lib 156738 2009-04-07 16:35:10Z ucko $ + LIB = valid + SRC = valid__ valid___ ++ ++DLL_LIB = xser xregexp +diff --git a/src/objects/variation/Makefile.variation.lib b/src/objects/variation/Makefile.variation.lib +index f21f84a..9ba5e9d 100644 +--- a/src/objects/variation/Makefile.variation.lib ++++ b/src/objects/variation/Makefile.variation.lib +@@ -1,2 +1,3 @@ + LIB = variation + SRC = variation__ variation___ ++DLL_LIB = xser general seq +diff --git a/src/objmgr/split/Makefile.id2_split.lib b/src/objmgr/split/Makefile.id2_split.lib +index fafa70a..8a53975 100644 +--- a/src/objmgr/split/Makefile.id2_split.lib ++++ b/src/objmgr/split/Makefile.id2_split.lib +@@ -17,6 +17,6 @@ LIB = id2_split + + CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE) + +-DLL_LIB = $(SOBJMGR_LIBS) ++DLL_LIB = $(SOBJMGR_LIBS) seqsplit xcompress + + WATCHERS = vasilche +diff --git a/src/objmgr/util/Makefile.util.lib b/src/objmgr/util/Makefile.util.lib +index 90eeee0..138e836 100644 +--- a/src/objmgr/util/Makefile.util.lib ++++ b/src/objmgr/util/Makefile.util.lib +@@ -10,3 +10,4 @@ LIB = xobjutil + + WATCHERS = ucko vasilche + ++DLL_LIB = xser xobjmgr +diff --git a/src/objtools/align/Makefile.xalntool.lib b/src/objtools/align/Makefile.xalntool.lib +index cb9846d..9c2a8f9 100644 +--- a/src/objtools/align/Makefile.xalntool.lib ++++ b/src/objtools/align/Makefile.xalntool.lib +@@ -6,3 +6,5 @@ ASN_DEP = seqset + + LIB = xalntool + SRC = alngraphic ++ ++DLL_LIB = access dbapi_driver general seq xhtml xncbi xobjmgr xobjutil xser # align_format axf blastinput +diff --git a/src/objtools/align_format/Makefile.align_format.lib b/src/objtools/align_format/Makefile.align_format.lib +index 4b3e59e..c67c352 100644 +--- a/src/objtools/align_format/Makefile.align_format.lib ++++ b/src/objtools/align_format/Makefile.align_format.lib +@@ -18,3 +18,5 @@ CPPFLAGS = $(ORIG_CPPFLAGS) + # LIB_OR_DLL = dll + + WATCHERS = zaretska jianye madden camacho ++ ++DLL_LIB = seqdb blastdb xser xhtml gene_info xnetblast blast_services ncbi_xloader_genbank xalnmgr xcgi xobjread xobjutil +diff --git a/src/objtools/alnmgr/Makefile.alnmgr.lib b/src/objtools/alnmgr/Makefile.alnmgr.lib +index e32c351..41355ff 100644 +--- a/src/objtools/alnmgr/Makefile.alnmgr.lib ++++ b/src/objtools/alnmgr/Makefile.alnmgr.lib +@@ -12,3 +12,4 @@ SRC = aln_builders aln_converters aln_generators aln_seqid aln_serial \ + + WATCHERS = todorov dicuccio grichenk + ++DLL_LIB = tables dbapi_driver ncbi_xcache_bdb seq seqset sequtil xncbi xobjmgr xobjutil xser # align_format axf +diff --git a/src/objtools/blast/blastdb_format/Makefile.blastdb_format.lib b/src/objtools/blast/blastdb_format/Makefile.blastdb_format.lib +index d8177ed..aa4d8e4 100644 +--- a/src/objtools/blast/blastdb_format/Makefile.blastdb_format.lib ++++ b/src/objtools/blast/blastdb_format/Makefile.blastdb_format.lib +@@ -18,3 +18,5 @@ CPPFLAGS = $(ORIG_CPPFLAGS) + # CXXFLAGS = $(FAST_CXXFLAGS) + # + # LIB_OR_DLL = dll ++ ++DLL_LIB = xncbi xser xobjutil seq seqdb +diff --git a/src/objtools/blast/gene_info_reader/Makefile.gene_info.lib b/src/objtools/blast/gene_info_reader/Makefile.gene_info.lib +index bf5fd1b..c32aca4 100644 +--- a/src/objtools/blast/gene_info_reader/Makefile.gene_info.lib ++++ b/src/objtools/blast/gene_info_reader/Makefile.gene_info.lib +@@ -4,3 +4,5 @@ WATCHERS = camacho + + LIB = gene_info + SRC = gene_info gene_info_reader file_utils ++ ++DLL_LIB = xncbi +diff --git a/src/objtools/blast/gene_info_writer/Makefile.gene_info_writer.lib b/src/objtools/blast/gene_info_writer/Makefile.gene_info_writer.lib +index b0a00dc..37569f8 100644 +--- a/src/objtools/blast/gene_info_writer/Makefile.gene_info_writer.lib ++++ b/src/objtools/blast/gene_info_writer/Makefile.gene_info_writer.lib +@@ -6,3 +6,5 @@ LIB = gene_info_writer + SRC = gene_info_writer + + ASN_DEP = blastdb ++ ++DLL_LIB = gene_info xncbi seqdb +diff --git a/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib b/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib +index 25898aa..0b0e478 100644 +--- a/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib ++++ b/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib +@@ -29,3 +29,5 @@ CXXFLAGS = $(FAST_CXXFLAGS) + LDFLAGS = $(FAST_LDFLAGS) + + WATCHERS = maning camacho ++ ++DLL_LIB = blastdb xobjmgr +diff --git a/src/objtools/blast/seqdb_writer/Makefile.writedb.lib b/src/objtools/blast/seqdb_writer/Makefile.writedb.lib +index 7b9c8e1..6dbdbaa 100644 +--- a/src/objtools/blast/seqdb_writer/Makefile.writedb.lib ++++ b/src/objtools/blast/seqdb_writer/Makefile.writedb.lib +@@ -13,3 +13,5 @@ CXXFLAGS = $(FAST_CXXFLAGS) + LDFLAGS = $(FAST_LDFLAGS) + + WATCHERS = maning camacho ++ ++DLL_LIB = seq blastdb seqdb xobjmgr xobjread xutil +diff --git a/src/objtools/blast/services/Makefile.blast_services.lib b/src/objtools/blast/services/Makefile.blast_services.lib +index 10a878c..7a70b22 100644 +--- a/src/objtools/blast/services/Makefile.blast_services.lib ++++ b/src/objtools/blast/services/Makefile.blast_services.lib +@@ -12,3 +12,4 @@ CFLAGS = $(FAST_CFLAGS) + CXXFLAGS = $(FAST_CXXFLAGS) + LDFLAGS = $(FAST_LDFLAGS) + ++DLL_LIB = xncbi xser xnetblast xnetblastcli +diff --git a/src/objtools/cddalignview/Makefile.cddalignview.lib b/src/objtools/cddalignview/Makefile.cddalignview.lib +index 8e39baa..f4d3a35 100644 +--- a/src/objtools/cddalignview/Makefile.cddalignview.lib ++++ b/src/objtools/cddalignview/Makefile.cddalignview.lib +@@ -11,3 +11,5 @@ SRC = \ + cav_seqset + + LIB = xcddalignview ++ ++DLL_LIB = cdd dbapi_driver general ncbimime seq seqset xncbi xser # align_format axf ncbi_xloader_bam +diff --git a/src/objtools/cleanup/Makefile.cleanup.lib b/src/objtools/cleanup/Makefile.cleanup.lib +index 663d755..ad7b3cf 100644 +--- a/src/objtools/cleanup/Makefile.cleanup.lib ++++ b/src/objtools/cleanup/Makefile.cleanup.lib +@@ -10,7 +10,7 @@ SRC = autogenerated_cleanup cleanup \ + cleanup_utils \ + newcleanupp + +-DLL_LIB = xregexp $(PCRE_LIB) ++DLL_LIB = xregexp $(PCRE_LIB) access biblio general pub seq seqset sequtil submit xobjmgr xobjutil xser + LIB = xcleanup + + LIBS = $(PCRE_LIBS) +diff --git a/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib b/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib +index 80af69f..704ed7a 100644 +--- a/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib ++++ b/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib +@@ -6,3 +6,6 @@ SRC = bdbloader cached_sequence local_blastdb_adapter + ASN_DEP = blastdb seqset + + WATCHERS = camacho ++ ++DLL_LIB = seqdb ++ +diff --git a/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib b/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib +index 80abb48..2ddec92 100644 +--- a/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib ++++ b/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib +@@ -6,3 +6,5 @@ SRC = bdbloader_rmt remote_blastdb_adapter + ASN_DEP = blastdb xnetblast + + WATCHERS = camacho ++ ++DLL_LIB = blast_services ncbi_xloader_blastdb xobjmgr +diff --git a/src/objtools/data_loaders/cdd/Makefile.ncbi_xloader_cdd.lib b/src/objtools/data_loaders/cdd/Makefile.ncbi_xloader_cdd.lib +index a51042b..fa92fc9 100644 +--- a/src/objtools/data_loaders/cdd/Makefile.ncbi_xloader_cdd.lib ++++ b/src/objtools/data_loaders/cdd/Makefile.ncbi_xloader_cdd.lib +@@ -9,3 +9,5 @@ LIB = ncbi_xloader_cdd + SRC = cdd + + ASN_DEP = seqset ++ ++DLL_LIB = dbapi_driver general seq seqset xconnect xncbi xobjmgr xser # align_format axf ncbi_xloader_bam +diff --git a/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib b/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib +index f2b2b49..864e4b1 100644 +--- a/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib ++++ b/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib +@@ -12,6 +12,6 @@ LIB = ncbi_xreader + LIB_OR_DLL = both + + # Dependencies for shared library +-DLL_LIB = ++DLL_LIB = xcompress xobjmgr seqsplit xconnect id1 id2 + + WATCHERS = vasilche +diff --git a/src/objtools/data_loaders/genbank/id2/Makefile.ncbi_xreader_id2.lib b/src/objtools/data_loaders/genbank/id2/Makefile.ncbi_xreader_id2.lib +index 0a29cbf..74c30dc 100644 +--- a/src/objtools/data_loaders/genbank/id2/Makefile.ncbi_xreader_id2.lib ++++ b/src/objtools/data_loaders/genbank/id2/Makefile.ncbi_xreader_id2.lib +@@ -15,3 +15,5 @@ CPPFLAGS = $(ORIG_CPPFLAGS) $(Z_INCLUDE) + # DLL_LIB = xconnect ncbi_xreader$(DLL) + + WATCHERS = vasilche ++ ++DLL_LIB = xncbi gene_info id2 ncbi_xreader xconnect xser +diff --git a/src/objtools/data_loaders/patcher/Makefile.ncbi_xloader_patcher.lib b/src/objtools/data_loaders/patcher/Makefile.ncbi_xloader_patcher.lib +index 8d09d8c..d6040ed 100644 +--- a/src/objtools/data_loaders/patcher/Makefile.ncbi_xloader_patcher.lib ++++ b/src/objtools/data_loaders/patcher/Makefile.ncbi_xloader_patcher.lib +@@ -7,3 +7,5 @@ ASN_DEP = seq seqset seqedit + + + WATCHERS = vasilche ++ ++DLL_LIB = dbapi_driver seq seqedit seqset xncbi xobjmgr xser # axf +diff --git a/src/objtools/data_loaders/trace/Makefile.xloader_trace.lib b/src/objtools/data_loaders/trace/Makefile.xloader_trace.lib +index d2debd5..33fed34 100644 +--- a/src/objtools/data_loaders/trace/Makefile.xloader_trace.lib ++++ b/src/objtools/data_loaders/trace/Makefile.xloader_trace.lib +@@ -9,3 +9,5 @@ LIB = ncbi_xloader_trace + SRC = trace_chgr + + ASN_DEP = id1 ++ ++DLL_LIB = dbapi_driver general id1 id1cli seq xncbi xobjmgr xser # align_format axf +diff --git a/src/objtools/edit/Makefile.edit.lib b/src/objtools/edit/Makefile.edit.lib +index 7ce0d11..f5458c5 100644 +--- a/src/objtools/edit/Makefile.edit.lib ++++ b/src/objtools/edit/Makefile.edit.lib +@@ -11,3 +11,5 @@ LIB = xobjedit + ASN_DEP = seqset + + WATCHERS = bollin ++ ++DLL_LIB = xncbi seq xobjutil xobjmgr +diff --git a/src/objtools/eutils/api/Makefile.eutils.lib b/src/objtools/eutils/api/Makefile.eutils.lib +index da71ea9..b444e72 100644 +--- a/src/objtools/eutils/api/Makefile.eutils.lib ++++ b/src/objtools/eutils/api/Makefile.eutils.lib +@@ -10,3 +10,5 @@ ASN_DEP = einfo esearch egquery epost elink esummary espell uilist \ + ehistory + + WATCHERS = grichenk ++ ++DLL_LIB = dbapi_driver xconnect xncbi xser # align_format axf ncbi_xloader_bam +diff --git a/src/objtools/eutils/egquery/Makefile.egquery.lib b/src/objtools/eutils/egquery/Makefile.egquery.lib +index 82b4ed0..7030a29 100644 +--- a/src/objtools/eutils/egquery/Makefile.egquery.lib ++++ b/src/objtools/eutils/egquery/Makefile.egquery.lib +@@ -4,3 +4,5 @@ LIB = egquery + SRC = egquery__ egquery___ + + WATCHERS = grichenk ++ ++DLL_LIB = xser +diff --git a/src/objtools/eutils/ehistory/Makefile.ehistory.lib b/src/objtools/eutils/ehistory/Makefile.ehistory.lib +index f99ca0f..5683a74 100644 +--- a/src/objtools/eutils/ehistory/Makefile.ehistory.lib ++++ b/src/objtools/eutils/ehistory/Makefile.ehistory.lib +@@ -4,3 +4,5 @@ LIB = ehistory + SRC = ehistory__ ehistory___ + + WATCHERS = grichenk ++ ++DLL_LIB = xser +diff --git a/src/objtools/eutils/einfo/Makefile.einfo.lib b/src/objtools/eutils/einfo/Makefile.einfo.lib +index e18413d..7eaee71 100644 +--- a/src/objtools/eutils/einfo/Makefile.einfo.lib ++++ b/src/objtools/eutils/einfo/Makefile.einfo.lib +@@ -4,3 +4,5 @@ LIB = einfo + SRC = einfo__ einfo___ + + WATCHERS = grichenk ++ ++DLL_LIB = xser +diff --git a/src/objtools/eutils/elink/Makefile.elink.lib b/src/objtools/eutils/elink/Makefile.elink.lib +index 87f352c..692835c 100644 +--- a/src/objtools/eutils/elink/Makefile.elink.lib ++++ b/src/objtools/eutils/elink/Makefile.elink.lib +@@ -4,3 +4,5 @@ LIB = elink + SRC = elink__ elink___ + + WATCHERS = grichenk ++ ++DLL_LIB = xser +diff --git a/src/objtools/eutils/epost/Makefile.epost.lib b/src/objtools/eutils/epost/Makefile.epost.lib +index 4a456ed..d73f41b 100644 +--- a/src/objtools/eutils/epost/Makefile.epost.lib ++++ b/src/objtools/eutils/epost/Makefile.epost.lib +@@ -4,3 +4,5 @@ LIB = epost + SRC = epost__ epost___ + + WATCHERS = grichenk ++ ++DLL_LIB = xser +diff --git a/src/objtools/eutils/esearch/Makefile.esearch.lib b/src/objtools/eutils/esearch/Makefile.esearch.lib +index bb5b64b..71912da 100644 +--- a/src/objtools/eutils/esearch/Makefile.esearch.lib ++++ b/src/objtools/eutils/esearch/Makefile.esearch.lib +@@ -4,3 +4,5 @@ LIB = esearch + SRC = esearch__ esearch___ + + WATCHERS = grichenk ++ ++DLL_LIB = xser +diff --git a/src/objtools/eutils/espell/Makefile.espell.lib b/src/objtools/eutils/espell/Makefile.espell.lib +index 7cf1a34..25be846 100644 +--- a/src/objtools/eutils/espell/Makefile.espell.lib ++++ b/src/objtools/eutils/espell/Makefile.espell.lib +@@ -4,3 +4,5 @@ LIB = espell + SRC = espell__ espell___ + + WATCHERS = grichenk ++ ++DLL_LIB = xser +diff --git a/src/objtools/eutils/esummary/Makefile.esummary.lib b/src/objtools/eutils/esummary/Makefile.esummary.lib +index 4d3e058..1f74c06 100644 +--- a/src/objtools/eutils/esummary/Makefile.esummary.lib ++++ b/src/objtools/eutils/esummary/Makefile.esummary.lib +@@ -4,3 +4,5 @@ LIB = esummary + SRC = esummary__ esummary___ + + WATCHERS = grichenk ++ ++DLL_LIB = xser +diff --git a/src/objtools/eutils/linkout/Makefile.linkout.lib b/src/objtools/eutils/linkout/Makefile.linkout.lib +index 19b2b8a..77dcc3c 100644 +--- a/src/objtools/eutils/linkout/Makefile.linkout.lib ++++ b/src/objtools/eutils/linkout/Makefile.linkout.lib +@@ -4,3 +4,5 @@ SRC = linkout__ linkout___ + LIB = linkout + + WATCHERS = grichenk ++ ++DLL_LIB = xser +diff --git a/src/objtools/eutils/uilist/Makefile.uilist.lib b/src/objtools/eutils/uilist/Makefile.uilist.lib +index b49c3c5..2ee63f0 100644 +--- a/src/objtools/eutils/uilist/Makefile.uilist.lib ++++ b/src/objtools/eutils/uilist/Makefile.uilist.lib +@@ -4,3 +4,5 @@ SRC = uilist__ uilist___ + LIB = uilist + + WATCHERS = grichenk ++ ++DLL_LIB = access dbapi_driver xncbi xser # align_format axf +diff --git a/src/objtools/format/Makefile.xformat.lib b/src/objtools/format/Makefile.xformat.lib +index a4fc469..fa58b3c 100644 +--- a/src/objtools/format/Makefile.xformat.lib ++++ b/src/objtools/format/Makefile.xformat.lib +@@ -19,3 +19,5 @@ SRC = accession_item basecount_item comment_item contig_item date_item \ + gather_iter html_anchor_item inst_info_map + + WATCHERS = ludwigf dicuccio kornbluh ++ ++DLL_LIB = submit connect xncbi gbseq xobjmgr xobjutil xalnmgr xconnect +diff --git a/src/objtools/lds/Makefile.lds.lib b/src/objtools/lds/Makefile.lds.lib +index e371035..689cfb4 100644 +--- a/src/objtools/lds/Makefile.lds.lib ++++ b/src/objtools/lds/Makefile.lds.lib +@@ -9,6 +9,6 @@ SRC = lds lds_reader lds_query \ + lds_coreobjreader lds_files lds_object lds_manager + + # Dependencies for shared library +-DLL_LIB = bdb ++DLL_LIB = bdb seq xobjread xobjmgr xobjutil + + WATCHERS = vasilche +diff --git a/src/objtools/manip/Makefile.xobjmanip.lib b/src/objtools/manip/Makefile.xobjmanip.lib +index 300ceb2..4a81ac9 100644 +--- a/src/objtools/manip/Makefile.xobjmanip.lib ++++ b/src/objtools/manip/Makefile.xobjmanip.lib +@@ -6,3 +6,5 @@ LIB = xobjmanip + SRC = sage_manip + + WATCHERS = dicuccio ++ ++DLL_LIB = xncbi general +diff --git a/src/objtools/readers/Makefile.xobjread.lib b/src/objtools/readers/Makefile.xobjread.lib +index 0fbffd4..4ca9fed 100644 +--- a/src/objtools/readers/Makefile.xobjread.lib ++++ b/src/objtools/readers/Makefile.xobjread.lib +@@ -19,5 +19,4 @@ SRC = read_util format_guess_ex \ + best_feat_finder source_mod_parser fasta_exception + + +-DLL_LIB = creaders +- ++DLL_LIB = creaders xncbi seq biblio seqset +diff --git a/src/objtools/readers/Makefile.xobjreadex.lib b/src/objtools/readers/Makefile.xobjreadex.lib +index 85eefe2..9f317ae 100644 +--- a/src/objtools/readers/Makefile.xobjreadex.lib ++++ b/src/objtools/readers/Makefile.xobjreadex.lib +@@ -8,4 +8,4 @@ LIB = xobjreadex + SRC = glimmer_reader idmapper idmapper_builtin idmapper_config \ + idmapper_database source_mod_parser_wrapper + +-DLL_LIB = xobjread ++DLL_LIB = xobjread xncbi xutil seq xobjmgr xobjutil +diff --git a/src/objtools/seqmasks_io/Makefile.seqmasks_io.lib b/src/objtools/seqmasks_io/Makefile.seqmasks_io.lib +index 687af1e..f48568c 100644 +--- a/src/objtools/seqmasks_io/Makefile.seqmasks_io.lib ++++ b/src/objtools/seqmasks_io/Makefile.seqmasks_io.lib +@@ -11,6 +11,6 @@ mask_writer_seqloc \ + mask_writer_blastdb_maskinfo + + ASN_DEP = seqset +-DLL_LIB = seqdb blastdb ++DLL_LIB = seqdb blastdb xobjread xobjutil + + WATCHERS = morgulis camacho +diff --git a/src/objtools/simple/Makefile.xobjsimple.lib b/src/objtools/simple/Makefile.xobjsimple.lib +index dab25d6..f676dc7 100644 +--- a/src/objtools/simple/Makefile.xobjsimple.lib ++++ b/src/objtools/simple/Makefile.xobjsimple.lib +@@ -10,3 +10,4 @@ ASN_DEP = seqset + LIB = xobjsimple + SRC = simple_om + ++DLL_LIB = xobjmgr ncbi_xloader_genbank +diff --git a/src/objtools/snputil/Makefile.snputil.lib b/src/objtools/snputil/Makefile.snputil.lib +index 15abef3..5ad1560 100644 +--- a/src/objtools/snputil/Makefile.snputil.lib ++++ b/src/objtools/snputil/Makefile.snputil.lib +@@ -9,3 +9,5 @@ SRC = snp_utils snp_bitfield \ + ASN_DEP = seqset + + WATCHERS = rudnev ++ ++DLL_LIB = general seq xncbi xobjmgr xser +diff --git a/src/objtools/validator/Makefile.validator.lib b/src/objtools/validator/Makefile.validator.lib +index 80a74d8..6eec94b 100644 +--- a/src/objtools/validator/Makefile.validator.lib ++++ b/src/objtools/validator/Makefile.validator.lib +@@ -19,3 +19,5 @@ NOOPT_CXX = $(CXX_WRAPPER) $(CXX) $(CXXFLAGS_ALL:-xO%=) + + lat_lon_country_map.o: $(srcdir)/lat_lon_country_map.cpp + $(NOOPT_CXX) $(srcdir)/lat_lon_country_map.cpp -o $@ $(CXX_FILTER) ++ ++DLL_LIB = xncbi xobjutil xalnmgr xformat taxon3 valerr valid +diff --git a/src/objtools/writers/Makefile.xobjwrite.lib b/src/objtools/writers/Makefile.xobjwrite.lib +index cd6596b..a7d0c01 100644 +--- a/src/objtools/writers/Makefile.xobjwrite.lib ++++ b/src/objtools/writers/Makefile.xobjwrite.lib +@@ -15,3 +15,4 @@ SRC = agp_write \ + + WATCHERS = ludwigf boukn + ++DLL_LIB = xobjutil xalnmgr +diff --git a/src/sample/app/asn/Makefile.sample_asn.lib b/src/sample/app/asn/Makefile.sample_asn.lib +index 0db9ebd..26e6ad9 100644 +--- a/src/sample/app/asn/Makefile.sample_asn.lib ++++ b/src/sample/app/asn/Makefile.sample_asn.lib +@@ -10,3 +10,5 @@ LIB = sample_asn + ASN_DEP = general + + WATCHERS = gouriano ++ ++DLL_LIB = access align_format axf dbapi_driver general xncbi xser +diff --git a/src/sample/app/soap/Makefile.soap_dataobj.lib b/src/sample/app/soap/Makefile.soap_dataobj.lib +index 4b87f51..c398ded 100644 +--- a/src/sample/app/soap/Makefile.soap_dataobj.lib ++++ b/src/sample/app/soap/Makefile.soap_dataobj.lib +@@ -2,3 +2,5 @@ LIB = soap_dataobj + SRC = soap_dataobj__ soap_dataobj___ + + WATCHERS = gouriano ++ ++DLL_LIB = access align_format axf dbapi_driver xncbi xser +diff --git a/src/sample/lib/asn_lib/Makefile.asn_sample_lib.lib b/src/sample/lib/asn_lib/Makefile.asn_sample_lib.lib +index f9d6103..4c22831 100644 +--- a/src/sample/lib/asn_lib/Makefile.asn_sample_lib.lib ++++ b/src/sample/lib/asn_lib/Makefile.asn_sample_lib.lib +@@ -2,3 +2,5 @@ LIB = asn_sample_lib + SRC = asn_sample_lib__ asn_sample_lib___ + + WATCHERS = gouriano ++ ++DLL_LIB = access align_format axf dbapi_driver xncbi xser +diff --git a/src/sample/lib/basic/Makefile.basic_sample_lib.lib b/src/sample/lib/basic/Makefile.basic_sample_lib.lib +index a6ba11a..364d9fc 100644 +--- a/src/sample/lib/basic/Makefile.basic_sample_lib.lib ++++ b/src/sample/lib/basic/Makefile.basic_sample_lib.lib +@@ -5,3 +5,5 @@ SRC = basic_sample_lib + + + WATCHERS = gouriano ++ ++DLL_LIB = xncbi +diff --git a/src/sample/lib/dtd/Makefile.dtd_sample_lib.lib b/src/sample/lib/dtd/Makefile.dtd_sample_lib.lib +index d2a27ef..a63a7e8 100644 +--- a/src/sample/lib/dtd/Makefile.dtd_sample_lib.lib ++++ b/src/sample/lib/dtd/Makefile.dtd_sample_lib.lib +@@ -2,3 +2,5 @@ LIB = dtd_sample_lib + SRC = dtd_sample_lib__ dtd_sample_lib___ + + WATCHERS = gouriano ++ ++DLL_LIB = access align_format axf dbapi_driver xncbi xser +diff --git a/src/sample/lib/xsd/Makefile.xsd_sample_lib.lib b/src/sample/lib/xsd/Makefile.xsd_sample_lib.lib +index 4b7b6e2..838e8ea 100644 +--- a/src/sample/lib/xsd/Makefile.xsd_sample_lib.lib ++++ b/src/sample/lib/xsd/Makefile.xsd_sample_lib.lib +@@ -2,3 +2,5 @@ LIB = xsd_sample_lib + SRC = xsd_sample_lib__ xsd_sample_lib___ + + WATCHERS = gouriano ++ ++DLL_LIB = access align_format axf dbapi_driver xncbi xser +diff --git a/src/serial/Makefile.serial.lib b/src/serial/Makefile.serial.lib +index 2563b5f..efad054 100644 +--- a/src/serial/Makefile.serial.lib ++++ b/src/serial/Makefile.serial.lib +@@ -19,3 +19,5 @@ SRC = \ + LIB = xser + + WATCHERS = gouriano ++ ++DLL_LIB = xncbi xutil +diff --git a/src/serial/soap/Makefile.soap.lib b/src/serial/soap/Makefile.soap.lib +index e77d4ee..3b28bc4 100644 +--- a/src/serial/soap/Makefile.soap.lib ++++ b/src/serial/soap/Makefile.soap.lib +@@ -8,3 +8,5 @@ SRC = soap_message soap_readhook soap_writehook soap_client \ + LIB = xsoap + + WATCHERS = gouriano ++ ++DLL_LIB = xncbi xutil xser xconnect +diff --git a/src/serial/soap/Makefile.soap_server.lib b/src/serial/soap/Makefile.soap_server.lib +index c961496..0ccb2f0 100644 +--- a/src/serial/soap/Makefile.soap_server.lib ++++ b/src/serial/soap/Makefile.soap_server.lib +@@ -9,3 +9,5 @@ LIB = xsoap_server + REQUIRES = cgi + + WATCHERS = gouriano ++ ++DLL_LIB = xncbi xutil xcgi xsoap xser +diff --git a/src/serial/test/Makefile.we_cpp.lib b/src/serial/test/Makefile.we_cpp.lib +index 9877691..599ef5d 100644 +--- a/src/serial/test/Makefile.we_cpp.lib ++++ b/src/serial/test/Makefile.we_cpp.lib +@@ -3,3 +3,4 @@ SRC = we_cpp__ we_cpp___ + + WATCHERS = gouriano + ++DLL_LIB = xncbi xutil xser +diff --git a/src/sra/data_loaders/bam/Makefile.ncbi_xloader_bam.lib b/src/sra/data_loaders/bam/Makefile.ncbi_xloader_bam.lib +index 4896661..8e2ad56 100644 +--- a/src/sra/data_loaders/bam/Makefile.ncbi_xloader_bam.lib ++++ b/src/sra/data_loaders/bam/Makefile.ncbi_xloader_bam.lib +@@ -12,7 +12,7 @@ ASN_DEP = seqset seq + + LIB_OR_DLL = both + +-DLL_LIB = $(SOBJMGR_LIBS) bamread$(STATIC) $(BAM_LIBS) $(CMPRS_LIB) ++DLL_LIB = $(SOBJMGR_LIBS) bamread$(STATIC) $(BAM_LIBS) $(CMPRS_LIB) xobjreadex + LIBS = $(CMPRS_LIBS) $(ORIG_LIBS) + + CPPFLAGS = $(SRA_INCLUDE) -DNCBI_XLOADER_BAM_EXPORTS $(ORIG_CPPFLAGS) +diff --git a/src/sra/sdk/libs/align/Makefile.align-writer.lib b/src/sra/sdk/libs/align/Makefile.align-writer.lib +index f2a2f58..f61b25a 100644 +--- a/src/sra/sdk/libs/align/Makefile.align-writer.lib ++++ b/src/sra/sdk/libs/align/Makefile.align-writer.lib +@@ -6,7 +6,7 @@ LIB = align-writer + SRC = dna-reverse-cmpl reader-cmn reader-refseq refseq-mgr writer-cmn \ + writer-refseq writer-alignment writer-sequence writer-ref writer-reference + +-DLL_LIB = wvdb wkdb load kfg kfs klib $(Z_LIB) ++DLL_LIB = wvdb wkdb load kfg kfs klib kapp $(Z_LIB) + LIBS = $(Z_LIBS) $(ORIG_LIBS) + + CPPFLAGS = $(SRA_INCLUDE) $(SRA_INTERNAL_CPPFLAGS) -D_LIBRARY $(ORIG_CPPFLAGS) +diff --git a/src/util/Makefile.util.lib b/src/util/Makefile.util.lib +index f103ff1..829a71c 100644 +--- a/src/util/Makefile.util.lib ++++ b/src/util/Makefile.util.lib +@@ -14,3 +14,5 @@ PROJ_TAG = core + LIBS = $(ORIG_LIBS) + + WATCHERS = vakatov ++ ++DLL_LIB = xncbi +diff --git a/src/util/compress/api/Makefile.compress.lib b/src/util/compress/api/Makefile.compress.lib +index ae22234..2ce803a 100644 +--- a/src/util/compress/api/Makefile.compress.lib ++++ b/src/util/compress/api/Makefile.compress.lib +@@ -6,7 +6,7 @@ LIB = xcompress + + CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE) + +-DLL_LIB = $(BZ2_LIB) $(Z_LIB) $(LZO_LIB) ++DLL_LIB = $(BZ2_LIB) $(Z_LIB) $(LZO_LIB) xutil xncbi + LIBS = $(BZ2_LIBS) $(Z_LIBS) $(LZO_LIBS) + + WATCHERS = ivanov +diff --git a/src/util/qparse/Makefile.xqueryparse.lib b/src/util/qparse/Makefile.xqueryparse.lib +index a003930..0505da7 100644 +--- a/src/util/qparse/Makefile.xqueryparse.lib ++++ b/src/util/qparse/Makefile.xqueryparse.lib +@@ -7,3 +7,5 @@ query_parser_bison.tab.c : query_parser_bison.y + bison -v -p ncbi_q_ -o query_parser_bison.tab.c query_parser_bison.y + + WATCHERS = kuznets ++ ++DLL_LIB = xncbi xutil +diff --git a/src/util/regexp/Makefile.regexp.lib b/src/util/regexp/Makefile.regexp.lib +index 0f8d5e8..83a82af 100644 +--- a/src/util/regexp/Makefile.regexp.lib ++++ b/src/util/regexp/Makefile.regexp.lib +@@ -10,3 +10,5 @@ LIB = regexp + CPPFLAGS = -I$(includedir)/util/regexp -DHAVE_CONFIG_H $(ORIG_CPPFLAGS) + + WATCHERS = ivanov ++ ++DLL_LIB = xncbi xutil +diff --git a/src/util/sequtil/Makefile.sequtil.lib b/src/util/sequtil/Makefile.sequtil.lib +index c068a32..453c911 100644 +--- a/src/util/sequtil/Makefile.sequtil.lib ++++ b/src/util/sequtil/Makefile.sequtil.lib +@@ -4,3 +4,5 @@ LIB = sequtil + SRC = sequtil sequtil_convert sequtil_convert_imp sequtil_manip sequtil_tables sequtil_shared + + WATCHERS = shomrat ++ ++DLL_LIB = xncbi xutil +diff --git a/src/util/xregexp/Makefile.xregexp.lib b/src/util/xregexp/Makefile.xregexp.lib +index 965fac4..3accea3 100644 +--- a/src/util/xregexp/Makefile.xregexp.lib ++++ b/src/util/xregexp/Makefile.xregexp.lib +@@ -6,7 +6,7 @@ LIB = xregexp + + CPPFLAGS = $(ORIG_CPPFLAGS) $(PCRE_INCLUDE) + +-DLL_LIB = $(PCRE_LIB) ++DLL_LIB = $(PCRE_LIB) xutil xncbi + LIBS = $(PCRE_LIBS) + + WATCHERS = ivanov diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-conf-opts.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-conf-opts.patch new file mode 100644 index 000000000..820960354 --- /dev/null +++ b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-conf-opts.patch @@ -0,0 +1,213 @@ + src/build-system/configure | 34 +++++++++++++++++++++++----------- + src/build-system/configure.ac | 33 ++++++++++++++++++++++----------- + 2 files changed, 45 insertions(+), 22 deletions(-) + +diff --git a/src/build-system/configure b/src/build-system/configure +index 82fc9ef..d31a4f2 100755 +--- a/src/build-system/configure ++++ b/src/build-system/configure +@@ -924,7 +924,7 @@ Optional Packages: + --without-distcc do not automatically use distcc if available + --without-ncbi-c do not use NCBI C Toolkit + --without-sss do not use NCBI SSS libraries +- --without-utils do not use NCBI SSS UTIL library ++ --without-sssutils do not use NCBI SSS UTIL library + --without-sssdb do not use NCBI SSS DB library + --with-included-sss use the in-tree copy of SSS + --with-z=DIR use zlib installation in DIR +@@ -2835,12 +2835,12 @@ check ncbi-public strip pch caution ccache distcc \ + ncbi-c wxwidgets wxwidgets-ucs fastcgi sss sssdb sssutils included-sss \ + geo included-geo \ + z bz2 lzo pcre gnutls openssl sybase sybase-local sybase-new \ +-ftds mysql orbacus freetype fltk opengl mesa glut glew glew-mx \ ++ftds mysql orbacus odbc freetype fltk opengl mesa glut glew glew-mx \ + bdb python jni sqlite3 icu boost boost-tag \ + sp expat sablot libxml libxslt xerces xalan oechem sge muparser hdf5 \ + gif jpeg tiff png xpm magic curl 3psw \ + local-lbsm ncbi-crypt connext \ +-serial objects dbapi app ctools gui algo internal gbench" ++serial objects dbapi app ctools gui algo internal gbench x" + + x_with_list=`echo "$x_with_list" | sed 's/\([^ ][^ ]*\)/--with-\1 --without-\1/g'` + +@@ -2864,6 +2864,7 @@ for x_arg in "$@" ; do + case "$x_arg" in + --with-extra-action= | --exec-prefix= | --with-projects= | --srcdir= \ + | --cache-file= | --build= | --host= | --target= | --with-runpath= \ ++ | --mandir= | --infodir= | --datadir= | --sysconfdir= | --localstatedir= \ + | --with-relative-runpath= | --x-includes= | --x-libraries= ) + { { echo "$as_me:$LINENO: error: $x_arg: requires value; use --help to show usage" >&5 + echo "$as_me: error: $x_arg: requires value; use --help to show usage" >&2;} +@@ -2876,6 +2877,7 @@ echo "$as_me: error: $x_arg: requires value; use --help to show usage" >&2;} + | --with-universal=* | --with-tcheck=* \ + | --cache-file=* | --build=* | --host=* | --prefix=* | --exec-prefix=* \ + | --libdir=* | --bindir=* | --includedir=* | --srcdir=* \ ++ | --mandir=* | --infodir=* | --datadir=* | --sysconfdir=* | --localstatedir=* \ + | [A-Z]*=* \ + | --with-z=* | --with-bz2=* | --with-lzo=* \ + | --with-pcre=* \ +@@ -3023,7 +3025,8 @@ echo "$as_me: error: --without-extra-action is not allowed" >&2;} + fi + + case "$with_projects" in +- "") if test -r projects; then ++ ""|yes) ++ if test -r projects; then + { echo "$as_me:$LINENO: using default projects file \"projects\"." >&5 + echo "$as_me: using default projects file \"projects\"." >&6;} + with_projects=projects +@@ -3049,6 +3052,16 @@ echo "$as_me: WARNING: default projects file \"projects\" is a dangling link." > + ;; + esac + ++if test -n "$with_projects"; then ++ case "$with_projects" in ++ /* ) abs_projects=$with_projects ;; ++ yes) abs_projects=$srcdir/projects ;; ++ * ) abs_projects=$srcdir/$with_projects ;; ++ esac ++ test -r "$abs_projects" || \ ++ as_fn_error $? "unable to read requested projects file \"$abs_projects\"." "$LINENO" 5 ++fi ++ + + #### Always define this + +@@ -32712,7 +32725,7 @@ else + sep=", " + fi + if test -n "$reason" -a "$with_internal" = "yes"; then +- if test -z "$with_projects" -o "$with_projects" = "no"; then ++ if test -z "$with_projects"; then + { { echo "$as_me:$LINENO: error: --with-internal: Cannot build INTERNAL projects: missing $reason" >&5 + echo "$as_me: error: --with-internal: Cannot build INTERNAL projects: missing $reason" >&2;} + { (exit 1); exit 1; }; } +@@ -34949,11 +34962,9 @@ if test "$with_flat_makefile" != "no"; then + else + cfm_flags='-remoteptb' + fi +- case "$with_projects" in +- yes ) cfm_flags="$cfm_flags -p projects" ;; +- no | '' ) ;; +- * ) cfm_flags="$cfm_flags -p $with_projects" ;; +- esac ++ if test -n "$with_projects"; then ++ cfm_flags="$cfm_flags -p $with_projects" ++ fi + if test "$with_configure_dialog" = yes; then + cfm_flags="$cfm_flags -cfg" + fi +@@ -34997,7 +35008,8 @@ lib) + esac + + if test -n "$with_projects"; then +- build_proj="To build selected projects: cd $builddir && make all_p" ++ build_proj="To build selected projects (as listed in \"$with_projects\"): ++ cd $builddir && make all_p" + fi + + cat << EOCONF +diff --git a/src/build-system/configure.ac b/src/build-system/configure.ac +index 7b733af..3b55bf5 100644 +--- a/src/build-system/configure.ac ++++ b/src/build-system/configure.ac +@@ -222,7 +222,7 @@ AC_ARG_WITH(ncbi-c, + AC_ARG_WITH(sss, + [ --without-sss do not use NCBI SSS libraries]) + AC_ARG_WITH(sssutils, +- [ --without-utils do not use NCBI SSS UTIL library]) ++ [ --without-sssutils do not use NCBI SSS UTIL library]) + AC_ARG_WITH(sssdb, + [ --without-sssdb do not use NCBI SSS DB library]) + AC_ARG_WITH(included-sss, +@@ -462,12 +462,12 @@ check ncbi-public strip pch caution ccache distcc \ + ncbi-c wxwidgets wxwidgets-ucs fastcgi sss sssdb sssutils included-sss \ + geo included-geo \ + z bz2 lzo pcre gnutls openssl sybase sybase-local sybase-new \ +-ftds mysql orbacus freetype fltk opengl mesa glut glew glew-mx \ ++ftds mysql orbacus odbc freetype fltk opengl mesa glut glew glew-mx \ + bdb python jni sqlite3 icu boost boost-tag \ + sp expat sablot libxml libxslt xerces xalan oechem sge muparser hdf5 \ + gif jpeg tiff png xpm magic curl 3psw \ + local-lbsm ncbi-crypt connext \ +-serial objects dbapi app ctools gui algo internal gbench" ++serial objects dbapi app ctools gui algo internal gbench x" + + changequote(, )dnl + x_with_list=`echo "$x_with_list" | sed 's/\([^ ][^ ]*\)/--with-\1 --without-\1/g'` +@@ -493,6 +493,7 @@ for x_arg in "$@" ; do + case "$x_arg" in + --with-extra-action= | --exec-prefix= | --with-projects= | --srcdir= \ + | --cache-file= | --build= | --host= | --target= | --with-runpath= \ ++ | --mandir= | --infodir= | --datadir= | --sysconfdir= | --localstatedir= \ + | --with-relative-runpath= | --x-includes= | --x-libraries= ) + AC_MSG_ERROR([$x_arg: requires value; use --help to show usage]) + ;; +@@ -503,6 +504,7 @@ for x_arg in "$@" ; do + | --with-universal=* | --with-tcheck=* \ + | --cache-file=* | --build=* | --host=* | --prefix=* | --exec-prefix=* \ + | --libdir=* | --bindir=* | --includedir=* | --srcdir=* \ ++ | --mandir=* | --infodir=* | --datadir=* | --sysconfdir=* | --localstatedir=* \ + | [[A-Z]*=*] \ + | --with-z=* | --with-bz2=* | --with-lzo=* \ + | --with-pcre=* \ +@@ -581,7 +583,8 @@ if test "$with_extra_action" = "no" ; then + fi + + case "$with_projects" in +- "") if test -r projects; then ++ ""|yes) ++ if test -r projects; then + AC_MSG_NOTICE([using default projects file "projects".]) + with_projects=projects + AC_SUBST(PROJECTS, "\$(top_srcdir)/projects") +@@ -599,6 +602,15 @@ case "$with_projects" in + * ) AC_SUBST(PROJECTS, "\$(top_srcdir)/$with_projects") ;; + esac + ++if test -n "$with_projects"; then ++ case "$with_projects" in ++ /* ) abs_projects=$with_projects ;; ++ yes) abs_projects=$srcdir/projects ;; ++ * ) abs_projects=$srcdir/$with_projects ;; ++ esac ++ test -r "$abs_projects" || \ ++ AC_MSG_ERROR([unable to read requested projects file "$abs_projects".]) ++fi + + #### Always define this + AC_DEFINE(NCBI_CXX_TOOLKIT, 1, [This is the NCBI C++ Toolkit.]) +@@ -6198,7 +6210,7 @@ else + sep=", " + fi + if test -n "$reason" -a "$with_internal" = "yes"; then +- if test -z "$with_projects" -o "$with_projects" = "no"; then ++ if test -z "$with_projects"; then + AC_MSG_ERROR([--with-internal: Cannot build INTERNAL projects: missing $reason]) + else + AC_MSG_WARN([--with-internal: Cannot build all INTERNAL projects: missing $reason]) +@@ -6807,11 +6819,9 @@ if test "$with_flat_makefile" != "no"; then + else + cfm_flags='-remoteptb' + fi +- case "$with_projects" in +- yes ) cfm_flags="$cfm_flags -p projects" ;; +- no | '' ) ;; +- * ) cfm_flags="$cfm_flags -p $with_projects" ;; +- esac ++ if test -n "$with_projects"; then ++ cfm_flags="$cfm_flags -p $with_projects" ++ fi + if test "$with_configure_dialog" = yes; then + cfm_flags="$cfm_flags -cfg" + fi +@@ -6854,7 +6864,8 @@ lib) + esac + + if test -n "$with_projects"; then +- build_proj="To build selected projects: cd $builddir && make all_p" ++ build_proj="To build selected projects (as listed in \"$with_projects\"): ++ cd $builddir && make all_p" + fi + + cat << EOCONF diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-fix-FreeTDS-upstream.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-fix-FreeTDS-upstream.patch new file mode 100644 index 000000000..fede70e51 --- /dev/null +++ b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-fix-FreeTDS-upstream.patch @@ -0,0 +1,19 @@ +--- src/app/agpconvert/Makefile.agpconvert.app.ori 2013-09-13 23:56:22.660032261 +0200 ++++ src/app/agpconvert/Makefile.agpconvert.app 2013-09-13 23:57:31.340032441 +0200 +@@ -6,13 +6,12 @@ + APP = agpconvert + SRC = agpconvert + +-LIB = xalgoseq xobjedit $(OBJREAD_LIBS) taxon1 xalnmgr xobjutil submit \ +- ncbi_xdbapi_ftds $(FTDS_LIB) tables xregexp $(PCRE_LIB) $(OBJMGR_LIBS) +-LIBS = $(FTDS_LIBS) $(CMPRS_LIBS) $(PCRE_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) ++LIB = $(OBJREAD_LIBS) taxon1 xregexp $(PCRE_LIB) $(OBJMGR_LIBS) ++LIBS = $(CMPRS_LIBS) $(PCRE_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) + + CXXFLAGS = $(FAST_CXXFLAGS) + LDFLAGS = $(FAST_LDFLAGS) + +-REQUIRES = objects algo ++REQUIRES = objects + + WATCHERS = xiangcha diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-fix-creaders-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-fix-creaders-linking.patch new file mode 100644 index 000000000..46c2e83fb --- /dev/null +++ b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-fix-creaders-linking.patch @@ -0,0 +1,11 @@ +--- src/objtools/alnmgr/demo/Makefile.alnmrg.app.ori 2013-09-13 23:51:34.340031508 +0200 ++++ src/objtools/alnmgr/demo/Makefile.alnmrg.app 2013-09-13 23:51:36.660031514 +0200 +@@ -5,7 +5,7 @@ + SRC = alnmrg + + LIB = xalnmgr $(OBJREAD_LIBS) ncbi_xloader_blastdb seqdb xobjutil submit blastdb \ +- tables $(OBJMGR_LIBS) ++ tables creaders $(OBJMGR_LIBS) + + LIBS = $(CMPRS_LIBS) $(DL_LIBS) $(NETWORK_LIBS) $(ORIG_LIBS) + diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-fix-svn-URL-upstream.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-fix-svn-URL-upstream.patch new file mode 100644 index 000000000..8bba91f1d --- /dev/null +++ b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-fix-svn-URL-upstream.patch @@ -0,0 +1,10 @@ +--- scripts/common/new_project.sh (revision 408264) ++++ scripts/common/new_project.sh (working copy) +@@ -6,7 +6,7 @@ + svn_revision=`echo '$Revision$' | sed "s%\\$[R]evision: *\\([^$][^$]*\\) \\$.*%\\1%"` + def_builddir="$NCBI/c++/Debug/build" + +-repository_url='https://svn.ncbi.nlm.nih.gov/repos/toolkit' ++repository_url='http://anonsvn.ncbi.nlm.nih.gov/repos/v1' + tmp_app_checkout_dir='tmp_app_sample' + stem='sample/app' diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-9.0.0-as-needed.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-9.0.0-as-needed.patch index f5d6a3d67..821380023 100644 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-9.0.0-as-needed.patch +++ b/sci-biology/ncbi-tools++/files/ncbi-tools++-9.0.0-as-needed.patch @@ -783,7 +783,7 @@ index 96325c4..5a72805 100644 LIB = xnetblastcli SRC = blastclient blastclient_ + -+DLL_LIB = xncbi xutil seqset connect xconnect xnetblast ++DLL_LIB = xncbi xutil seqset xconnect xnetblast diff --git a/src/objects/blastdb/Makefile.blastdb.lib b/src/objects/blastdb/Makefile.blastdb.lib index be2c0d1..2884db2 100644 --- a/src/objects/blastdb/Makefile.blastdb.lib diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-9.0.0-fix-creaders-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-9.0.0-fix-creaders-linking.patch new file mode 100644 index 000000000..b3b57975e --- /dev/null +++ b/sci-biology/ncbi-tools++/files/ncbi-tools++-9.0.0-fix-creaders-linking.patch @@ -0,0 +1,10 @@ +--- src/objtools/alnmgr/demo/Makefile.alnmrg.app (revision 413271) ++++ src/objtools/alnmgr/demo/Makefile.alnmrg.app (working copy) +@@ -4,7 +4,7 @@ + APP = alnmrg + SRC = alnmrg + LIB = xalnmgr xobjread ncbi_xloader_blastdb seqdb xobjutil submit blastdb \ +- tables $(OBJMGR_LIBS) ++ tables creaders $(OBJMGR_LIBS) + + LIBS = $(CMPRS_LIBS) $(DL_LIBS) $(NETWORK_LIBS) $(ORIG_LIBS) diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-9.0.0-fix-svn-URL-upstream.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-9.0.0-fix-svn-URL-upstream.patch new file mode 100644 index 000000000..8bba91f1d --- /dev/null +++ b/sci-biology/ncbi-tools++/files/ncbi-tools++-9.0.0-fix-svn-URL-upstream.patch @@ -0,0 +1,10 @@ +--- scripts/common/new_project.sh (revision 408264) ++++ scripts/common/new_project.sh (working copy) +@@ -6,7 +6,7 @@ + svn_revision=`echo '$Revision$' | sed "s%\\$[R]evision: *\\([^$][^$]*\\) \\$.*%\\1%"` + def_builddir="$NCBI/c++/Debug/build" + +-repository_url='https://svn.ncbi.nlm.nih.gov/repos/toolkit' ++repository_url='http://anonsvn.ncbi.nlm.nih.gov/repos/v1' + tmp_app_checkout_dir='tmp_app_sample' + stem='sample/app' diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-9.0.0-fix-undef-reference-to-GenBankReaders_Register_Id1.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-9.0.0-fix-undef-reference-to-GenBankReaders_Register_Id1.patch new file mode 100644 index 000000000..be496254a --- /dev/null +++ b/sci-biology/ncbi-tools++/files/ncbi-tools++-9.0.0-fix-undef-reference-to-GenBankReaders_Register_Id1.patch @@ -0,0 +1,10 @@ +--- src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib 2013-09-13 21:58:59.420013862 +0200 ++++ src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib 2013-09-13 21:59:56.060014010 +0200 +@@ -10,6 +10,6 @@ + LIB_OR_DLL = both + + # Dependencies for shared library +-DLL_LIB = ncbi_xreader$(DLL) ++DLL_LIB = ncbi_xreader$(DLL) $(GENBANK_LDEP) + + WATCHERS = vasilche diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-9.0.0-remove-LZO-definition-upstream.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-9.0.0-remove-LZO-definition-upstream.patch new file mode 100644 index 000000000..95d3f7461 --- /dev/null +++ b/sci-biology/ncbi-tools++/files/ncbi-tools++-9.0.0-remove-LZO-definition-upstream.patch @@ -0,0 +1,10 @@ +--- src/connect/ncbi_gnutls.c 2013-09-14 09:49:41.260005353 +0200 ++++ src/connect/ncbi_gnutls.c 2013-09-14 09:49:46.950005368 +0200 +@@ -112,7 +112,6 @@ + 0 + }; + static const int kGnuTlsCompPrio[] = { +- GNUTLS_COMP_LZO, + GNUTLS_COMP_ZLIB, + GNUTLS_COMP_NULL, + 0 diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild new file mode 100644 index 000000000..f217ab346 --- /dev/null +++ b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild @@ -0,0 +1,311 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools++/ncbi-tools++-0.2010.06.15-r1.ebuild,v 1.3 2012/11/05 11:22:49 jlec Exp $ + +EAPI=5 + +inherit eutils flag-o-matic multilib toolchain-funcs + +MY_TAG="Jun_15_2010" +MY_Y="${MY_TAG/*_/}" +MY_PV="12_0_0" +MY_P="ncbi_cxx--${MY_PV}" +#ftp://ftp.ncbi.nlm.nih.gov/toolbox/ncbi_tools++/ARCHIVE/9_0_0/ncbi_cxx--9_0_0.tar.gz + +DESCRIPTION="NCBI C++ Toolkit, including NCBI BLAST+" +HOMEPAGE="http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=toolkit" +SRC_URI=" + ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/ARCHIVE/${MY_PV}/ncbi_cxx--${MY_PV}.tar.gz" +# http://dev.gentoo.org/~jlec/distfiles/${PN}-${PV#0.}-asneeded.patch.xz" + +LICENSE="public-domain" +SLOT="0" +IUSE=" + debug static-libs static threads pch + test wxwidgets odbc + berkdb boost bzip2 cppunit curl expat fastcgi fltk freetype ftds gif + glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python + sablotron sqlite sqlite3 ssl tiff xerces xalan xml xpm xslt X" +#KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +KEYWORDS="" + +# sys-libs/db should be compiled with USE=cxx +DEPEND=" + berkdb? ( sys-libs/db:4.3[cxx] ) + ftds? ( dev-db/freetds ) + boost? ( dev-libs/boost ) + curl? ( net-misc/curl ) + sqlite? ( dev-db/sqlite ) + sqlite3? ( dev-db/sqlite:3 ) + mysql? ( virtual/mysql ) + gnutls? ( net-libs/gnutls[lzo] ) + ssl? ( dev-libs/openssl ) + fltk? ( x11-libs/fltk ) + opengl? ( virtual/opengl ) + mesa? ( media-libs/mesa + media-libs/glew + ) + glut? ( media-libs/freeglut ) + freetype? ( media-libs/freetype ) + fastcgi? ( www-apache/mod_fastcgi ) + python? ( dev-lang/python ) + cppunit? ( dev-util/cppunit ) + icu? ( dev-libs/icu ) + expat? ( dev-libs/expat ) + sablotron? ( app-text/sablotron ) + xml? ( dev-libs/libxml2 ) + xslt? ( dev-libs/libxslt ) + xerces? ( dev-libs/xerces-c ) + xalan? ( dev-libs/xalan-c ) + muparser? ( dev-cpp/muParser ) + hdf5? ( sci-libs/hdf5 ) + gif? ( media-libs/giflib ) + jpeg? ( virtual/jpeg ) + png? ( media-libs/libpng ) + tiff? ( media-libs/tiff ) + xpm? ( x11-libs/libXpm ) + dev-libs/lzo + app-arch/bzip2 + dev-libs/libpcre" +# USE flags which should be added somehow: wxWindows wxWidgets SP ORBacus ODBC OEChem sge + + +# seems muParser is required, also glew is required. configure exitss otherwise + +RDEPEND="${DEPEND}" + +S="${WORKDIR}/${MY_P}" + +src_prepare() { +# filter-ldflags -Wl,--as-needed +# append-ldflags -Wl,--no-undefined +# sed -i -e 's/-print-file-name=libstdc++.a//' \ +# -e '/sed/ s/\([gO]\[0-9\]\)\*/\1\\+/' \ +# src/build-system/configure || die +# epatch \ +# "${FILESDIR}"/${PN}-${PV#0.}-fix-order-of-libs.patch \ +# "${FILESDIR}"/curl-types.patch \ +# "${FILESDIR}"/malloc_initialize_upstream_fix.patch \ +# "${FILESDIR}"/respect_CXXFLAGS_configure.ac.patch \ +# "${FILESDIR}"/respect_CXXFLAGS_configure.patch \ +# "${FILESDIR}"/report_project_settings_configure.ac.patch \ +# "${FILESDIR}"/report_project_settings_configure.patch \ +# "${FILESDIR}"/make_install.patch + +# "${FILESDIR}"/${PN}-${PV#0.}-disable_test_compress.patch + +# "${FILESDIR}"/${PN}-${PV#0.}-gcc46.patch \ +# "${FILESDIR}"/${PN}-${PV#0.}-gcc47.patch \ +# "${WORKDIR}"/${PN}-${PV#0.}-asneeded.patch \ +# "${FILESDIR}"/${PN}-${PV#0.}-libpng15.patch \ +# "${FILESDIR}"/${PN}-${PV#0.}-glibc-214.patch + +# use prefix && append-ldflags -Wl,-rpath,"${EPREFIX}/usr/$(get_libdir)/${PN}" + + +# The conf-opts.patch and as-needed.patch need to be adjusted for 12.0.0 line numbers + local PATCHES=( + #"${FILESDIR}"/${P}-conf-opts.patch + #"${FILESDIR}"/${P}-as-needed.patch + "${FILESDIR}"/${P}-fix-creaders-linking.patch + "${FILESDIR}"/${P}-fix-svn-URL-upstream.patch + "${FILESDIR}"/${P}-fix-FreeTDS-upstream.patch + ) + epatch ${PATCHES[@]} + + tc-export CXX CC + +# cd src/build-system || die +# eaclocal -I. +# eautoconf +} + +src_configure() { + local myconf=() + #--without-optimization turn off optimization flags in non-debug mode + #--with-profiling build profiled versions of libs and apps + #--with-tcheck(=DIR) build for Intel Thread Checker (in DIR) + #--with-plugin-auto-load always enable the plugin manager by default + #--with-bundles build bundles in addition to dylibs on Mac OS X + #--with-bin-release build executables suitable for public release + # no dll and such + #--with-64 compile to 64-bit code + #--with-universal build universal binaries on Mac OS X + #--with-universal=CPUs build universal binaries targeting the given CPUs + #--without-exe do not build executables + #--with-relative-runpath=P specify an executable-relative DLL search path + #--with-hard-runpath hard-code runtime path, ignoring LD_LIBRARY_PATH + #--with-limited-linker don't attempt to build especially large projects + #--with-extra-action= script to call after the configuration is complete + #--with-autodep automatic generation of dependencies (GNU make) + #--with-fake-root=DIR appear to have been built under DIR + #--with-build-root-sfx=X add a user-specified suffix to the build dir name + #--without-execopy do not copy built executables to the BIN area + #--with-lib-rebuilds ensure that apps use up-to-date libraries + #--with-lib-rebuilds=ask ask whether to update each app's libraries + #--without-deactivation keep old copies of libraries that no longer build + #--without-makefile-auto-update do not auto-update generated makefiles + #--with-projects=FILE build projects listed in FILE by default + #--without-flat-makefile do not generate an all-encompassing flat makefile + #--with-configure-dialog allow interactive flat makefile project selection + #--with-saved-settings=F load configuration settings from the file F + #--with-check-tools=... use the specified tools for testing + #--with-ncbi-public ensure compatibility for all in-house platforms + #--with-sybase-local=DIR use local SYBASE install (DIR is optional) + #--with-sybase-new use newer SYBASE install (12.5 rather than 12.0) + #--without-ftds-renamed do not rename Sybase DBLIB symbols in built-in FTDS + #--without-sp do not use SP libraries + #--without-orbacus do not use ORBacus CORBA libraries + #--with-orbacus=DIR use ORBacus installation in DIR + #--with-jni(=JDK-DIR) build Java bindings (against the JDK in JDK-DIR) + #--with-sablot=DIR use Sablotron installation in DIR + #--without-sablot, do not use Sablotron + #--with-oechem=DIR use OpenEye OEChem installation in DIR + #--without-oechem do not use OEChem + #--with-sge=DIR use Sun Grid Engine installation in DIR + #--without-sge do not use Sun Grid Engine + #--with-magic=DIR use libmagic installation in DIR + #--without-magic do not use libmagic + #--without-local-lbsm turn off support for IPC with locally running LBSMD + #--without-ncbi-crypt use a dummy stubbed-out version of ncbi_crypt + #--without-connext do not build non-public CONNECT library extensions + #--without-serial do not build the serialization library and tools + #--without-objects do not generate/build serializeable objects from ASNs + #--without-dbapi do not build database connectivity libraries + #--without-app do not build standalone applications like ID1_FETCH + #--without-gui do not build most graphical projects + #--without-algo do not build CPU-intensive algorithms + #--without-internal do not build internal projects + #--with-gbench ensure that Genome Workbench can be built + #--without-gbench do not build Genome Workbench + myconf+=( + --with-dll + --with-lfs + --with-build-root="${S}"_build + --without-suffix + --without-hostspec + --without-version + --with-bincopy + --without-strip + --without-ccache + --without-distcc +# --with-ncbi-c + --without-ctools +# --with-sss +# --with-sssutils +# --with-sssdb +# --with-included-sss + --with-z="${EPREFIX}/usr" + --with-bz2="${EPREFIX}/usr" + --with-muparser="${EPREFIX}/usr" + --without-sybase + --with-autodep +# --with-3psw=std:netopt favor standard (system) builds of the above pkgs + $(use_with debug) + $(use_with debug max-debug) + $(use_with debug symbols) + $(use_with static-libs static) + $(use_with static static-exe) + $(use_with threads mt) + $(use_with prefix runpath "${EPREFIX}/usr/$(get_libdir)/ncbi_cxx") + $(use_with test check) + $(use_with pch) + $(use_with lzo lzo "${EPREFIX}/usr") + $(use_with pcre pcre "${EPREFIX}/usr") + $(use_with gnutls gnutls "${EPREFIX}/usr") + $(use_with ssl openssl "${EPREFIX}/usr") + $(use_with ftds ftds "${EPREFIX}/usr") + $(use_with mysql mysql "${EPREFIX}/usr") + $(use_with fltk fltk "${EPREFIX}/usr") + $(use_with opengl opengl "${EPREFIX}/usr") + $(use_with mesa mesa "${EPREFIX}/usr") + $(use_with opengl glut "${EPREFIX}/usr") + $(use_with opengl glew "${EPREFIX}/usr") + $(use_with opengl glew-mx) + $(use_with wxwidgets wxwidgets "${EPREFIX}/usr") + $(use_with wxwidgets wxwidgets-ucs) + $(use_with freetype freetype "${EPREFIX}/usr") + $(use_with fastcgi fastcgi "${EPREFIX}/usr") + $(use_with berkdb bdb "${EPREFIX}/usr") + $(use_with odbc odbc "${EPREFIX}/usr") + $(use_with python python "${EPREFIX}/usr") + $(use_with boost boost "${EPREFIX}/usr") + $(use_with sqlite sqlite3 "${EPREFIX}/usr") + $(use_with icu icu "${EPREFIX}/usr") + $(use_with expat expat "${EPREFIX}/usr") + $(use_with xml libxml "${EPREFIX}/usr") + $(use_with xml libxslt "${EPREFIX}/usr") + $(use_with xerces xerces "${EPREFIX}/usr") + $(use_with hdf5 hdf5 "${EPREFIX}/usr") + $(use_with xalan xalan "${EPREFIX}/usr") +# $(use_with gif gif "${EPREFIX}/usr") + $(use_with jpeg jpeg "${EPREFIX}/usr") + $(use_with tiff tiff "${EPREFIX}/usr") + $(use_with png png "${EPREFIX}/usr") + $(use_with xpm xpm "${EPREFIX}/usr") + $(use_with curl curl "${EPREFIX}/usr") +# $(use_with X x "${EPREFIX}/usr") + $(use_with X x) + ) + + # http://www.ncbi.nlm.nih.gov/books/NBK7167/ + use test || myconf+=( --with-projects="${FILESDIR}"/disable-testsuite-compilation.txt ) + + # TODO + # copy optimization -O options from CXXFLAGS to DEF_FAST_FLAGS and pass that also to configure + # otherwise your -O2 will be dropped in some subdirectories and repalced by e.g. -O9 + + einfo "bash ./src/build-system/configure --srcdir="${S}" --prefix="${EPREFIX}/usr" --libdir=/usr/lib64 ${myconf[@]}" + +# bash \ +# ./src/build-system/configure \ +# cd src/build-system || die + econf \ + --srcdir="${S}" \ + --prefix="${EPREFIX}/usr" \ + --libdir=/usr/lib64 \ + ${myconf[@]} || die +#--without-debug \ +# --with-bin-release \ +# --with-bincopy \ +# --without-static \ +# --with-dll \ +# --with-mt \ +# --with-lfs \ +# --prefix="${ED}"/usr \ +# --libdir="${ED}"/usr/$(get_libdir)/"${PN}" \ +# ${myconf} LDFLAGS="-Wl,--no-as-needed" \ +# || die +# econf ${myconf[@]} +} + +src_compile() { + # all_r would ignore the --with-projects contents and build more + # emake all_r -C GCC*-Release*/build || die + # all_p with compile only selected/required components +# cd "${S}"_build &&\ + emake all_p -C "${S}"_build/build +# emake all_p -C GCC*-Release*/build || die "gcc-4.5.3 crashes at src/objects/valerr/ValidError.cpp:226:1: internal compiler error: Segmentation fault, right?" +} + +src_install() { + rm -rvf "${S}"_build/lib/ncbi || die + emake install prefix="${ED}/usr" libdir="${ED}/usr/$(get_libdir)/${PN}" + +# dobin "${S}"_build/bin/* +# dolib.so "${S}"_build/lib/*so* +# dolib.a "${S}"_build/lib/*.a +# doheader "${S}"_build/inc/* + + # File collisions with sci-biology/ncbi-tools + rm -f "${ED}"/usr/bin/{asn2asn,rpsblast,test_regexp} + mv "${ED}"/usr/bin/seedtop "${ED}"/usr/bin/seedtop2 + + echo "LDPATH=${EPREFIX}/usr/$(get_libdir)/${PN}" > ${S}/99${PN} + doenvd "${S}/99${PN}" +} + +pkg_postinst() { + einfo 'Please run "source /etc/profile" before using this package in the current shell.' + einfo 'Documentation is at http://www.ncbi.nlm.nih.gov/books/NBK7167/' +} diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild index 8c190e48b..4e1ee2e3e 100644 --- a/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild +++ b/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild @@ -24,7 +24,7 @@ IUSE=" debug static-libs static threads pch test wxwidgets odbc berkdb boost bzip2 cppunit curl expat fastcgi fltk freetype ftds gif - glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python + glut gnutls hdf5 icu lzo jpeg mesa mysql muparser opengl pcre png python sablotron sqlite sqlite3 ssl tiff xerces xalan xml xpm xslt X" #KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" KEYWORDS="" @@ -42,7 +42,9 @@ DEPEND=" ssl? ( dev-libs/openssl ) fltk? ( x11-libs/fltk ) opengl? ( virtual/opengl ) - mesa? ( media-libs/mesa ) + mesa? ( media-libs/mesa + media-libs/glew + ) glut? ( media-libs/freeglut ) freetype? ( media-libs/freetype ) fastcgi? ( www-apache/mod_fastcgi ) @@ -67,6 +69,9 @@ DEPEND=" dev-libs/libpcre" # USE flags which should be added somehow: wxWindows wxWidgets SP ORBacus ODBC OEChem sge + +# seems muParser is required, also glew is required. configure exitss otherwise + RDEPEND="${DEPEND}" S="${WORKDIR}/${MY_P}" @@ -100,6 +105,10 @@ src_prepare() { local PATCHES=( "${FILESDIR}"/${P}-conf-opts.patch "${FILESDIR}"/${P}-as-needed.patch + "${FILESDIR}"/${P}-fix-creaders-linking.patch + "${FILESDIR}"/${P}-fix-svn-URL-upstream.patch + "${FILESDIR}"/${P}-fix-undef-reference-to-GenBankReaders_Register_Id1.patch + "${FILESDIR}"/${P}-remove-LZO-definition-upstream.patch ) epatch ${PATCHES[@]} @@ -190,7 +199,17 @@ src_configure() { --with-muparser="${EPREFIX}/usr" --without-sybase --with-autodep + +# due to \*-fix-undef-reference-to-GenBankReaders_Register_Id1.patch +# ./configure ... --with-flat-makefile +# cd .../build +# make -f Makefile.flat +# + --with-flat-makefile # --with-3psw=std:netopt favor standard (system) builds of the above pkgs + + +# TODO: should improve the ssl/openssl/gmutls logic like is in net-misc/vpnc $(use_with debug) $(use_with debug max-debug) $(use_with debug symbols) @@ -254,6 +273,7 @@ src_configure() { --srcdir="${S}" \ --prefix="${EPREFIX}/usr" \ --libdir=/usr/lib64 \ + ${myconf} LDFLAGS="-Wl,-rpath-link,${S}_build/lib -Wl,--no-as-needed" \ ${myconf[@]} || die #--without-debug \ # --with-bin-release \ @@ -274,7 +294,14 @@ src_compile() { # emake all_r -C GCC*-Release*/build || die # all_p with compile only selected/required components # cd "${S}"_build &&\ - emake all_p -C "${S}"_build/build + + # disabling this because we need to take the flat Makefile route + # emake all_p -C "${S}"_build/build + + # take the flat Makefile route + emake -f Makefile.flat -C "${S}"_build/build + + # emake all_p -C GCC*-Release*/build || die "gcc-4.5.3 crashes at src/objects/valerr/ValidError.cpp:226:1: internal compiler error: Segmentation fault, right?" } diff --git a/sci-biology/psychopy/Manifest b/sci-biology/psychopy/Manifest index ced74875f..c306e0274 100644 --- a/sci-biology/psychopy/Manifest +++ b/sci-biology/psychopy/Manifest @@ -1 +1,3 @@ DIST PsychoPy-1.75.01.zip 3512277 SHA256 c86c617bcd9a215f1fe3d1420563a9bc1c8c6707b477481f885437a68a56d211 SHA512 3a57dcff426d9bbeeababd7699d2fe99fc36025d45b4f52abb8ae4544454314dacb00b52b16f94168c86a255f9ac469fad297590b6e466931d5de12e7520f684 WHIRLPOOL a0f258c293937efbd6cbbc325663a1de93961de349e0113562c20d54a957c686590256d7c7a2e0ebea7a497090569ba0e2b777165e9cfe908af82a90991bb939 +DIST PsychoPy-1.77.02.zip 6313389 SHA256 37313ca13e6062146979dbc79dde79306377a08958b47ea1477957373914f1a1 SHA512 11c305d69763c7eca236c53ccef56780637ad2d53801764dada52565a4e07949422722cf7d8691b615d515c6eeee1c29e2ec44fc312fb299fc2bea17b5a15b44 WHIRLPOOL 568cd06a9ad511ceeb0f0293296d4a98549855960be82e25de57b576bbf6614f37253358dcc44909570a73b298df0651920ab2378e0145eb8bd69186922a745c +DIST PsychoPy-1.78.00.zip 6376071 SHA256 ac74ea948f400a4a962a6abde7e7360fce5738a0f44aec4a0ff636d00976cc25 SHA512 ec2cd1c2094488d2b02c94070c7bc3d50e12e597c0107d2f64d49522e43a12c81b060b7a8abc15e83d50736776ee9d3d7190b78d39c58ee8f8be88b32330c5e2 WHIRLPOOL 9395a55bb820d2d326f4d95e12fb7513fbc4038eea25d0fd182e7e909e86d153374ac14293e89162761f0655b14bb8ca2abfa7fdf3df3e1951bec11e469db1f7 diff --git a/sci-biology/psychopy/psychopy-1.75.01.ebuild b/sci-biology/psychopy/psychopy-1.75.01.ebuild index f4469cee4..db7ffd360 100644 --- a/sci-biology/psychopy/psychopy-1.75.01.ebuild +++ b/sci-biology/psychopy/psychopy-1.75.01.ebuild @@ -28,13 +28,15 @@ RDEPEND=" dev-python/wxpython[${PYTHON_USEDEP}] dev-python/setuptools[${PYTHON_USEDEP}] dev-python/lxml[${PYTHON_USEDEP}] - app-admin/eselect dev-python/pyglet[${PYTHON_USEDEP}] - dev-python/pygame[${PYTHON_USEDEP}]" + dev-python/pygame[${PYTHON_USEDEP}] + " -DEPEND="app-arch/unzip +DEPEND="app-admin/eselect + app-arch/unzip dev-python/setuptools[${PYTHON_USEDEP}] - test? ( ${RDEPEND} )" + test? ( ${RDEPEND} ) + " RESTRICT="test" # interactive, opens lots of windows @@ -43,7 +45,7 @@ S="${WORKDIR}/${MY_P}" python_install_all() { distutils-r1_python_install_all doicon psychopy/monitors/psychopy.ico - make_desktop_entry psychopyapp.py PsychoPy psychopy "Science;Biology" + make_desktop_entry psychopyapp.py PsychoPy psychopy } pkg_postinst() { diff --git a/sci-biology/psychopy/psychopy-1.77.02.ebuild b/sci-biology/psychopy/psychopy-1.77.02.ebuild new file mode 100644 index 000000000..db7ffd360 --- /dev/null +++ b/sci-biology/psychopy/psychopy-1.77.02.ebuild @@ -0,0 +1,56 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI="5" + +PYTHON_COMPAT=( python2_7 ) + +inherit distutils-r1 gnome2-utils eutils + +MY_P="PsychoPy-${PV}" + +DESCRIPTION="Python experimental psychology toolkit" +HOMEPAGE="http://www.psychopy.org/" +SRC_URI="http://psychopy.googlecode.com/files/${MY_P}.zip" + +LICENSE="GPL-3+" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="test" + +RDEPEND=" + dev-python/numpy[lapack,${PYTHON_USEDEP}] + sci-libs/scipy[${PYTHON_USEDEP}] + dev-python/matplotlib[${PYTHON_USEDEP}] + dev-python/pyopengl[${PYTHON_USEDEP}] + virtual/python-imaging[${PYTHON_USEDEP}] + dev-python/wxpython[${PYTHON_USEDEP}] + dev-python/setuptools[${PYTHON_USEDEP}] + dev-python/lxml[${PYTHON_USEDEP}] + dev-python/pyglet[${PYTHON_USEDEP}] + dev-python/pygame[${PYTHON_USEDEP}] + " + +DEPEND="app-admin/eselect + app-arch/unzip + dev-python/setuptools[${PYTHON_USEDEP}] + test? ( ${RDEPEND} ) + " + +RESTRICT="test" # interactive, opens lots of windows + +S="${WORKDIR}/${MY_P}" + +python_install_all() { + distutils-r1_python_install_all + doicon psychopy/monitors/psychopy.ico + make_desktop_entry psychopyapp.py PsychoPy psychopy +} + +pkg_postinst() { + gnome2_icon_cache_update +} +pkg_postrm() { + gnome2_icon_cache_update +} diff --git a/sci-biology/psychopy/psychopy-1.78.00.ebuild b/sci-biology/psychopy/psychopy-1.78.00.ebuild new file mode 100644 index 000000000..584a533a9 --- /dev/null +++ b/sci-biology/psychopy/psychopy-1.78.00.ebuild @@ -0,0 +1,56 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI="5" + +PYTHON_COMPAT=( python2_7 ) + +inherit distutils-r1 gnome2-utils eutils + +MY_P="PsychoPy-${PV}" + +DESCRIPTION="Python experimental psychology toolkit" +HOMEPAGE="http://www.psychopy.org/" +SRC_URI="http://sourceforge.net/projects/psychpy/files/PsychoPy/${MY_P}.zip" + +LICENSE="GPL-3+" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="test" + +RDEPEND=" + dev-python/numpy[lapack,${PYTHON_USEDEP}] + sci-libs/scipy[${PYTHON_USEDEP}] + dev-python/matplotlib[${PYTHON_USEDEP}] + dev-python/pyopengl[${PYTHON_USEDEP}] + virtual/python-imaging[${PYTHON_USEDEP}] + dev-python/wxpython[${PYTHON_USEDEP}] + dev-python/setuptools[${PYTHON_USEDEP}] + dev-python/lxml[${PYTHON_USEDEP}] + dev-python/pyglet[${PYTHON_USEDEP}] + dev-python/pygame[${PYTHON_USEDEP}] + " + +DEPEND="app-admin/eselect + app-arch/unzip + dev-python/setuptools[${PYTHON_USEDEP}] + test? ( ${RDEPEND} ) + " + +RESTRICT="test" # interactive, opens lots of windows + +S="${WORKDIR}/${MY_P}" + +python_install_all() { + distutils-r1_python_install_all + doicon psychopy/monitors/psychopy.ico + make_desktop_entry psychopyapp.py PsychoPy psychopy +} + +pkg_postinst() { + gnome2_icon_cache_update +} +pkg_postrm() { + gnome2_icon_cache_update +} diff --git a/sci-biology/psychopy/psychopy-9999.ebuild b/sci-biology/psychopy/psychopy-9999.ebuild index cc0241660..512d34757 100644 --- a/sci-biology/psychopy/psychopy-9999.ebuild +++ b/sci-biology/psychopy/psychopy-9999.ebuild @@ -14,12 +14,13 @@ EGIT_REPO_URI="https://github.com/psychopy/psychopy.git" LICENSE="GPL-3+" SLOT="0" -KEYWORDS="~amd64 ~x86" +KEYWORDS="" -DEPEND="dev-python/setuptools[${PYTHON_USEDEP}]" +DEPEND="dev-python/setuptools[${PYTHON_USEDEP}] + app-admin/eselect + " RDEPEND="${DEPEND} - app-admin/eselect virtual/python-imaging[${PYTHON_USEDEP}] dev-python/lxml[${PYTHON_USEDEP}] dev-python/matplotlib[${PYTHON_USEDEP}] @@ -28,12 +29,13 @@ RDEPEND="${DEPEND} dev-python/pyglet[${PYTHON_USEDEP}] dev-python/pyopengl[${PYTHON_USEDEP}] dev-python/wxpython[${PYTHON_USEDEP}] - sci-libs/scipy[${PYTHON_USEDEP}]" + sci-libs/scipy[${PYTHON_USEDEP}] + " python_install_all() { distutils-r1_python_install_all newicon -s scalable psychopy/monitors/psychopy-icon.svg psychopy.svg - make_desktop_entry psychopyApp.py PsychoPy psychopy "Science;Biology" + make_desktop_entry psychopyApp.py PsychoPy psychopy } pkg_postinst() { diff --git a/sci-chemistry/freeon/ChangeLog b/sci-chemistry/freeon/ChangeLog index 0067c486a..26eff87ac 100644 --- a/sci-chemistry/freeon/ChangeLog +++ b/sci-chemistry/freeon/ChangeLog @@ -2,6 +2,11 @@ # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*freeon-20130912 (14 Sep 2013) + + 14 Sep 2013; Nicolas Bock <nicolasbock@gmail.com> +freeon-20130912.ebuild: + sci-chemistry/freeon-20130912: Added new version. + 17 Jun 2013; Honza Macháček <Hloupy.Honza@centrum.cz> freeon-2012.05.03.ebuild, freeon-9999.ebuild, +files/freeon-2012.05.03-no_internal_hdf5.patch, diff --git a/sci-chemistry/freeon/Manifest b/sci-chemistry/freeon/Manifest index 8cf18b96f..bf6c69ce7 100644 --- a/sci-chemistry/freeon/Manifest +++ b/sci-chemistry/freeon/Manifest @@ -1 +1,2 @@ +DIST freeon-20130912.tar.bz2 6057644 SHA256 1b0501721c40a1f503f358aec7bde72120ebe86820752666d6cf69d0256f7213 SHA512 3a28c6e3db34d77c84fdaddd98b4a2543bad3ed5167008073aa9ced9f1693731b3839add38929233a128a057933dac478a4363556e948ca8ab15bbeb0145abef WHIRLPOOL f7a5709ce5bc795b8a375f35075ed3e3aa3662517ed18e1f664ed1272ceef294d72ff35f8a08c3539c7d20c74411ff7761d46fc142565bb8a79a19b15b2d6a33 DIST freeon-beta-2012-05-03.tar.bz2 15259173 SHA256 48a4657fd99aed25f90fd68e50e515b691b5c09d2b7c8305ddfb35bd1d2ba17c SHA512 30b5d5406df3eb0bd44166e78e16df2013e40b024f0350caefaf08d5c157308896d6ade66a7184f7c8e93c5db6c39c7f3a73340d48b06c5acb6272de525ce18a WHIRLPOOL 55aa72b03b414be40987fab416bf17c3cc4f9b2783501830ffc8c27b987c73fa471878024f04139266c69d9c76f16476737b2241f294ec9b32f828d831b0b7ac diff --git a/sci-chemistry/freeon/freeon-20130912.ebuild b/sci-chemistry/freeon/freeon-20130912.ebuild new file mode 100644 index 000000000..956c7662b --- /dev/null +++ b/sci-chemistry/freeon/freeon-20130912.ebuild @@ -0,0 +1,38 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +AUTOTOOLS_AUTORECONF=1 + +FORTRAN_STANDARD=90 + +inherit autotools-utils fortran-2 + +DESCRIPTION="an experimental suite of programs for linear scaling quantum chemistry." +HOMEPAGE="http://www.freeon.org" +SRC_URI="http://download.savannah.gnu.org/releases/${PN}/${PN}-${PV}.tar.bz2" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="static-libs" + +RDEPEND=" + sys-libs/zlib + sci-libs/hdf5 + virtual/blas + virtual/lapack" +DEPEND="${DEPEND} + virtual/pkgconfig" + +S="${WORKDIR}/${PN}-${PV}" + +src_configure() { + local myeconfargs=( + --with-lapacklibs="$($(tc-getPKG_CONFIG) --libs lapack)" + ) + #TODO mv BasisSets from /usr to /usr/share/freeon/ + autotools-utils_src_configure +} diff --git a/sci-chemistry/namd/ChangeLog b/sci-chemistry/namd/ChangeLog new file mode 100644 index 000000000..495468268 --- /dev/null +++ b/sci-chemistry/namd/ChangeLog @@ -0,0 +1,11 @@ +# ChangeLog for sci-chemistry/namd +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*namd-2.9 (14 Sep 2013) + + 14 Sep 2013; Nicolas Bock <nicolasbock@gmail.com> + +files/namd-2.7-iml-dec.patch, +files/namd-2.9-gentoo.patch, +metadata.xml, + +namd-2.9.ebuild: + sci-chemistry/namd-2.9: Version bump; ported patches from namd-2.7_beta2-r1 + and bumped EAPI to 5. diff --git a/sci-chemistry/namd/Manifest b/sci-chemistry/namd/Manifest new file mode 100644 index 000000000..738c167a3 --- /dev/null +++ b/sci-chemistry/namd/Manifest @@ -0,0 +1 @@ +DIST NAMD_2.9_Source.tar.gz 8814042 SHA256 9ba6a1f87d4600a62847728d7c223295be214f9a72b5bb62552f74d644108424 SHA512 0644814a2799b560d9dcf807ba0047325bc9f0a26e3831b0465d95180784f038d69595e036daac85d59cd919c92d11a0343031975d99deb1fa3052c8a649bdd6 WHIRLPOOL 5494ccb2ee2f2792fe52ad7dcfe6da9d11453f0a9b0859d30698dea56b00d92fae73465967f82bd708abee5cd4ff50b0a6ffde86451e859e2f515af203e09286 diff --git a/sci-chemistry/namd/files/namd-2.7-iml-dec.patch b/sci-chemistry/namd/files/namd-2.7-iml-dec.patch new file mode 100644 index 000000000..e5ee3bd6c --- /dev/null +++ b/sci-chemistry/namd/files/namd-2.7-iml-dec.patch @@ -0,0 +1,24 @@ +diff --git a/src/flipbinpdb.c b/src/flipbinpdb.c +index 94b71ba..01a2529 100644 +--- a/src/flipbinpdb.c ++++ b/src/flipbinpdb.c +@@ -9,6 +9,7 @@ + #include <sys/mman.h> + #include <fcntl.h> + #include <stdio.h> ++#include <stdlib.h> + + #ifndef MAP_FILE + #define MAP_FILE 0 +diff --git a/src/flipdcd.c b/src/flipdcd.c +index 8ec85b7..1c23433 100644 +--- a/src/flipdcd.c ++++ b/src/flipdcd.c +@@ -13,6 +13,7 @@ + #include <sys/mman.h> + #include <fcntl.h> + #include <stdio.h> ++#include <stdlib.h> + + #ifndef MAP_FILE + #define MAP_FILE 0 diff --git a/sci-chemistry/namd/files/namd-2.9-gentoo.patch b/sci-chemistry/namd/files/namd-2.9-gentoo.patch new file mode 100644 index 000000000..583cc5264 --- /dev/null +++ b/sci-chemistry/namd/files/namd-2.9-gentoo.patch @@ -0,0 +1,151 @@ +diff -Naur NAMD_2.9_Source.original/Make.charm NAMD_2.9_Source/Make.charm +--- NAMD_2.9_Source.original/Make.charm 2012-02-29 19:12:11.000000000 -0700 ++++ NAMD_2.9_Source/Make.charm 2013-09-13 21:23:26.000000000 -0600 +@@ -2,5 +2,5 @@ + # The config script will override this setting if there is a directory + # called charm-6.4.0 or charm in the NAMD base directory. + +-CHARMBASE = /Projects/namd2/charm-6.4.0 ++CHARMBASE = /usr/include/charm-6.4.0 + +diff -Naur NAMD_2.9_Source.original/Makefile NAMD_2.9_Source/Makefile +--- NAMD_2.9_Source.original/Makefile 2012-04-27 09:53:24.000000000 -0600 ++++ NAMD_2.9_Source/Makefile 2013-09-13 21:30:15.000000000 -0600 +@@ -344,10 +344,10 @@ + $(DSTDIR)/stringhash.o + + # definitions for Charm routines +-CHARMC = $(CHARM)/bin/charmc +-CHARMXI = $(CHARM)/bin/charmc +-CHARMINC = $(CHARM)/include $(COPTD)CMK_OPTIMIZE=1 +-CHARMLIB = $(CHARM)/lib ++CHARMC = /usr/bin/charmc ++CHARMXI = /usr/bin/charmc ++CHARMINC = /usr/include/gentoo-charm $(COPTD)CMK_OPTIMIZE=1 ++CHARMLIB = /usr/gentoo-libdir + CHARM_MODULES = -module NeighborLB -module HybridLB -module RefineLB -module GreedyLB + #CHARM_MODULES = -module msa -module NeighborLB -module HybridLB -module RefineLB -module GreedyLB + #MSA = -DCHARM_HAS_MSA +@@ -370,7 +370,7 @@ + + # Add new executables here. + +-BINARIES = namd2 psfgen sortreplicas charmrun flipdcd flipbinpdb ++BINARIES = namd2 psfgen sortreplicas flipdcd flipbinpdb + + # This should be rebuilt at every compile, but not on Win32. + BUILDINFO = $(DSTDIR)/buildinfo +@@ -386,7 +386,7 @@ + + namd2: $(MKINCDIR) $(MKDSTDIR) $(OBJS) $(LIBS) + $(MAKEBUILDINFO) +- $(CHARMC) -verbose -ld++-option \ ++ $(CHARMC) $(LDFLAGS) -verbose -ld++-option \ + "$(COPTI)$(CHARMINC) $(COPTI)$(INCDIR) $(COPTI)$(SRCDIR) $(CXXOPTS)" \ + "$(CHARM_MODULES)" -language charm++ \ + $(BUILDINFO).o \ +@@ -402,16 +402,9 @@ + $(EXTRALINKLIBS) \ + -lm -o namd2 + +-charmrun: $(CHARM)/bin/charmrun # XXX +- $(COPY) $(CHARM)/bin/charmrun $@ +- + $(LIBCUDARTSO): + $(COPY) $(CUDASODIR)/$(LIBCUDARTSO) $@; + +-WINDOWSBINARIES = namd2.exe psfgen.exe sortreplicas.exe +-# WINDOWSBINARIES = namd2.exe psfgen.exe charmd.exe charmd_faceless.exe charmrun.exe +-windowsbinaries: $(WINDOWSBINARIES) +- + namd2.exe: $(MKINCDIR) $(MKDSTDIR) $(OBJS) $(LIBS) $(TCLDLL) + $(MAKEBUILDINFO) + $(CHARMC) -verbose \ +@@ -434,11 +427,8 @@ + charmd_faceless.exe: + $(COPY) $(CHARM)/bin/charmd_faceless.exe charmd_faceless.exe + +-charmrun.exe: +- $(COPY) $(CHARM)/bin/charmrun.exe charmrun.exe +- + psfgen: $(MKDSTDIR) $(SBOBJS) $(PLUGINOBJS) +- $(CC) $(SBCFLAGS) -o psfgen $(SBOBJS) $(PLUGINOBJS) $(TCLLIB) $(TCLAPPLIB) -lm ++ $(CC) $(SBCFLAGS) $(LDFLAGS) -o psfgen $(SBOBJS) $(PLUGINOBJS) $(TCLLIB) $(TCLAPPLIB) -lm + + psfgen.exe: $(MKDSTDIR) $(SBOBJS) $(PLUGINOBJS) $(TCLDLL) + $(CC) $(SBCFLAGS) -o psfgen $(SBOBJS) $(PLUGINOBJS) $(TCLLIB) $(TCLAPPLIB) -lm +@@ -456,7 +446,7 @@ + $(CC) $(CFLAGS) -o diffbinpdb $(SRCDIR)/diffbinpdb.c -lm + + flipdcd: $(SRCDIR)/flipdcd.c +- $(CC) $(CFLAGS) -o $@ $(SRCDIR)/flipdcd.c || \ ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(SRCDIR)/flipdcd.c || \ + echo "#!/bin/sh\necho unavailable on this platform" > $@; \ + chmod +x $@ + +@@ -466,7 +456,7 @@ + chmod +x $@ + + fixdcd: $(SRCDIR)/fixdcd.c +- $(CC) $(CFLAGS) -o fixdcd $(SRCDIR)/fixdcd.c ++ $(CC) $(CFLAGS) $(LDFLAGS) -o fixdcd $(SRCDIR)/fixdcd.c + + dumpdcd: $(SRCDIR)/dumpdcd.c + $(CC) $(CFLAGS) -o dumpdcd $(SRCDIR)/dumpdcd.c +@@ -665,9 +655,7 @@ + + DOC_FILES = README.txt announce.txt license.txt notes.txt + +-RELEASE_FILES = $(LIBCUDARTSO) flipdcd flipbinpdb sortreplicas psfgen charmrun namd2 +- +-WINDOWS_RELEASE_FILES = $(LIBCUDARTSO) $(WINDOWSBINARIES) $(TCLDLL) ++RELEASE_FILES = $(LIBCUDARTSO) flipdcd flipbinpdb sortreplicas psfgen namd2 + + release: all + $(ECHO) Creating release $(RELEASE_DIR_NAME) +@@ -678,17 +666,9 @@ + for f in `find $(RELEASE_DIR_NAME)/lib -name CVS`; do \ + /bin/rm -rf $$f; \ + done +- if [ -r $(CHARM)/bin/charmd ]; then \ +- $(COPY) $(CHARM)/bin/charmd $(RELEASE_DIR_NAME); \ +- fi +- if [ -r $(CHARM)/bin/charmd_faceless ]; then \ +- $(COPY) $(CHARM)/bin/charmd_faceless $(RELEASE_DIR_NAME); \ +- fi + chmod -R a+rX $(RELEASE_DIR_NAME) + tar cf $(RELEASE_DIR_NAME).tar $(RELEASE_DIR_NAME) + gzip $(RELEASE_DIR_NAME).tar +- echo $(CHARM) +- ls -l $(CHARM)/lib + -for f in $(RELEASE_FILES); do echo $$f; $(LDD) $(RELEASE_DIR_NAME)/$$f; done + + winrelease: winall +diff -Naur NAMD_2.9_Source.original/arch/Linux-x86_64.fftw NAMD_2.9_Source/arch/Linux-x86_64.fftw +--- NAMD_2.9_Source.original/arch/Linux-x86_64.fftw 2009-02-21 21:16:04.000000000 -0700 ++++ NAMD_2.9_Source/arch/Linux-x86_64.fftw 2013-09-13 20:55:02.000000000 -0600 +@@ -1,7 +1,7 @@ + +-FFTDIR=/Projects/namd2/fftw/linux-x86_64 ++FFTDIR=/usr + FFTINCL=-I$(FFTDIR)/include +-FFTLIB=-L$(FFTDIR)/lib -lsrfftw -lsfftw ++FFTLIB=-L$(FFTDIR)/gentoo-libdir -lsrfftw -lsfftw + FFTFLAGS=-DNAMD_FFTW + FFT=$(FFTINCL) $(FFTFLAGS) + +diff -Naur NAMD_2.9_Source.original/arch/Linux-x86_64.tcl NAMD_2.9_Source/arch/Linux-x86_64.tcl +--- NAMD_2.9_Source.original/arch/Linux-x86_64.tcl 2011-06-17 14:38:43.000000000 -0600 ++++ NAMD_2.9_Source/arch/Linux-x86_64.tcl 2013-09-13 20:56:30.000000000 -0600 +@@ -1,9 +1,9 @@ + + #TCLDIR=/Projects/namd2/tcl/tcl8.5.9-linux-x86_64 +-TCLDIR=/Projects/namd2/tcl/tcl8.5.9-linux-x86_64-threaded ++TCLDIR=/usr + TCLINCL=-I$(TCLDIR)/include + #TCLLIB=-L$(TCLDIR)/lib -ltcl8.5 -ldl +-TCLLIB=-L$(TCLDIR)/lib -ltcl8.5 -ldl -lpthread ++TCLLIB=-L$(TCLDIR)/gentoo-libdir -ltcl8.5 -ldl -lpthread + TCLFLAGS=-DNAMD_TCL + TCL=$(TCLINCL) $(TCLFLAGS) + diff --git a/sci-chemistry/namd/metadata.xml b/sci-chemistry/namd/metadata.xml new file mode 100644 index 000000000..e42d0af60 --- /dev/null +++ b/sci-chemistry/namd/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> +</pkgmetadata> diff --git a/sci-chemistry/namd/namd-2.9.ebuild b/sci-chemistry/namd/namd-2.9.ebuild new file mode 100644 index 000000000..85114c26c --- /dev/null +++ b/sci-chemistry/namd/namd-2.9.ebuild @@ -0,0 +1,105 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit eutils multilib toolchain-funcs flag-o-matic + +DESCRIPTION="A powerful and highly parallelized molecular dynamics code" +LICENSE="namd" +HOMEPAGE="http://www.ks.uiuc.edu/Research/namd/" + +MY_PN="NAMD" +MY_PV="2.9" + +SRC_URI="${MY_PN}_${MY_PV}_Source.tar.gz" + +SLOT="0" +KEYWORDS="~amd64" +IUSE="" + +RESTRICT="fetch" + +DEPEND=" + app-shells/tcsh + sys-cluster/charm + sci-libs/fftw:2.1 + dev-lang/tcl" + +RDEPEND=${DEPEND} + +NAMD_ARCH="Linux-x86_64-g++" + +NAMD_DOWNLOAD="http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=NAMD" + +S="${WORKDIR}/${MY_PN}_${MY_PV}_Source" + +pkg_nofetch() { + echo + einfo "Please download ${MY_PN}_${MY_PV}_Source.tar.gz from" + einfo "${NAMD_DOWNLOAD}" + einfo "after agreeing to the license and then move it to" + einfo "${DISTDIR}" + einfo "Be sure to select the ${MY_PV} version!" + echo +} + +src_prepare() { + CHARM_VERSION=$(best_version sys-cluster/charm | cut -d- -f3) + + # apply a few small fixes to make NAMD compile and + # link to the proper libraries + epatch "${FILESDIR}"/namd-2.9-gentoo.patch + epatch "${FILESDIR}"/namd-2.7-iml-dec.patch + sed \ + -e "s:charm-.\+:charm-${CHARM_VERSION}:" \ + -i Make.charm || die + + rm -f charm-6.4.0.tar || die + + # proper compiler and cflags + sed \ + -e "s/g++/$(tc-getCXX)/" \ + -e "s/gcc/$(tc-getCC)/" \ + -e "s/CXXOPTS = -O3 -m64 -fexpensive-optimizations -ffast-math/CXXOPTS = ${CXXFLAGS}/" \ + -e "s/COPTS = -O3 -m64 -fexpensive-optimizations -ffast-math/COPTS = ${CFLAGS}/" \ + -i arch/${NAMD_ARCH}.arch || die + + sed \ + -e "s/gentoo-libdir/$(get_libdir)/g" \ + -e "s/gentoo-charm/charm-${CHARM_VERSION}/g" \ + -i Makefile || die "Failed gentooizing Makefile." + sed -e "s/gentoo-libdir/$(get_libdir)/g" -i arch/Linux-x86_64.fftw || die + sed -e "s/gentoo-libdir/$(get_libdir)/g" -i arch/Linux-x86_64.tcl || die +} + +src_configure() { + # configure + ./config ${NAMD_ARCH} || die +} + +src_compile() { + # build namd + cd "${S}/${NAMD_ARCH}" + emake +} + +src_install() { + dodoc announce.txt license.txt notes.txt + cd "${S}/${NAMD_ARCH}" + + # the binaries + dobin ${PN}2 psfgen flipbinpdb flipdcd +} + +pkg_postinst() { + echo + einfo "For detailed instructions on how to run and configure" + einfo "NAMD please consults the extensive documentation at" + einfo "http://www.ks.uiuc.edu/Research/namd/" + einfo "and the NAMD tutorials available at" + einfo "http://www.ks.uiuc.edu/Training/Tutorials/" + einfo "Have fun :)" + echo +} diff --git a/sci-libs/fftw/ChangeLog b/sci-libs/fftw/ChangeLog new file mode 100644 index 000000000..5bac2521e --- /dev/null +++ b/sci-libs/fftw/ChangeLog @@ -0,0 +1,18 @@ +# ChangeLog for sci-libs/fftw +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 07 Sep 2013; Christoph Junghans <ottxor@gentoo.org> fftw-3.3.3-r3.ebuild, + fftw-9999.ebuild: + final clean up + + 02 Sep 2013; Christoph Junghans <ottxor@gentoo.org> fftw-3.3.3-r3.ebuild, + fftw-9999.ebuild: + clean up + +*fftw-3.3.3-r3 (01 Sep 2013) +*fftw-9999 (01 Sep 2013) + + 01 Sep 2013; Christoph Junghans <ottxor@gentoo.org> +fftw-3.3.3-r3.ebuild, + +fftw-9999.ebuild, +files/fftw-3.3.3-install-header.patch, +metadata.xml: + import from gx86 diff --git a/sci-libs/fftw/Manifest b/sci-libs/fftw/Manifest new file mode 100644 index 000000000..2aab3f825 --- /dev/null +++ b/sci-libs/fftw/Manifest @@ -0,0 +1 @@ +DIST fftw-3.3.3.tar.gz 3920661 SHA256 85cdfc0a0ba10d8fa4f0f8e733aac1a5936c859832a9e3d5c0731fb5c54a97f3 SHA512 1d88b6376ba8c15cceafd3381de1d181a974b921b72b31dd89c297e5771e8d665aa3c121ef2504a70e7b0bb562b1e0612ac2a02121c412d27df06c4d687507c4 WHIRLPOOL b410cb4d854988f9a57f08344d9207ece4ebf218ec6fa605036235e472bef91f5037d852793fa6a7bc0f8a6a7081dc1e71b25b15ab1259e299bb95affca40d3b diff --git a/sci-libs/fftw/fftw-3.3.3-r3.ebuild b/sci-libs/fftw/fftw-3.3.3-r3.ebuild new file mode 100644 index 000000000..fb359955f --- /dev/null +++ b/sci-libs/fftw/fftw-3.3.3-r3.ebuild @@ -0,0 +1,187 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-libs/fftw/fftw-3.3.3-r2.ebuild,v 1.3 2013/06/27 14:30:29 aballier Exp $ + +EAPI=5 + +#AUTOTOOLS_AUTORECONF=1 +FORTRAN_NEEDED=fortran + +inherit autotools-multilib eutils flag-o-matic fortran-2 multibuild toolchain-funcs versionator + +DESCRIPTION="Fast C library for the Discrete Fourier Transform" +HOMEPAGE="http://www.fftw.org/" + +if [[ ${PV} = *9999 ]]; then + inherit git-2 + EGIT_REPO_URI="https://github.com/FFTW/fftw3.git" + KEYWORDS="" + AUTOTOOLS_AUTORECONF=1 +else + SRC_URI="http://www.fftw.org/${P}.tar.gz" + KEYWORDS="~alpha ~amd64 ~arm ~hppa ~ia64 ~mips ~ppc ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~x86-macos" +fi + +LICENSE="GPL-2" +SLOT="3.0" +IUSE="altivec avx doc fma fortran mpi neon openmp quad sse sse2 static-libs test threads zbus" + +RDEPEND=" + mpi? ( virtual/mpi ) + abi_x86_32? ( !<=app-emulation/emul-linux-x86-soundlibs-20130224-r2 + !app-emulation/emul-linux-x86-soundlibs[-abi_x86_32(-)] )" +DEPEND="${RDEPEND} + test? ( dev-lang/perl )" + +#can go once mpi is multlib +MULTILIB_WRAPPED_HEADERS=( + /usr/include/fftw3-mpi.h + /usr/include/fftw3l-mpi.f03 + /usr/include/fftw3-mpi.f03 + /usr/include/fftw3q.f03 +) + +pkg_setup() { + # XXX: this looks like it should be used with BUILD_TYPE!=binary + + if use openmp; then + if [[ $(tc-getCC) == *gcc ]] && ! tc-has-openmp; then + ewarn "OpenMP is not available in your current selected gcc" + die "need openmp capable gcc" + fi + FORTRAN_NEED_OPENMP=1 + fi + + fortran-2_pkg_setup + + MULTIBUILD_VARIANTS=( single double longdouble ) + if use quad; then + if [[ $(tc-getCC) == *gcc ]] && ! version_is_at_least 4.6 $(gcc-version); then + ewarn "quad precision only available for gcc >= 4.6" + die "need quad precision capable gcc" + fi + MULTIBUILD_VARIANTS+=( quad ) + fi +} + +src_prepare() { + # fix info file for category directory + [[ ${PV} = *9999 ]] || sed -i \ + -e 's/Texinfo documentation system/Libraries/' \ + doc/fftw3."info" || die "failed to fix info file" + + autotools-utils_src_prepare +} + +src_configure() { + local x + + # filter -Os according to docs + replace-flags -Os -O2 + + my_configure() { + #a bit hacky improve after #483758 is solved + local x=${BUILD_DIR%-${ABI}} + x=${x##*-} + # there is no abi_x86_32 port of virtual/mpi right now + local enable_mpi=$(use_enable mpi) + multilib_is_native_abi || enable_mpi="--disable-mpi" + + #jlec reported USE=quad on abi_x86_32 has too less registers + #stub Makefiles + if use amd64 && ! multilib_is_native_abi && [[ $x = quad ]]; then + mkdir -p "${BUILD_DIR}/tests" || die + echo "all: ;" > "${BUILD_DIR}/Makefile" || die + echo "install: ;" >> "${BUILD_DIR}/Makefile" || die + echo "smallcheck: ;" > "${BUILD_DIR}/tests/Makefile" || die + return 0 + fi + + myeconfargs=( + $(use_enable fma) + $(use_enable fortran) + $(use_enable zbus mips-zbus-timer) + $(use_enable threads) + $(use_enable openmp) + ) + if [[ $x == single ]]; then + #altivec, sse, single-paired only work for single + myeconfargs+=( + --enable-single + $(use_enable altivec) + $(use_enable avx) + $(use_enable sse) + ${enable_mpi} + $(use_enable neon) + ) + elif [[ $x == double ]]; then + myeconfargs+=( + $(use_enable avx) + $(use_enable sse2) + ${enable_mpi} + ) + elif [[ $x == longdouble ]]; then + myeconfargs+=( + --enable-long-double + ${enable_mpi} + ) + elif [[ $x == quad ]]; then + #quad does not support mpi + myeconfargs+=( --enable-quad-precision ) + else + die "${x} precision not implemented in this ebuild" + fi + + autotools-utils_src_configure + } + + multibuild_foreach_variant multilib_parallel_foreach_abi my_configure +} + +src_compile() { + multibuild_foreach_variant autotools-multilib_src_compile +} + +src_test () { + # We want this to be a reasonably quick test, but that is still hard... + ewarn "This test series will take 30 minutes on a modern 2.5Ghz machine" + # Do not increase the number of threads, it will not help your performance + #local testbase="perl check.pl --nthreads=1 --estimate" + # ${testbase} -${p}d || die "Failure: $n" + multibuild_foreach_variant autotools-multilib_src_compile -C tests smallcheck +} + +src_install () { + local u x + DOCS=( AUTHORS ChangeLog NEWS README TODO COPYRIGHT CONVENTIONS ) + HTML_DOCS=( doc/html/ ) + + #copied from autotools-multilib_secure_install + my_abi_src_install() { + autotools-utils_src_install + #https://github.com/FFTW/fftw3/pull/6 + # f03 are installed unconditionally, not a big problem as the quad + # header is the only one to be wrapped. + [[ ${BUILD_DIR} = *-quad* ]] || rm -f "${ED}/usr/include/fftw3q.f03" + if [[ ${#MULTIBUILD_VARIANTS[@]} -gt 1 ]]; then + multilib_prepare_wrappers + multilib_check_headers + fi + } + multibuild_foreach_variant multilib_foreach_abi my_abi_src_install + multilib_install_wrappers + + if use doc; then + dodoc doc/*.pdf + insinto /usr/share/doc/${PF}/faq + doins -r doc/FAQ/fftw-faq.html/* + else + rm -r "${ED}"/usr/share/doc/${PF}/html + fi + + for x in "${ED}"/usr/lib*/pkgconfig/*.pc; do + for u in $(usev mpi) $(usev threads) $(usex openmp omp ""); do + sed -e "s|-lfftw3[flq]\?|&_$u &|" "$x" > "${x%.pc}_$u.pc" || die + done + done +} diff --git a/sci-libs/fftw/fftw-9999.ebuild b/sci-libs/fftw/fftw-9999.ebuild new file mode 100644 index 000000000..fb359955f --- /dev/null +++ b/sci-libs/fftw/fftw-9999.ebuild @@ -0,0 +1,187 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-libs/fftw/fftw-3.3.3-r2.ebuild,v 1.3 2013/06/27 14:30:29 aballier Exp $ + +EAPI=5 + +#AUTOTOOLS_AUTORECONF=1 +FORTRAN_NEEDED=fortran + +inherit autotools-multilib eutils flag-o-matic fortran-2 multibuild toolchain-funcs versionator + +DESCRIPTION="Fast C library for the Discrete Fourier Transform" +HOMEPAGE="http://www.fftw.org/" + +if [[ ${PV} = *9999 ]]; then + inherit git-2 + EGIT_REPO_URI="https://github.com/FFTW/fftw3.git" + KEYWORDS="" + AUTOTOOLS_AUTORECONF=1 +else + SRC_URI="http://www.fftw.org/${P}.tar.gz" + KEYWORDS="~alpha ~amd64 ~arm ~hppa ~ia64 ~mips ~ppc ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~x86-macos" +fi + +LICENSE="GPL-2" +SLOT="3.0" +IUSE="altivec avx doc fma fortran mpi neon openmp quad sse sse2 static-libs test threads zbus" + +RDEPEND=" + mpi? ( virtual/mpi ) + abi_x86_32? ( !<=app-emulation/emul-linux-x86-soundlibs-20130224-r2 + !app-emulation/emul-linux-x86-soundlibs[-abi_x86_32(-)] )" +DEPEND="${RDEPEND} + test? ( dev-lang/perl )" + +#can go once mpi is multlib +MULTILIB_WRAPPED_HEADERS=( + /usr/include/fftw3-mpi.h + /usr/include/fftw3l-mpi.f03 + /usr/include/fftw3-mpi.f03 + /usr/include/fftw3q.f03 +) + +pkg_setup() { + # XXX: this looks like it should be used with BUILD_TYPE!=binary + + if use openmp; then + if [[ $(tc-getCC) == *gcc ]] && ! tc-has-openmp; then + ewarn "OpenMP is not available in your current selected gcc" + die "need openmp capable gcc" + fi + FORTRAN_NEED_OPENMP=1 + fi + + fortran-2_pkg_setup + + MULTIBUILD_VARIANTS=( single double longdouble ) + if use quad; then + if [[ $(tc-getCC) == *gcc ]] && ! version_is_at_least 4.6 $(gcc-version); then + ewarn "quad precision only available for gcc >= 4.6" + die "need quad precision capable gcc" + fi + MULTIBUILD_VARIANTS+=( quad ) + fi +} + +src_prepare() { + # fix info file for category directory + [[ ${PV} = *9999 ]] || sed -i \ + -e 's/Texinfo documentation system/Libraries/' \ + doc/fftw3."info" || die "failed to fix info file" + + autotools-utils_src_prepare +} + +src_configure() { + local x + + # filter -Os according to docs + replace-flags -Os -O2 + + my_configure() { + #a bit hacky improve after #483758 is solved + local x=${BUILD_DIR%-${ABI}} + x=${x##*-} + # there is no abi_x86_32 port of virtual/mpi right now + local enable_mpi=$(use_enable mpi) + multilib_is_native_abi || enable_mpi="--disable-mpi" + + #jlec reported USE=quad on abi_x86_32 has too less registers + #stub Makefiles + if use amd64 && ! multilib_is_native_abi && [[ $x = quad ]]; then + mkdir -p "${BUILD_DIR}/tests" || die + echo "all: ;" > "${BUILD_DIR}/Makefile" || die + echo "install: ;" >> "${BUILD_DIR}/Makefile" || die + echo "smallcheck: ;" > "${BUILD_DIR}/tests/Makefile" || die + return 0 + fi + + myeconfargs=( + $(use_enable fma) + $(use_enable fortran) + $(use_enable zbus mips-zbus-timer) + $(use_enable threads) + $(use_enable openmp) + ) + if [[ $x == single ]]; then + #altivec, sse, single-paired only work for single + myeconfargs+=( + --enable-single + $(use_enable altivec) + $(use_enable avx) + $(use_enable sse) + ${enable_mpi} + $(use_enable neon) + ) + elif [[ $x == double ]]; then + myeconfargs+=( + $(use_enable avx) + $(use_enable sse2) + ${enable_mpi} + ) + elif [[ $x == longdouble ]]; then + myeconfargs+=( + --enable-long-double + ${enable_mpi} + ) + elif [[ $x == quad ]]; then + #quad does not support mpi + myeconfargs+=( --enable-quad-precision ) + else + die "${x} precision not implemented in this ebuild" + fi + + autotools-utils_src_configure + } + + multibuild_foreach_variant multilib_parallel_foreach_abi my_configure +} + +src_compile() { + multibuild_foreach_variant autotools-multilib_src_compile +} + +src_test () { + # We want this to be a reasonably quick test, but that is still hard... + ewarn "This test series will take 30 minutes on a modern 2.5Ghz machine" + # Do not increase the number of threads, it will not help your performance + #local testbase="perl check.pl --nthreads=1 --estimate" + # ${testbase} -${p}d || die "Failure: $n" + multibuild_foreach_variant autotools-multilib_src_compile -C tests smallcheck +} + +src_install () { + local u x + DOCS=( AUTHORS ChangeLog NEWS README TODO COPYRIGHT CONVENTIONS ) + HTML_DOCS=( doc/html/ ) + + #copied from autotools-multilib_secure_install + my_abi_src_install() { + autotools-utils_src_install + #https://github.com/FFTW/fftw3/pull/6 + # f03 are installed unconditionally, not a big problem as the quad + # header is the only one to be wrapped. + [[ ${BUILD_DIR} = *-quad* ]] || rm -f "${ED}/usr/include/fftw3q.f03" + if [[ ${#MULTIBUILD_VARIANTS[@]} -gt 1 ]]; then + multilib_prepare_wrappers + multilib_check_headers + fi + } + multibuild_foreach_variant multilib_foreach_abi my_abi_src_install + multilib_install_wrappers + + if use doc; then + dodoc doc/*.pdf + insinto /usr/share/doc/${PF}/faq + doins -r doc/FAQ/fftw-faq.html/* + else + rm -r "${ED}"/usr/share/doc/${PF}/html + fi + + for x in "${ED}"/usr/lib*/pkgconfig/*.pc; do + for u in $(usev mpi) $(usev threads) $(usex openmp omp ""); do + sed -e "s|-lfftw3[flq]\?|&_$u &|" "$x" > "${x%.pc}_$u.pc" || die + done + done +} diff --git a/sci-libs/fftw/files/fftw-3.3.3-install-header.patch b/sci-libs/fftw/files/fftw-3.3.3-install-header.patch new file mode 100644 index 000000000..4456c189e --- /dev/null +++ b/sci-libs/fftw/files/fftw-3.3.3-install-header.patch @@ -0,0 +1,35 @@ +From f450afa1cc0bb962abecfc1ffdbef8e1f7b748e4 Mon Sep 17 00:00:00 2001 +From: Christoph Junghans <ottxor@gentoo.org> +Date: Sat, 31 Aug 2013 21:21:28 -0600 +Subject: [PATCH] Only install f03 header of the active precision + +--- + api/Makefile.am | 11 ++++++++++- + 1 file changed, 10 insertions(+), 1 deletion(-) + +diff --git a/api/Makefile.am b/api/Makefile.am +index e4eaad7..bb6c042 100644 +--- a/api/Makefile.am ++++ b/api/Makefile.am +@@ -4,8 +4,17 @@ AM_CFLAGS = $(STACK_ALIGN_CFLAGS) + + EXTRA_DIST = f03api.sh genf03.pl fftw3.f03.in + +-include_HEADERS = fftw3.h fftw3.f fftw3l.f03 fftw3q.f03 ++include_HEADERS = fftw3.h fftw3.f ++noinst_HEADERS = fftw3l.f03 fftw3q.f03 ++if LDOUBLE ++include_HEADERS += fftw3l.f03 ++else ++if QUAD ++include_HEADERS += fftw3q.f03 ++else + nodist_include_HEADERS = fftw3.f03 ++endif ++endif + noinst_LTLIBRARIES = libapi.la + + # pkgincludedir = $(includedir)/fftw3@PREC_SUFFIX@ +-- +1.8.1.5 + diff --git a/sci-libs/fftw/metadata.xml b/sci-libs/fftw/metadata.xml new file mode 100644 index 000000000..50e74c164 --- /dev/null +++ b/sci-libs/fftw/metadata.xml @@ -0,0 +1,23 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci</herd> + <longdescription lang="en"> + The Fastest Fourier Transform in the West is a C subroutine library + for computing the Discrete Fourier Transform (DFT) in one or more + dimensions, of both real and complex data, and of arbitrary input + size. It is becoming the FFT library of choice for most + applications. Benchmarks, performed on a variety of platforms, show + that FFTW's performance is typically superior to that of other + publicly available FFT software. +</longdescription> + <use> + <flag name="avx">Adds support for Advanced Vector Extensions</flag> + <flag name="fma">Use the Fused Multiply Add instruction set (fma3/fma4 either one)</flag> + <flag name="quad">Build quadruple precision lib</flag> + <flag name="zbus">Adds support for ZBus cycle-counter of mips</flag> + </use> + <upstream> + <remote-id type="freecode">fftw</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/itk/ChangeLog b/sci-libs/itk/ChangeLog new file mode 100644 index 000000000..618618847 --- /dev/null +++ b/sci-libs/itk/ChangeLog @@ -0,0 +1,9 @@ +# ChangeLog for sci-libs/itk +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*itk-4.4.2 (12 Sep 2013) + + 12 Sep 2013; Sébastien Fabbro <bicatali@gentoo.org> +itk-4.4.2.ebuild, + -files/itk-4.4-v3compat_I2VI_const-fix.patch, -itk-4.4.0.ebuild, metadata.xml: + sci-libs/itk: Version bump. Cleaned-up ebuild and metadata.xml diff --git a/sci-libs/itk/Manifest b/sci-libs/itk/Manifest new file mode 100644 index 000000000..2a83eb01b --- /dev/null +++ b/sci-libs/itk/Manifest @@ -0,0 +1 @@ +DIST InsightToolkit-4.4.2.tar.gz 231905134 SHA256 071a7929c295b80bc8a6ab80d50c06cdfb0e6aafd936103c6d0a4a086cf8bec3 SHA512 c65beca4dd60aa769871bb3089cbb421729a2dcbd8bd3ec42c378ed60828e4327f1faf062f77bcca34306315a1daee6bc29d858dab9aea1c08f4843405fd21e3 WHIRLPOOL 4036bce61d0900ef2f1484ca06e9b513f6154c2233122e41fe694c648dd6eef53510749bf75368f9851a4dbd45777ca7033ad43f28c86259d5efae9e0d4200bd diff --git a/sci-libs/itk/itk-4.4.2.ebuild b/sci-libs/itk/itk-4.4.2.ebuild new file mode 100644 index 000000000..542216b7e --- /dev/null +++ b/sci-libs/itk/itk-4.4.2.ebuild @@ -0,0 +1,116 @@ +# Copyright 2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +PYTHON_COMPAT=( python{2_5,2_6,2_7} ) + +inherit eutils toolchain-funcs cmake-utils python-single-r1 + +MYP=InsightToolkit-${PV} + +DESCRIPTION="NLM Insight Segmentation and Registration Toolkit" +HOMEPAGE="http://www.itk.org" +SRC_URI="mirror://sourceforge/${PN}/${MYP}.tar.gz" + +RESTRICT="primaryuri" + +LICENSE="Apache-2.0" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="debug examples fftw itkv3compat python review sse2 test" + +RDEPEND=" + sci-libs/hdf5[cxx] + virtual/jpeg + media-libs/libpng + media-libs/tiff:0 + sys-libs/zlib + fftw? ( sci-libs/fftw:3.0 ) +" +DEPEND="${RDEPEND} + python? ( ${PYTHON_DEPS} + >=dev-lang/swig-2.0 + >=dev-cpp/gccxml-0.9.0_pre20120309 ) +" + +S="${WORKDIR}/${MYP}" + +pkg_pretend() { + if [[ -z ${ITK_COMPUTER_MEMORY_SIZE} ]]; then + elog "To tune ITK to make the best use ouf working memory you can set" + elog " ITK_COMPUTER_MEMORY_SIZE=XX" + elog "in make.conf, default is 1 (unit is GB)" + fi + if use python && [[ -z ${ITK_WRAP_DIMS} ]]; then + elog "For Python language bindings, you can define the dimensions" + elog "you want to create bindings for by setting" + elog " ITK_WRAP_DIMS=X;Y;Z..." + elog "in make.conf, default is 2;3 for 2D and 3D data" + fi +} + +src_configure() { + local mycmakeargs=( + -DWRAP_ITK_JAVA=OFF + -DWRAP_ITK_TCL=OFF + -DITK_USE_SYSTEM_HDF5=ON + -DITK_USE_SYSTEM_JPEG=ON + -DITK_USE_SYSTEM_PNG=ON + -DITK_USE_SYSTEM_TIFF=ON + -DITK_USE_SYSTEM_ZLIB=ON + -DITK_USE_SYSTEM_GCCXML=ON + -DITK_USE_SYSTEM_SWIG=ON + -DITK_BUILD_ALL_MODULES=ON + -DBUILD_SHARED_LIBS=ON + -DBUILD_EXAMPLES=OFF + -DITK_COMPUTER_MEMORY_SIZE="${ITK_COMPUTER_MEMORY_SIZE:-1}" + $(cmake-utils_use_build test TESTING) + $(cmake-utils_use review ITK_USE_REVIEW) + $(cmake-utils_use itkv3compat ITKV3_COMPATIBILITY) + $(cmake-utils_use sse2 VNL_CONFIG_ENABLE_SSE2) + ) + if use fftw; then + mycmakeargs+=( + -DUSE_FFTWD=ON + -DUSE_FFTWF=ON + -DUSE_SYSTEM_FFTW=ON + -DITK_WRAP_double=ON + -DITK_WRAP_vector_double=ON + -DITK_WRAP_covariant_vector_double=ON + -DITK_WRAP_complex_double=ON + ) + fi + if use python; then + mycmakeargs+=( + -DITK_WRAP_PYTHON=ON + -DITK_WRAP_DIMS="${ITK_WRAP_DIMS:-2;3}" + ) + else + mycmakeargs+=( + -DITK_WRAP_PYTHON=OFF + ) + fi + cmake-utils_src_configure +} + +src_install() { + cmake-utils_src_install + + if use examples; then + insinto /usr/share/doc/${PF}/examples + docompress -x /usr/share/doc/${PF}/examples + doins -r "${S}"/Examples/* + fi + + echo "ITK_DATA_ROOT=${EROOT}/usr/share/${PN}/data" > ${T}/40${PN} + local ldpath="${EROOT}/usr/$(get_libdir)/InsightToolkit" + if use python; then + echo "PYTHONPATH=${EROOT}/usr/$(get_libdir)/InsightToolkit/WrapITK/Python" >> ${T}/40${PN} + ldpath="${ldpath}:${EROOT}/usr/$(get_libdir)/InsightToolkit/WrapITK/lib" + fi + echo "LDPATH=${ldpath}" >> ${T}/40${PN} + + doenvd "${T}"/40${PN} +} diff --git a/sci-libs/itk/metadata.xml b/sci-libs/itk/metadata.xml new file mode 100644 index 000000000..e941d4802 --- /dev/null +++ b/sci-libs/itk/metadata.xml @@ -0,0 +1,18 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> +<herd>sci-biology</herd> +<maintainer> + <email>maintainer-wanted@gentoo.org</email> +</maintainer> +<longdescription lang="en"> + Insight Segmentation and Registration Toolkit (ITK) is a library + that provides developers with an extensive suite of tools for image + analysis. +</longdescription> +<use> + <flag name="itkv3compat">Enable compatibility with ITK version 3</flag> + <flag name="review">Enable compilation of methods under review</flag> +</use> +</pkgmetadata> + diff --git a/sci-libs/modglue/ChangeLog b/sci-libs/modglue/ChangeLog index 732b78492..eb811e97d 100644 --- a/sci-libs/modglue/ChangeLog +++ b/sci-libs/modglue/ChangeLog @@ -2,6 +2,10 @@ # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 03 Sep 2013; François Bissey <francois.bissey@canterbury.ac.nz> + modglue-1.16.ebuild: + Fix PATCHES definition, it shouldn't include 'epatch' + 03 Mar 2013; Justin Lecher <jlec@gentoo.org> modglue-1.16.ebuild, metadata.xml: Move to EPAI=5 and virtual/pkgconfig; clean usage of autotools-utils.eclass @@ -39,4 +43,3 @@ 03 Apr 2009; Francois Bissey <f.r.bissey@massey.ac.nz> ChangeLog: Initial import for the science overlay - diff --git a/sci-libs/modglue/Manifest b/sci-libs/modglue/Manifest index 05141a4d3..9c45f3be3 100644 --- a/sci-libs/modglue/Manifest +++ b/sci-libs/modglue/Manifest @@ -1 +1 @@ -DIST modglue-1.16.tar.gz 89987 SHA256 1da62910d7171cb5547c0757c366e5338f889c0155c33375e891df75e2ee429e +DIST modglue-1.16.tar.gz 89987 SHA256 1da62910d7171cb5547c0757c366e5338f889c0155c33375e891df75e2ee429e SHA512 2ac93f771f99b33f6339ceb55ba95c034c37d84b3d8ee6a56a8c75e7b6129cf3a218adb5539df37da2c5f645983eb7c141c9716ad5c94699e2f44396609d7f2a WHIRLPOOL 39f399b30c3762fa6522444051f81bb8d484448681735e8e1c0d304f0f8ebc5e281853257dffc506ab3f864025cab373b608720e0645ed8397ec7fc2fe8625af diff --git a/sci-libs/modglue/modglue-1.16.ebuild b/sci-libs/modglue/modglue-1.16.ebuild index afabe76c7..ab4602cd4 100644 --- a/sci-libs/modglue/modglue-1.16.ebuild +++ b/sci-libs/modglue/modglue-1.16.ebuild @@ -25,12 +25,12 @@ AUTOTOOLS_IN_SOURCE_BUILD=1 PATCHES=( # Respect LDFLAGS - epatch "${FILESDIR}"/${P}-ldflags.patch + "${FILESDIR}"/${P}-ldflags.patch # fix parallel make. test are made at the same time as the library?? - epatch "${FILESDIR}"/${P}-parallelmake.patch + "${FILESDIR}"/${P}-parallelmake.patch # take care of the lib/lib64 problem. Without this modglue installs # stuff in /usr/usr/lib64 on 64bits systems. - epatch "${FILESDIR}"/${P}-lib64.patch + "${FILESDIR}"/${P}-lib64.patch ) src_install() { diff --git a/sci-libs/nibabel/metadata.xml b/sci-libs/nibabel/metadata.xml new file mode 100644 index 000000000..7ffd788e6 --- /dev/null +++ b/sci-libs/nibabel/metadata.xml @@ -0,0 +1,19 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> +<herd>sci</herd> +<maintainer> + <email>h.chr@mail.ru</email> + <name>Horea Christian</name> +</maintainer> +<longdescription lang="en"> + The package provides read and write access to some common medical and + neuroimaging file formats, including: ANALYZE (plain, SPM99, SPM2), GIFTI, + NIfTI1, MINC, MGH and ECAT as well as PAR/REC. It can read and write Freesurfer + geometry, and read Freesurfer morphometry and annotation files. There is some + very limited support for DICOM. NiBabel is the successor of PyNIfTI. +</longdescription> +<use> + <flag name="dicom">Adds limited read support for the DICOM imaging format.</flag> +</use> +</pkgmetadata> diff --git a/sci-libs/nibabel/nibabel-9999.ebuild b/sci-libs/nibabel/nibabel-9999.ebuild new file mode 100644 index 000000000..0070d0bfd --- /dev/null +++ b/sci-libs/nibabel/nibabel-9999.ebuild @@ -0,0 +1,40 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI="5" + +PYTHON_COMPAT=( python{2_6,2_7,3_2,3_3} ) + +inherit distutils-r1 git-2 + +DESCRIPTION="Access a cacophony of neuro-imaging file formats" +HOMEPAGE="http://nipy.org/nibabel/" +EGIT_REPO_URI="https://github.com/nipy/nibabel.git" + +LICENSE="MIT" +SLOT="0" +IUSE="dicom doc test" + +RDEPEND=" + dev-python/numpy[${PYTHON_USEDEP}] + sci-libs/scipy[${PYTHON_USEDEP}] + dev-python/nose[${PYTHON_USEDEP}] + dicom? ( + sci-libs/pydicom[${PYTHON_USEDEP}] + virtual/python-imaging[${PYTHON_USEDEP}] + ) + " + +DEPEND=" + dev-python/setuptools[${PYTHON_USEDEP}] + test? ( ${RDEPEND} ) + doc? ( dev-python/sphinx[${PYTHON_USEDEP}] ) + " + +python_test() { + distutils-r1_install_for_testing + cd "${BUILD_DIR}" || die + echo "backend: Agg" > matplotlibrc + MPLCONFIGDIR=. nosetests || die +} diff --git a/sci-libs/nipy/Manifest b/sci-libs/nipy/Manifest new file mode 100644 index 000000000..e2730eee9 --- /dev/null +++ b/sci-libs/nipy/Manifest @@ -0,0 +1 @@ +DIST nipy-0.3.0.tar.gz 2143887 SHA256 74fef65c832795a35e1757d8bd852177fae190517a964afcb0812cfc1107d155 SHA512 3eaab4628bfa1706c99d516242387e1a27330bbf03b5b79da80d9a5e697b4e779f8f059e6f7bcc4253c5ad7af1bf6c600bcc5bd87db95d2e38f445d1f4416106 WHIRLPOOL 8a27c42abd8c7ae5ce66b8cfb0686b79e3208950107fcc5090d88fa2c23bf15d4ce4ae5b598f6f51c6e70122c40a343b9b7b2950ef09aefaeb22e24efd854af0 diff --git a/sci-libs/nipy/metadata.xml b/sci-libs/nipy/metadata.xml new file mode 100644 index 000000000..ac599a834 --- /dev/null +++ b/sci-libs/nipy/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> +<herd>sci</herd> +<maintainer> + <email>h.chr@mail.ru</email> + <name>Horea Christian</name> +</maintainer> +<longdescription lang="en"> + NIPY is a python project for analysis of structural and functional neuroimaging data. +</longdescription> +</pkgmetadata> diff --git a/sci-libs/nipy/nipy-0.3.0.ebuild b/sci-libs/nipy/nipy-0.3.0.ebuild new file mode 100644 index 000000000..4d68e2a82 --- /dev/null +++ b/sci-libs/nipy/nipy-0.3.0.ebuild @@ -0,0 +1,37 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI="5" + +PYTHON_COMPAT=( python{2_6,2_7,3_2} ) +DISTUTILS_NO_PARALLEL_BUILD=true + +inherit distutils-r1 eutils multilib flag-o-matic + + +DESCRIPTION="Neuroimaging tools for Python" +HOMEPAGE="http://nipy.org/" +SRC_URI="mirror://pypi/${P:0:1}/${PN}/${P}.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +DEPEND="dev-python/setuptools[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}]" +RDEPEND="${DEPEND} + sci-libs/scipy[${PYTHON_USEDEP}] + dev-python/sympy[${PYTHON_USEDEP}] + >=sci-libs/nibabel-1.2[${PYTHON_USEDEP}]" + +python_prepare_all() { + distutils-r1_python_prepare_all + # bug #397605 + [[ ${CHOST} == *-darwin* ]] \ + && append-ldflags -bundle "-undefined dynamic_lookup" \ + || append-ldflags -shared + + # nipy uses the horrible numpy.distutils automagic +} diff --git a/sci-libs/nipy/nipy-9999.ebuild b/sci-libs/nipy/nipy-9999.ebuild new file mode 100644 index 000000000..6d752cbde --- /dev/null +++ b/sci-libs/nipy/nipy-9999.ebuild @@ -0,0 +1,36 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-libs/scikits_image/scikits_image-0.8.2.ebuild,v 1.3 2013/06/18 04:33:25 patrick Exp $ + +EAPI=5 + +PYTHON_COMPAT=( python{2_6,2_7,3_2} ) +DISTUTILS_NO_PARALLEL_BUILD=true + +inherit distutils-r1 multilib git-2 flag-o-matic + +DESCRIPTION="Neuroimaging tools for Python" +HOMEPAGE="http://nipy.org/" +EGIT_REPO_URI="https://github.com/nipy/nipy" + +LICENSE="BSD" +SLOT="0" +IUSE="" +KEYWORDS="" + +DEPEND="dev-python/setuptools[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}]" +RDEPEND="${DEPEND} + sci-libs/scipy[${PYTHON_USEDEP}] + dev-python/sympy[${PYTHON_USEDEP}] + >=sci-libs/nibabel-1.2[${PYTHON_USEDEP}]" + +python_prepare_all() { + distutils-r1_python_prepare_all + # bug #397605 + [[ ${CHOST} == *-darwin* ]] \ + && append-ldflags -bundle "-undefined dynamic_lookup" \ + || append-ldflags -shared + + # nipy uses the horrible numpy.distutils automagic +} diff --git a/sci-libs/nipype/metadata.xml b/sci-libs/nipype/metadata.xml new file mode 100644 index 000000000..d41e11fc9 --- /dev/null +++ b/sci-libs/nipype/metadata.xml @@ -0,0 +1,21 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> +<herd>sci</herd> +<maintainer> + <email>h.chr@mail.ru</email> + <name>Horea Christian</name> +</maintainer> +<longdescription lang="en"> + Nipype, an open-source, community-developed initiative under the + umbrella of NiPy, is a Python project that provides a uniform interface + to existing neuroimaging software and facilitates interaction between + these packages within a single workflow. Nipype provides an environment + that encourages interactive exploration of algorithms from different + packages (e.g., SPM, FSL, FreeSurfer, Camino, MRtrix, MNE, AFNI, Slicer), + eases the design of workflows within and between packages, and reduces + the learning curve necessary to use different packages. Nipype is + creating a collaborative platform for neuroimaging software development + in a high-level language and addressing limitations of existing pipeline systems. +</longdescription> +</pkgmetadata> diff --git a/sci-libs/nipype/nipype-9999.ebuild b/sci-libs/nipype/nipype-9999.ebuild new file mode 100644 index 000000000..7afb3b5f0 --- /dev/null +++ b/sci-libs/nipype/nipype-9999.ebuild @@ -0,0 +1,33 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-libs/scikits_image/scikits_image-0.8.2.ebuild,v 1.3 2013/06/18 04:33:25 patrick Exp $ + +EAPI=5 + +# pyamg missing py3 support +# PYTHON_COMPAT=( python{2_6,2_7,3_2,3_3} ) +PYTHON_COMPAT=( python{2_6,2_7} ) + +inherit distutils-r1 git-2 + +DESCRIPTION="Neuroimaging in Python: Pipelines and Interfaces" +HOMEPAGE="http://nipy.sourceforge.net/nipype/" +EGIT_REPO_URI="https://github.com/nipy/nipype" + +LICENSE="BSD" +SLOT="0" + +DEPEND=" + dev-python/setuptools[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] + >=sci-libs/nibabel-1.2[${PYTHON_USEDEP}]" +RDEPEND=" + sci-libs/scipy[${PYTHON_USEDEP}] + dev-python/traits[${PYTHON_USEDEP}] + dev-python/networkx[${PYTHON_USEDEP}]" + +python_test() { + nosetests -v || die +} + + diff --git a/sci-libs/pydicom/Manifest b/sci-libs/pydicom/Manifest new file mode 100644 index 000000000..c6ce98860 --- /dev/null +++ b/sci-libs/pydicom/Manifest @@ -0,0 +1 @@ +DIST pydicom-0.9.8.zip 466418 SHA256 d73852cd6f2a0f95c5bd096806ca517f3c152f117638528dcbf7527793853141 SHA512 baba1963069caebd5f124e545356f07993733b4bd2e11d06e22b57b796bb48ad21734a72c0b4ced8e5607b40047ccc929886e449c956047cb293e5fb27038cbe WHIRLPOOL fba24f994ea76ab13bfa6432ba69afd61ca250c1f05573782d660b7c1b0db9aadfa15d6bce5a4a26b38f8cbdce7db16b1d00857f8f1bc4e54190217a8bedaa97 diff --git a/sci-libs/pydicom/pydicom-0.9.8.ebuild b/sci-libs/pydicom/pydicom-0.9.8.ebuild new file mode 100644 index 000000000..1a31eb262 --- /dev/null +++ b/sci-libs/pydicom/pydicom-0.9.8.ebuild @@ -0,0 +1,20 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 +PYTHON_COMPAT=( python2_7 ) + +inherit distutils-r1 + +DESCRIPTION="A pure python package for parsing DICOM files" +HOMEPAGE="https://code.google.com/p/pydicom/" +SRC_URI="https://pydicom.googlecode.com/files/${P}.zip" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +RDEPEND="" +DEPEND="" diff --git a/sci-misc/sfst/Manifest b/sci-misc/sfst/Manifest index 3fea2be41..4e69fd2b3 100644 --- a/sci-misc/sfst/Manifest +++ b/sci-misc/sfst/Manifest @@ -1,4 +1,4 @@ DIST SFST-1.4.2.tar.gz 490458 SHA256 0f3040f9e79faa7fee083d3344a87db533dfd84340b43eb86e79a208c70ad7be SHA512 9466d929e33141db7e2e19eb9dbcdf095a561677ba0e0ae9158a813a92ac3b389462a47a253fca5c61d14413c2559e0f1cfe3d3222f456836b5b5f93b33b42ea WHIRLPOOL e1aa43b8902812a75aa8d4ac598aa029cf38e23e52c9cc8c140eda03d5b514bcc5cc60f820b0eedd00d060b175aff74e05ce72c860337297553a228ab3b6425b -DIST SFST-1.4.6g.tar.gz 486283 SHA256 5ed88df7ca993fc62e9ca85464ffc78fde83425344826e26debc984f32621bf8 SHA512 cd92a952389e5ec1cf965362b249f992bc20dca58c9dd3f8cc873ccbdc80507d4962681725943d2611956d92c116338a0b46f18653d89486f0a4986fb58fbd13 WHIRLPOOL 79f0dadb16f12507b58bf3971df0b6aba42f2f7b5fe95a796e6d2c15ddfdf95fc30dea4e387f77080f440810acdbfbba0ebe29f3fe7de1102f79edfec540129c +DIST SFST-1.4.6g.tar.gz 486334 SHA256 53441e785be6d00b96021f455a7c6d4e40793afdade87f40be02305583a2b7a3 SHA512 8535ffd7b0a62dd27bc24d95d048afc7f56c81bfc3c989255a3d65b18a7be99c6b474a6ca0c196f7dc68eea4e4a5e1d744413252d909a9db2f0be843bb8fc518 WHIRLPOOL cd5a9756cb4bfb588cafa7bcb54a43e786af79befb68af574c7b578d51d4aefcd77be62bdc94b5fc5e35be401f5cbab1ea801aedb27f08fdc0addfcc680c9254 DIST sfst.el 4752 SHA256 b47ff59f5ff24482dbbb2f1e71a8b9ca234c4154487f83eb2118f1a62bb9eb5f SHA512 88c808044919d49b7c647c16caffb0e67d6fae9ae948434247dbcef7d78168a7b67e7a5b64c5dbeb634f273d6b8ccb93d449af097a1418a6d48a7852f6ad9bbe WHIRLPOOL c8075858fde4c0986acdebab6e5935b1a8022065db09f722d0844d5a020414e8b19d3f321a6f1eeb96e4609643ed4dc62375d8c11be471b5d2e6b7212f6af273 DIST vim-mode.tar.gz 1104 SHA256 a62ba91c40da75be389a334db62cc2b4904bedfac657b185012b10f3f55dfe09 SHA512 8b808553dbf7a6d6aebb0d6382339bfbe56584effe0b1b0b9096969f81324305e4b66760188dc8fdfbb69118aa5688c66e2bd880dabb57b494068fd620ff540d WHIRLPOOL 252b7bd1110f3522caf0e2921550a52a552611227fd0da0029485f6eaf467ad476758deaee2774cf3c0e882d5dca63b82362e3e5a8fd378171286f7c1682fa77 diff --git a/sci-physics/lammps/ChangeLog b/sci-physics/lammps/ChangeLog index 5bc3b87a6..b53b891d5 100644 --- a/sci-physics/lammps/ChangeLog +++ b/sci-physics/lammps/ChangeLog @@ -2,6 +2,11 @@ # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*lammps-20130830 (02 Sep 2013) + + 02 Sep 2013; Nicolas Bock <nicolasbock@gmail.com> +lammps-20130830.ebuild: + sci-physics/lammps: Version bump to 20130830. + *lammps-20130816 (13 Aug 2013) 13 Aug 2013; Nicolas Bock <nicolasbock@gmail.com> +lammps-20130816.ebuild: diff --git a/sci-physics/lammps/Manifest b/sci-physics/lammps/Manifest index ffdd74013..3cd74ecb9 100644 --- a/sci-physics/lammps/Manifest +++ b/sci-physics/lammps/Manifest @@ -1,4 +1,5 @@ DIST lammps-11Jul13.tar.gz 47802661 SHA256 98516d69ec12463ee3884c2e71b7704dcc2f4cf6dc2be43531452f94d9b29f4d SHA512 b5df81063516f93ec3bb347f3e1601a5e4862b8c227adf7778d76a890ef8f8f989b6a75f8363bdd5f30fbed090d0589c70b3a45b791d0312065bf3405c33d0d7 WHIRLPOOL 73ea6b0d248a7c92531a5ce6d7ac516dc277a8ae2bf7ed7bdb253f8dd1c47fc983a0f112ceabde424778ee21cd8f1e5eb2722a1bab9293213415c4b4950d6a4a DIST lammps-16Aug13.tar.gz 48337879 SHA256 740d35046961df7ea2dd39e2b7a28e5ff1414f283ac9f568986bd1f2b8b036d9 SHA512 1e56751b94e2af8487c77066846cad7e3a98b7f990a90db9b57e32dc8e3c0a4b9be3431a92f393962fb703ce4957c1d2580545e27549e47a3207e88ec158aa8d WHIRLPOOL d3d442d1d7e9e0267de2a637fd44c87df6dc8eaad61de28cc1aa75d93b49b7877c1de21df251fc8d812e36391f2c5d5e7a75b4b349e6749e9efb9b5266edeb77 DIST lammps-1Jul13.tar.gz 47784757 SHA256 9a41b6bdc6b5288e711d0ff877f18a028a6ae9981c3cf7b7ab77df344d5ac5e2 SHA512 de9dd48926a53127f53862df7f604599e0ec6cbe6e7661b83126239d5c63775e76c12e6f0677d286204696fb1734cc57370483f052b1060a5db9d8dc3765ae84 WHIRLPOOL 05eb83d8fe4fb7affe8331b987c6d87d3437fe265e1f50554970265ed4df1dd22d931e9bb8461df6e0ea3d19bb3458623dc40b0ee1a13b297ad3e3a611055dda +DIST lammps-30Aug13.tar.gz 48632345 SHA256 8d20ab00412feda5c9869de0188c52fb77f1faa51b317f09706eff35e651d961 SHA512 9722a3a4a7adc3387014650bd5a3ed18f3081065791507d0c39227a394f375f10a8ffbb5510fac24fcc6e84a40b98c0ad21d576969824284e65be94c445e5a24 WHIRLPOOL 50c6f4aed0ef21aa9078eb16ea15f6d6a89bc24316a40183ac993fbf3fecca2c55a5bcf1715cfbecff24ea07e96c55ba082679b11926c50f6ac2da2ec17547e4 DIST lammps-8Jul13.tar.gz 47801224 SHA256 1ae1c27e4ac47a732f3141f3106f395e3fcaa07e05039f15adc01bfbba1aa5e5 SHA512 32c693e7e4dc00f674f910fc2890e85dfd71171da99a993aa8b7ce71aa0f5cd0974e28654a00585190b5a0c47d3fd24eb63d3d2d143f48a88e76e0fca740e99c WHIRLPOOL 12b67892ca7f98255c4aac7183fedddcefb62aa5835787185443b07eab7641e7177c2c2095309336b0fbcae552b6993d3208c0246b13ce0f71084a21b4ab271b diff --git a/sci-physics/lammps/lammps-20130830.ebuild b/sci-physics/lammps/lammps-20130830.ebuild new file mode 100644 index 000000000..fa960e384 --- /dev/null +++ b/sci-physics/lammps/lammps-20130830.ebuild @@ -0,0 +1,115 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-physics/lammps/lammps-20130526.ebuild,v 1.1 2013/06/26 23:53:11 ottxor Exp $ + +EAPI=5 + +FORTRAN_NEEDED="package-meam" + +inherit eutils fortran-2 + +convert_month() { + case $1 in + 01) echo Jan + ;; + 02) echo Feb + ;; + 03) echo Mar + ;; + 04) echo Apr + ;; + 05) echo May + ;; + 06) echo Jun + ;; + 07) echo Jul + ;; + 08) echo Aug + ;; + 09) echo Sep + ;; + 10) echo Oct + ;; + 11) echo Nov + ;; + 12) echo Dec + ;; + *) echo unknown + ;; + esac +} + +MY_P=${PN}-$((10#${PV:6:2}))$(convert_month ${PV:4:2})${PV:2:2} + +DESCRIPTION="Large-scale Atomic/Molecular Massively Parallel Simulator" +HOMEPAGE="http://lammps.sandia.gov/" +SRC_URI="http://lammps.sandia.gov/tars/${MY_P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64" +IUSE="doc examples gzip lammps-memalign mpi package-dipole package-meam package-rigid" + +DEPEND="mpi? ( virtual/mpi )" +RDEPEND="${DEPEND}" + +S="${WORKDIR}/${MY_P}" + +lmp_emake() { + local LAMMPS_INCLUDEFLAGS="$(usex gzip '-DLAMMPS_GZIP' '')" + LAMMPS_INCLUDEFLAGS+="$(usex lammps-memalign ' -DLAMMPS_MEMALIGN' '')" + + # Note: The lammps makefile uses CC to indicate the C++ compiler. + emake \ + ARCHIVE=$(tc-getAR) \ + CC=$(usex mpi "mpic++" "$(tc-getCXX)") \ + F90=$(usex mpi "mpif90" "$(tc-getFC)") \ + LINK=$(usex mpi "mpic++" "$(tc-getCXX)") \ + CCFLAGS="${CXXFLAGS}" \ + F90FLAGS="${FCFLAGS}" \ + LINKFLAGS="${LDFLAGS}" \ + LMP_INC="${LAMMPS_INCLUDEFLAGS}" \ + MPI_INC=$(usex mpi '' "-I../STUBS") \ + MPI_PATH=$(usex mpi '' '-L../STUBS') \ + MPI_LIB=$(usex mpi '' '-lmpi_stubs') \ + "$@" +} + +src_compile() { + # Compile stubs for serial version. + use mpi || lmp_emake -C src stubs + + # Build optional packages. + if use package-meam; then + lmp_emake -C src yes-meam + lmp_emake -j1 -C lib/meam -f Makefile.gfortran + fi + use package-dipole && emake -C src yes-dipole + use package-rigid && emake -C src yes-rigid + + # Compile. + lmp_emake -C src serial +} + +src_install() { + newbin "src/lmp_serial" "lmp" + + local LAMMPS_POTENTIALS="/usr/share/${PF}/potentials" + insinto "${LAMMPS_POTENTIALS}" + doins potentials/* + echo "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS}" > 99lammps + doenvd 99lammps + + if use examples; then + local LAMMPS_EXAMPLES="/usr/share/${PF}/examples" + elog "The examples can be found in ${LAMMPS_EXAMPLES}" + insinto "${LAMMPS_EXAMPLES}" + doins -r examples/* + fi + + dodoc README + if use doc; then + dodoc doc/Manual.pdf + dohtml -r doc/* + fi +} diff --git a/sys-cluster/charm/ChangeLog b/sys-cluster/charm/ChangeLog index 60a0d00f3..618de1d01 100644 --- a/sys-cluster/charm/ChangeLog +++ b/sys-cluster/charm/ChangeLog @@ -2,6 +2,35 @@ # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 14 Sep 2013; Nicolas Bock <nicolasbock@gmail.com> + files/charm-6.5.1-fix-string-parsing.patch: + sys-cluster/charm-6.5.1: Small fix in patch to make printing less verbose. + + 11 Sep 2013; Nicolas Bock <nicolasbock@gmail.com> + files/charm-6.5.1-fix-string-parsing.patch: + sys-cluster/charm-6.5.1: Fix patch for the last time. + + 11 Sep 2013; Nicolas Bock <nicolasbock@gmail.com> + files/charm-6.5.1-fix-string-parsing.patch: + sys-cluster/charm-6.5.1-r1: Backported patch just added to correct upstream + version. + + 11 Sep 2013; Nicolas Bock <nicolasbock@gmail.com> + +files/charm-6.5.1-fix-string-parsing.patch, charm-6.5.1-r1.ebuild: + sys-cluster/charm-6.5.1-r1: Added patch from ticket 294. + +*charm-6.5.1-r1 (11 Sep 2013) + + 11 Sep 2013; Nicolas Bock <nicolasbock@gmail.com> +charm-6.5.1-r1.ebuild, + charm-6.5.1.ebuild: + Version bump to sys-cluster/charm-6.5.1-r1 to push CkMigrationMgr patch to + users. + + 11 Sep 2013; Nicolas Bock <nicolasbock@gmail.com> + +files/charm-6.5.1-CkReductionMgr.patch, charm-6.5.1.ebuild: + Added patch to fix bug in CkReductionMgr::reduceMessages(). This issues has + been reported upstream (issue #287). + 23 Jul 2013; Nicolas Bock <nicolasbock@gmail.com> +files/charm-6.5.1-cleanup-config.patch, charm-6.5.1.ebuild: sys-cluster/charm-6.5.1: Added patch to fix config.h The added patch diff --git a/sys-cluster/charm/charm-6.5.1-r1.ebuild b/sys-cluster/charm/charm-6.5.1-r1.ebuild new file mode 100644 index 000000000..25b056000 --- /dev/null +++ b/sys-cluster/charm/charm-6.5.1-r1.ebuild @@ -0,0 +1,195 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sys-cluster/charm/charm-6.5.0.ebuild,v 1.1 2013/06/26 23:58:38 ottxor Exp $ + +EAPI=5 + +inherit eutils flag-o-matic fortran-2 multilib toolchain-funcs + +DESCRIPTION="Message-passing parallel language and runtime system" +HOMEPAGE="http://charm.cs.uiuc.edu/" +SRC_URI="http://charm.cs.uiuc.edu/distrib/${P}.tar.gz" + +LICENSE="charm" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="charmdebug charmtracing charmproduction cmkopt doc examples mlogft mpi numa smp static-libs syncft tcp" + +RDEPEND="mpi? ( virtual/mpi )" +DEPEND=" + ${RDEPEND} + doc? ( + >=app-text/poppler-0.12.3-r3[utils] + dev-tex/latex2html + virtual/tex-base + )" + +REQUIRED_USE=" + cmkopt? ( !charmdebug !charmtracing ) + charmproduction? ( !charmdebug !charmtracing )" + +FORTRAN_STANDARD="90" + +get_opts() { + local CHARM_OPTS + + # TCP instead of default UDP for socket comunication + # protocol + CHARM_OPTS+="$(usex tcp ' tcp' '')" + + # enable direct SMP support using shared memory + CHARM_OPTS+="$(usex smp ' smp' '')" + + CHARM_OPTS+="$(usex mlogft ' mlogft' '')" + CHARM_OPTS+="$(usex syncft ' syncft' '')" + + # Build shared libraries by default. + CHARM_OPTS+=" --build-shared" + + if use charmproduction; then + CHARM_OPTS+=" --with-production" + else + if use charmdebug; then + CHARM_OPTS+=" --enable-charmdebug" + fi + + if use charmtracing; then + CHARM_OPTS+=" --enable-tracing --enable-tracing-commthread" + fi + fi + + CHARM_OPTS+="$(usex numa ' --with-numa' '')" + echo $CHARM_OPTS +} + +src_prepare() { + sed \ + -e "/CMK_CF90/s:f90:$(usex mpi "mpif90" "$(tc-getFC)"):g" \ + -e "/CMK_CXX/s:g++:$(usex mpi "mpic++" "$(tc-getCXX)"):g" \ + -e "/CMK_CC/s:gcc:$(usex mpi "mpicc" "$(tc-getCC)"):g" \ + -e '/CMK_F90_MODINC/s:-p:-I:g' \ + -e "/CMK_LD/s:\"$: ${LDFLAGS} \":g" \ + -i src/arch/$(usex mpi "mpi" "net")-linux*/*sh || die + + sed \ + -e "s:-o conv-cpm:${LDFLAGS} &:g" \ + -e "s:-o charmxi:${LDFLAGS} &:g" \ + -e "s:-o charmrun-silent:${LDFLAGS} &:g" \ + -e "s:-o charmrun-notify:${LDFLAGS} &:g" \ + -e "s:-o charmrun:${LDFLAGS} &:g" \ + -e "s:-o charmd_faceless:${LDFLAGS} &:g" \ + -e "s:-o charmd:${LDFLAGS} &:g" \ + -i \ + src/scripts/Makefile \ + src/arch/net/charmrun/Makefile || die + + # CMK optimization + use cmkopt && append-cppflags -DCMK_OPTIMIZE=1 + + # Fix QA notice. Filed report with upstream. + append-cflags -DALLOCA_H + + epatch "${FILESDIR}/charm-6.5.1-cleanup-config.patch" + epatch "${FILESDIR}/charm-6.5.1-CkReductionMgr.patch" + epatch "${FILESDIR}/charm-6.5.1-fix-string-parsing.patch" +} + +src_compile() { + # Build charmm++ first. + einfo "running ./build charm++ $(usex mpi 'mpi' 'net')-linux$(usex amd64 '-amd64' '') $(get_opts) ${MAKEOPTS} ${CFLAGS}" + ./build charm++ $(usex mpi "mpi" "net")-linux$(usex amd64 "-amd64" '') \ + $(get_opts) ${MAKEOPTS} ${CFLAGS} || die "Failed to build charm++" + + # make pdf/html docs + if use doc; then + cd "${S}"/doc + make doc || die "failed to create pdf/html docs" + fi +} + +src_test() { + make -C tests/charm++ test TESTOPTS="++local" || die +} + +src_install() { + # Make charmc play well with gentoo before we move it into /usr/bin. + epatch "${FILESDIR}/charm-6.5.0-charmc-gentoo.patch" + + sed -e "s|gentoo-include|${P}|" \ + -e "s|gentoo-libdir|$(get_libdir)|g" \ + -e "s|VERSION|${P}/VERSION|" \ + -i ./src/scripts/charmc || die "failed patching charmc script" + + # In the following, some of the files are symlinks to ../tmp which we need + # to dereference first (see bug 432834). + + local i + + # Install binaries. + for i in bin/*; do + if [[ -L ${i} ]]; then + i=$(readlink -e "${i}") || die + fi + dobin "${i}" + done + + # Install headers. + insinto /usr/include/${P} + for i in include/*; do + if [[ -L ${i} ]]; then + i=$(readlink -e "${i}") || die + fi + doins "${i}" + done + + # Install static libs. Charm has a lot of .o "libs" that it requires at + # runtime. + if use static-libs; then + for i in lib/*.{a,o}; do + if [[ -L ${i} ]]; then + i=$(readlink -e "${i}") || die + fi + dolib "${i}" + done + fi + + # Install shared libs. + for i in lib_so/*; do + if [[ -L ${i} ]]; then + i=$(readlink -e "${i}") || die + fi + dolib.so "${i}" + done + + # Basic docs. + dodoc CHANGES README + + # Install examples. + if use examples; then + find examples/ -name 'Makefile' | xargs sed \ + -r "s:(../)+bin/charmc:/usr/bin/charmc:" -i || \ + die "Failed to fix examples" + find examples/ -name 'Makefile' | xargs sed \ + -r "s:./charmrun:./charmrun ++local:" -i || \ + die "Failed to fix examples" + insinto /usr/share/doc/${PF}/examples + doins -r examples/charm++/* + fi + + # Install pdf/html docs + if use doc; then + cd "${S}"/doc + # Install pdfs. + insinto /usr/share/doc/${PF}/pdf + doins doc/pdf/* + # Install html. + docinto html + dohtml -r doc/html/* + fi +} + +pkg_postinst() { + einfo "Please test your charm installation by copying the" + einfo "content of /usr/share/doc/${PF}/examples to a" + einfo "temporary location and run 'make test'." +} diff --git a/sys-cluster/charm/files/charm-6.5.1-CkReductionMgr.patch b/sys-cluster/charm/files/charm-6.5.1-CkReductionMgr.patch new file mode 100644 index 000000000..8387180f0 --- /dev/null +++ b/sys-cluster/charm/files/charm-6.5.1-CkReductionMgr.patch @@ -0,0 +1,34 @@ +From f9cc5724818141201ba201e698c21aea62ecd362 Mon Sep 17 00:00:00 2001 +From: Nicolas Bock <nicolasbock@gmail.com> +Date: Thu, 5 Sep 2013 04:04:06 -0600 +Subject: [PATCH] Fixed bug in CkReductionMgr::reduceMessages(). + +The first contribution of a child node is a single message. In this case +CkReductionMgr::reduceMessages() simply returns the message without calling +the reducer. However, when using the CkReduction::set reducer this behavior is +incorrect, and instead the reducer should be called even for one single +message so that the message is wrapped into a setElement struct. In the +current implementation, the reduction becomes corrupted because the +CkReduction::set() method one tier up in the reduction sizes the remote +contribution incorrectly assuming a setElement struct and not a simple +message. +--- + src/ck-core/ckreduction.C | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/src/ck-core/ckreduction.C b/src/ck-core/ckreduction.C +index f2ac8cd..d94f5b1 100644 +--- a/src/ck-core/ckreduction.C ++++ b/src/ck-core/ckreduction.C +@@ -862,7 +862,7 @@ CkReductionMsg *CkReductionMgr::reduceMessages(void) + else + {//Use the reducer to reduce the messages + //if there is only one msg to be reduced just return that message +- if(nMsgs == 1){ ++ if(nMsgs == 1 && msgArr[0]->reducer != CkReduction::set) { + ret = msgArr[0]; + }else{ + if (msgArr[0]->reducer == CkReduction::random) { +-- +1.8.1.5 + diff --git a/sys-cluster/charm/files/charm-6.5.1-fix-string-parsing.patch b/sys-cluster/charm/files/charm-6.5.1-fix-string-parsing.patch new file mode 100644 index 000000000..06bdf0df1 --- /dev/null +++ b/sys-cluster/charm/files/charm-6.5.1-fix-string-parsing.patch @@ -0,0 +1,50 @@ +From 7a8bf20508f54a223c13e62c7c485a7de4aaeba0 Mon Sep 17 00:00:00 2001 +From: Nicolas Bock <nicolasbock@gmail.com> +Date: Wed, 11 Sep 2013 14:13:30 -0600 +Subject: [PATCH] charmrun.c: parsing of strings now parses "\n" into '\n' + +Since gdb lacks anything like ';' to separate several commands in one line, +the commands need to be separated by a newline character. I have added some +parsing logic so that the string "\n" will now be translated into the +character '\n'. +--- + src/arch/net/charmrun/charmrun.c | 24 ++++++++++++++++++++++-- + 1 file changed, 22 insertions(+), 2 deletions(-) + +diff --git a/src/arch/net/charmrun/charmrun.c b/src/arch/net/charmrun/charmrun.c +index 6837712..bf370c1 100644 +--- a/src/arch/net/charmrun/charmrun.c ++++ b/src/arch/net/charmrun/charmrun.c +@@ -454,8 +454,28 @@ static int pparam_setdef(def, value) + if (*p) return -1; + return 0; + case 's' : +- *def->where.s = strdup(value); +- return 0; ++ { ++ /* Parse input string and convert a literal "\n" into '\n'. */ ++ *def->where.s = (char*) calloc(strlen(value)+1, sizeof(char)); ++ char* parsed_value = (char*) *def->where.s; ++ int i; ++ int j = 0; ++ for(i = 0; i < strlen(value); i++) ++ { ++ if(i+1 < strlen(value)) ++ { ++ if(value[i] == '\\' && value[i+1] == 'n') ++ { ++ parsed_value[j++] = '\n'; ++ i++; ++ continue; ++ } ++ } ++ parsed_value[j++] = value[i]; ++ } ++ return 0; ++ } + case 'f' : + *def->where.f = strtol(value, &p, 10); + if (*p) return -1; +-- +1.8.1.5 + |