diff options
97 files changed, 1007 insertions, 967 deletions
diff --git a/app-admin/eselect/ChangeLog b/app-admin/eselect/ChangeLog index 47d1515ce..79d1aacfc 100644 --- a/app-admin/eselect/ChangeLog +++ b/app-admin/eselect/ChangeLog @@ -2,6 +2,14 @@ # Copyright 1999-2015 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 $ +*eselect-1.4.4-r102 (06 Jun 2015) + + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> +eselect-1.4.4-r102.ebuild, + -eselect-1.4.4-r100.ebuild, -eselect-1.4.4-r101.ebuild, + -files/eselect-1.4.2-alternatives.patch, + files/eselect-1.4.4-alternatives.patch: + app-admin/eselect: Add latest patch + *eselect-1.4.4-r101 (24 May 2015) 24 May 2015; Justin Lecher <jlec@gentoo.org> +eselect-1.4.4-r101.ebuild, diff --git a/app-admin/eselect/eselect-1.4.4-r100.ebuild b/app-admin/eselect/eselect-1.4.4-r100.ebuild deleted file mode 100644 index 8001cf173..000000000 --- a/app-admin/eselect/eselect-1.4.4-r100.ebuild +++ /dev/null @@ -1,72 +0,0 @@ -# Copyright 1999-2015 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="http://dev.gentoo.org/~ulm/eselect/${P}.tar.xz" - -LICENSE="GPL-2+ || ( GPL-2+ CC-BY-SA-3.0 )" -SLOT="0" -KEYWORDS="~alpha ~amd64 ~arm ~arm64 ~hppa ~ia64 ~m68k ~mips ~ppc ~ppc64 ~s390 ~sh ~sparc ~x86 ~ppc-aix ~amd64-fbsd ~sparc-fbsd ~x86-fbsd ~x64-freebsd ~x86-freebsd ~hppa-hpux ~ia64-hpux ~x86-interix ~amd64-linux ~arm-linux ~ia64-linux ~x86-linux ~ppc-macos ~x64-macos ~x86-macos ~m68k-mint ~sparc-solaris ~sparc64-solaris ~x64-solaris ~x86-solaris" -IUSE="doc emacs vim-syntax" - -RDEPEND="sys-apps/sed - || ( - sys-apps/coreutils - sys-freebsd/freebsd-bin - app-misc/realpath - )" -DEPEND="${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}"/${PN}-1.4.2-alternatives.patch - AT_M4DIR="." eautoreconf -} - -src_compile() { - emake - use doc && emake html -} - -src_install() { - emake DESTDIR="${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 || die - 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 "${EROOT}/var/lib/gentoo/news" - fi -} diff --git a/app-admin/eselect/eselect-1.4.4-r101.ebuild b/app-admin/eselect/eselect-1.4.4-r102.ebuild index 67b835c52..67b835c52 100644 --- a/app-admin/eselect/eselect-1.4.4-r101.ebuild +++ b/app-admin/eselect/eselect-1.4.4-r102.ebuild diff --git a/app-admin/eselect/files/eselect-1.4.2-alternatives.patch b/app-admin/eselect/files/eselect-1.4.2-alternatives.patch deleted file mode 100644 index 3f4a34bcf..000000000 --- a/app-admin/eselect/files/eselect-1.4.2-alternatives.patch +++ /dev/null @@ -1,616 +0,0 @@ -Index: bin/eselect.in -=================================================================== ---- bin/eselect.in (revision 863) -+++ bin/eselect.in (working copy) -@@ -22,10 +22,15 @@ - # Where are modules installed by default? - ESELECT_DEFAULT_MODULES_PATH="${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/app-admin/eselect/files/eselect-1.4.4-alternatives.patch b/app-admin/eselect/files/eselect-1.4.4-alternatives.patch index 71c2e67da..b2b943274 100644 --- a/app-admin/eselect/files/eselect-1.4.4-alternatives.patch +++ b/app-admin/eselect/files/eselect-1.4.4-alternatives.patch @@ -226,10 +226,10 @@ index 027ef73..a5fe373 100644 @$(dosed) $< > $@ diff --git a/libs/alternatives-common.bash.in b/libs/alternatives-common.bash.in new file mode 100644 -index 0000000..99de48e +index 0000000..64d74df --- /dev/null +++ b/libs/alternatives-common.bash.in -@@ -0,0 +1,372 @@ +@@ -0,0 +1,488 @@ +# Copyright 2015 Gentoo Foundation +# Copyright 2008 Mike Kelly +# Copyright 2009, 2013 David Leverton @@ -238,7 +238,7 @@ index 0000000..99de48e + +inherit config output path-manipulation + -+ALTERNATIVESDIR_ROOTLESS="@sysconfdir@/env.d/alternatives" ++: "${ALTERNATIVESDIR_ROOTLESS:=@sysconfdir@/env.d/alternatives}" +ALTERNATIVESDIR="${EROOT%/}${ALTERNATIVESDIR_ROOTLESS}" + +get_current_provider() { @@ -298,7 +298,8 @@ index 0000000..99de48e + [[ -d ${p} && ! -L ${p} ]] || continue + p=${p##*/} + -+ importance=$(< "${ALTERNATIVESDIR}/${ALTERNATIVE}/${p}/_importance") ++ [[ -e "${ALTERNATIVESDIR}/${ALTERNATIVE}/${p}/_importance" ]] && ++ importance=$(< "${ALTERNATIVESDIR}/${ALTERNATIVE}/${p}/_importance") + importance=${importance:-0} + [[ "${importance}" =~ ^[0123456789]+(\.[0123456789]+)*$ ]] || die "_importance (${importance}) for ${p} is not a dot-separated list of integers" + @@ -466,6 +467,117 @@ index 0000000..99de48e + return 0 +} + ++### add action ### ++alternatives_describe_add() { ++ echo "Add provider to selected alternative" ++} ++ ++alternatives_describe_add_parameters() { ++ echo "<provider> <importance> <source> <target> [<source> <target> [...]]" ++} ++ ++alternatives_describe_add_options() { ++ echo "<provider> : the name of the alternative provider" ++ echo "<importance> : interger value, representing the importance of the provider" ++ echo "<source> : source of the symlink" ++ echo "<target> : destination for the symlink" ++} ++ ++alternatives_do_add() { ++ [[ -z "${ALTERNATIVE}" ]] && die "Need to set ALTERNATIVE in the eselect module" ++ ++ (( $# >= 4 )) && (( ($#-2)%2 == 0)) || \ ++ die "exactly 3+N*2 arguments where N>=1 required" ++ local provider=${1} ++ local importance=${2} ++ shift 2 ++ local index src target ret=0 ++ local provider_dir="${ALTERNATIVESDIR}/${ALTERNATIVE}/${provider}" ++ ++ # Creating base dir ++ if [[ ! -e "${provider_dir}" ]]; then ++ mkdir -p "${provider_dir}" || die "Failed to create ${provider_dir}" ++ elif [[ ! -d "${provider_dir}" ]]; then ++ die "${provider_dir} exists but is a file" ++ else ++ die "${provider_dir} already present. You need ot remove it before adding it again" ++ fi ++ ++ # Make sure importance is a signed integer ++ if [[ -n ${importance} ]] && ! [[ ${importance} =~ ^[0-9]+(\.[0-9]+)*$ ]]; then ++ die "Invalid importance (${importance}) detected" ++ else ++ # Setting importance ++ echo ${importance} > "${provider_dir}/_importance" ++ fi ++ ++ # Process source-target pairs ++ while (( $# >= 2 )); do ++ src=${1//+(\/)/\/}; target=${2//+(\/)/\/} ++ if [[ ${src} != /* ]]; then ++ die "Source path must be absolute, but got ${src}" ++ else ++ local reltarget= dir=${provider_dir}${src%/*} ++ while [[ -n ${dir} ]]; do ++ reltarget+=../ ++ dir=${dir%/*} ++ done ++ ++ reltarget=${reltarget%/} ++ [[ ${target} == /* ]] || reltarget+=${src%/*}/ ++ reltarget+=${target} ++ mkdir -p "${provider_dir}${src%/*}" || die "Failed to create ${provider_dir}${src%/*}" ++ ln -sf "${reltarget}" "${provider_dir}${src}" || die "Failed to create symlink" ++ # The -e test will fail if existing symlink points to non-existing target, ++ # so check for -L also. ++ # Say ${ED}/sbin/init exists and links to /bin/systemd (which doesn't exist yet). ++# if [[ -e ${ED}${src} || -L ${ED}${src} ]]; then ++# local fulltarget=${target} ++# [[ ${fulltarget} != /* ]] && fulltarget=${src%/*}/${fulltarget} ++# if [[ -e ${ED}${fulltarget} || -L ${ED}${fulltarget} ]]; then ++# die "${src} defined as provider for ${fulltarget}, but both already exist in \${ED}" ++# else ++# mv "${ED}${src}" "${ED}${fulltarget}" || die ++# fi ++# fi ++ fi ++ shift 2 ++ done ++} ++ ++alternatives_options_add() { ++ _options_parameters ${FUNCNAME#alternatives_} "$@" ++} ++ ++### remove action ### ++ ++alternatives_describe_remove() { ++ echo "Remove a provider for selected alternative" ++} ++ ++alternatives_describe_remove_parameters() { ++ echo "<provider>" ++} ++ ++alternatives_describe_remove_options() { ++ echo "<provider> : the name of the alternative provider to be removed" ++} ++ ++alternatives_do_remove() { ++ [[ -z "${ALTERNATIVE}" ]] && die "Need to set ALTERNATIVE in the eselect module" ++ ++ if [[ -d "${ALTERNATIVESDIR}/${ALTERNATIVE}/${provider}" ]]; then ++ rm -r "${ALTERNATIVESDIR}/${ALTERNATIVE}/${provider}" || \ ++ die "Failed to remove '${provider}' for '${ALTERNATIVE}'" ++ else ++ einfo "'${provider}' is not a provider for '${ALTERNATIVE}'" ++ fi ++} ++ ++alternatives_options_remove() { ++ _options_parameters ${FUNCNAME#alternatives_} "$@" ++} ++ +### update action ### + +# available in both "eselect alternatives" and individual modules @@ -502,6 +614,10 @@ index 0000000..99de48e + [[ -n ${best} && -n ${1} && -z ${ignore} ]] && die -q "Cannot specify both --best and a provider" + + if [[ -n ${best} ]] ; then ++ # set best provider ++ : # fall through to "switch to first available" loop below ++ elif [[ $# == "0" ]] && [[ -z ${cur} ]]; then ++ # if nothing is specified + : # fall through to "switch to first available" loop below + elif [[ ${cur} == ${1} && -z ${ignore} ]]; then + # if current provider was just updated, reselect it since it could have changed @@ -541,13 +657,13 @@ index 0000000..99de48e + +alternatives_options_update() { + _options_parameters ${FUNCNAME#alternatives_} "$@" -+ if [[ -n ${ALTERNATIVE} ]]; then -+ get_providers -+ else -+ for alt in ${ALTERNATIVESDIR_ROOTLESS}/_*/*/_importance; do -+ echo ${alt} | cut -d/ -f5 -+ done | sort -u -+ fi ++ if [[ -n ${ALTERNATIVE} ]]; then ++ get_providers ++ else ++ for alt in ${ALTERNATIVESDIR_ROOTLESS}/_*/*/_importance; do ++ echo ${alt} | cut -d/ -f5 ++ done | sort -u ++ fi +} + +### unset action stub ### @@ -604,10 +720,10 @@ index 0000000..99de48e +# vim: set ft=eselect sw=4 sts=4 ts=4 et tw=80 : diff --git a/libs/alternatives.bash.in b/libs/alternatives.bash.in new file mode 100644 -index 0000000..c2512e1 +index 0000000..1b5a2b0 --- /dev/null +++ b/libs/alternatives.bash.in -@@ -0,0 +1,249 @@ +@@ -0,0 +1,293 @@ +# Copyright 2015 Gentoo Foundation +# Copyright 2008 Mike Kelly +# Copyright 2009, 2013 David Leverton @@ -726,6 +842,50 @@ index 0000000..c2512e1 + get_providers +} + ++### add action ### ++ ++describe_add() { ++ alternatives_describe_add ++} ++ ++describe_add_parameters() { ++ alternatives_describe_add_parameters ++} ++ ++describe_add_options() { ++ alternatives_describe_add_options ++} ++ ++do_add() { ++ alternatives_do_add ++ ++ # make sure we have something selected ++ eselect ${provider} show > /dev/null || eselect ${provider} update --best ++} ++ ++### remove action ### ++ ++describe_remove() { ++ alternatives_describe_remove ++} ++ ++describe_remove_parameters() { ++ alternatives_describe_remove_parameters ++} ++ ++describe_remove_options() { ++ alternatives_describe_remove_options ++} ++ ++do_remove() { ++ alternatives_do_remove ++ ++# if no provider is present, remove whole Alternative ++ if ! eselect ${provider} update --best > /dev/null; then ++ eselect alternatives remove ${ALTERNATIVE} ++ fi ++} ++ +### update action ### + +# all functions implemented in alternatives-common.bash as defined for @@ -803,7 +963,7 @@ index 0000000..c2512e1 + + local idx=${!} + if [[ ${idx} == +(-|+|[[:digit:]]) ]]; then -+ idx=${1#+(-|+)} ++ idx=${1#+(-|+)} + providers=( $(get_providers) ) + (( ${idx} <= ${#providers[@]} )) || die -q "The given provider with index (${idx}) does not exist" + provider=${providers[${idx}-1]} @@ -871,10 +1031,10 @@ index 73960c4..4da6465 100644 env.eselect \ diff --git a/modules/alternatives.eselect b/modules/alternatives.eselect new file mode 100644 -index 0000000..b1c219f +index 0000000..912bb3d --- /dev/null +++ b/modules/alternatives.eselect -@@ -0,0 +1,50 @@ +@@ -0,0 +1,165 @@ +# Copyright 2015 Gentoo Foundation +# Copyright 2008 Mike Kelly +# Copyright 2009, 2013 David Leverton @@ -896,11 +1056,11 @@ index 0000000..b1c219f + ENDOFTEXT +} + -+### update action ### -+ +# all functions implemented in alternatives-common.bash as defined for +# both "eselect alternatives" and individual modules + ++### update action ### ++ +describe_update() { + alternatives_describe_update +} @@ -925,6 +1085,121 @@ index 0000000..b1c219f + alternatives_options_update +} + ++### create action ### ++ ++describe_create() { ++ echo "Create a new alternative" ++} ++ ++describe_create_parameters() { ++ echo "<alternative>" ++} ++ ++describe_create_options() { ++ echo "<alternative> : the name of the alternative to create" ++} ++ ++do_create() { ++ [[ $# == 1 ]] || die "Need exactly one alternative name" ++ ++ local auto_dir="${ESELECT_AUTO_GENERATED_MODULES_PATH}" ++ local auto_file="${auto_dir}/${1}.eselect" ++ ++ if [[ ! -e "${auto_file}" ]]; then ++ if [[ ! -e "${auto_dir}" ]]; then ++ mkdir -p "${auto_dir}" || die "Failed to create ${auto_dir}" ++ elif [[ ! -d "${auto_dir}" ]]; then ++ die "${auto_dir} exists but is a file" ++ fi ++ cat >> ${auto_file} <<- ENDOFTEXT ++ DESCRIPTION="${DESCRIPTION} for ${1}" ++ VERSION="${VERSION}" ++ MAINTAINER="${MAINTAINER}" ++ ESELECT_MODULE_GROUP="Alternatives" ++ ++ ALTERNATIVE="${1}" ++ ++ inherit alternatives ++ ENDOFTEXT ++ fi ++} ++ ++### delete action ### ++ ++describe_delete() { ++ echo "Delete an existing alternative" ++} ++ ++describe_delete_parameters() { ++ echo "<alternative>" ++} ++ ++describe_delete_options() { ++ echo "<alternative> : the name of the alternative to delete" ++} ++ ++do_delete() { ++ [[ $# == 1 ]] || die "Need exactly one alternative name" ++ ++ local auto_dir="${ESELECT_AUTO_GENERATED_MODULES_PATH}" ++ local auto_file="${auto_dir}/${1}.eselect" ++ ++ if [[ -e "${auto_file}" ]]; then ++ rm "${auto_file}" || die "Failed to remove alternative: ${1}" ++ fi ++} ++ ++### add action ### ++ ++describe_add() { ++ alternatives_describe_add ++} ++ ++describe_add_parameters() { ++ echo "<alternative> $(alternatives_describe_add_parameters)" ++} ++ ++describe_add_options() { ++ echo "<alternative> : the name of the alternative to add a provider for" ++ alternatives_describe_add_options ++} ++ ++do_add() { ++ local ALTERNATIVE=$1 ++ shift ++ [[ -z "${ALTERNATIVE}" ]] && die -q "Missing required parameter 'alternative'" ++ alternatives_do_add "$@" ++} ++ ++options_add() { ++ alternatives_options_add ++} ++ ++### remove action ### ++ ++describe_remove() { ++ alternatives_describe_remove ++} ++ ++describe_remove_parameters() { ++ echo "<alternative> $(alternatives_describe_remove_parameters)" ++} ++ ++describe_remove_options() { ++ echo "<alternative> : the name of the alternative to remove a provider from" ++ alternatives_describe_remove_options ++} ++ ++do_remove() { ++ local ALTERNATIVE=$1 ++ shift ++ [[ -z "${ALTERNATIVE}" ]] && die -q "Missing required parameter 'alternative'" ++ alternatives_do_remove "$@" ++} ++ ++options_remove() { ++ alternatives_options_remove ++} diff --git a/modules/modules.eselect b/modules/modules.eselect index 038f630..eb73e16 100644 --- a/modules/modules.eselect diff --git a/app-misc/aa/ChangeLog b/app-misc/aa/ChangeLog new file mode 100644 index 000000000..e1e42cb39 --- /dev/null +++ b/app-misc/aa/ChangeLog @@ -0,0 +1,11 @@ +# ChangeLog for app-misc/aa +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 24 May 2015; Justin Lecher <jlec@gentoo.org> aa-0.ebuild: + app-misc/aa: Fix usage + +*aa-0 (24 May 2015) + + 24 May 2015; Justin Lecher <jlec@gentoo.org> +aa-0.ebuild, +metadata.xml: + app-misc/aa: Dummy package diff --git a/app-misc/aa/aa-0.ebuild b/app-misc/aa/aa-0.ebuild new file mode 100644 index 000000000..142e1c7a6 --- /dev/null +++ b/app-misc/aa/aa-0.ebuild @@ -0,0 +1,33 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit alternatives-2 + +DESCRIPTION="AA" +HOMEPAGE="http://www.gentoo.org" +SRC_URI="" + +SLOT="0" +LICENSE="BSD" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +RDEPEND="" +DEPEND="${RDEPEND} +" + +S="${WORKDIR}" + +src_install() { + cat > aa <<- EOF + #!/bin/bash + echo "aa" + EOF + + dobin aa + + alternatives_for alternatives-2 aa 0 /usr/bin/alternatives aa +} diff --git a/app-misc/aa/metadata.xml b/app-misc/aa/metadata.xml new file mode 100644 index 000000000..7bc6ee8ea --- /dev/null +++ b/app-misc/aa/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer> + <email>jlec@gentoo.org</email> + <name>Justin Lecher</name> + </maintainer> +</pkgmetadata> diff --git a/app-misc/bb/ChangeLog b/app-misc/bb/ChangeLog new file mode 100644 index 000000000..9b385c022 --- /dev/null +++ b/app-misc/bb/ChangeLog @@ -0,0 +1,11 @@ +# ChangeLog for app-misc/bb +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 24 May 2015; Justin Lecher <jlec@gentoo.org> bb-0.ebuild: + app-misc/bb: Fix usage + +*bb-0 (24 May 2015) + + 24 May 2015; Justin Lecher <jlec@gentoo.org> +bb-0.ebuild, +metadata.xml: + app-misc/bb: Dummy package diff --git a/app-misc/bb/bb-0.ebuild b/app-misc/bb/bb-0.ebuild new file mode 100644 index 000000000..befb22737 --- /dev/null +++ b/app-misc/bb/bb-0.ebuild @@ -0,0 +1,33 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit alternatives-2 + +DESCRIPTION="BB" +HOMEPAGE="http://www.gentoo.org" +SRC_URI="" + +SLOT="0" +LICENSE="BSD" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +RDEPEND="" +DEPEND="${RDEPEND} +" + +S="${WORKDIR}" + +src_install() { + cat > bb <<- EOF + #!/bin/bash + echo "bb" + EOF + + dobin bb + + alternatives_for alternatives-2 bb 0 /usr/bin/alternatives aa +} diff --git a/app-misc/bb/metadata.xml b/app-misc/bb/metadata.xml new file mode 100644 index 000000000..7bc6ee8ea --- /dev/null +++ b/app-misc/bb/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer> + <email>jlec@gentoo.org</email> + <name>Justin Lecher</name> + </maintainer> +</pkgmetadata> diff --git a/dev-cpp/icnc/ChangeLog b/dev-cpp/icnc/ChangeLog index 8de9e15ef..72d7f2105 100644 --- a/dev-cpp/icnc/ChangeLog +++ b/dev-cpp/icnc/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-cpp/icnc: Add github to remote-id in metadata.xml + 08 Feb 2015; Christoph Junghans <ottxor@gentoo.org> icnc-9999.ebuild: fix bug #539318 diff --git a/dev-cpp/icnc/metadata.xml b/dev-cpp/icnc/metadata.xml index 745b9e1ce..c3e80bdd7 100644 --- a/dev-cpp/icnc/metadata.xml +++ b/dev-cpp/icnc/metadata.xml @@ -1,8 +1,11 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <maintainer> - <email>ottxor@gentoo.org</email> - <name>Christoph Junghans</name> - </maintainer> + <maintainer> + <email>ottxor@gentoo.org</email> + <name>Christoph Junghans</name> + </maintainer> + <upstream> + <remote-id type="github">icnc/icnc</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-java/gluegen/ChangeLog b/dev-java/gluegen/ChangeLog index 4982a6bbb..d23d7be03 100644 --- a/dev-java/gluegen/ChangeLog +++ b/dev-java/gluegen/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-java/gluegen: Add github to remote-id in metadata.xml + 03 Apr 2015; Guillaume Horel <guillaume.horel@gmail.com> +files/2.2.4-dont-copy-jars.patch, +files/2.2.4-dont-strip.patch, +files/2.2.4-dont-test-archive.patch, gluegen-2.2.4.ebuild: diff --git a/dev-java/gluegen/metadata.xml b/dev-java/gluegen/metadata.xml index d29f3a9fd..d6bbcc249 100644 --- a/dev-java/gluegen/metadata.xml +++ b/dev-java/gluegen/metadata.xml @@ -13,4 +13,7 @@ on the IR before glue code emission. GlueGen is currently powerful enough to bind even low-level APIs such as the Java Native Interface (JNI) and the AWT Native Interface (JAWT) back up to the Java programming language. </longdescription> + <upstream> + <remote-id type="github">sgothel/gluegen</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-java/jogl/ChangeLog b/dev-java/jogl/ChangeLog index 84ec1abb4..411673c12 100644 --- a/dev-java/jogl/ChangeLog +++ b/dev-java/jogl/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-java/jogl: Add github to remote-id in metadata.xml + 03 Apr 2015; Guillaume Horel <guillaume.horel@gmail.com> -files/disable-applet.diff, -files/jogl-2.2.4-notests.patch, jogl-2.2.4.ebuild: diff --git a/dev-java/jogl/metadata.xml b/dev-java/jogl/metadata.xml index 975a649d1..cb3e7c1dd 100644 --- a/dev-java/jogl/metadata.xml +++ b/dev-java/jogl/metadata.xml @@ -9,4 +9,7 @@ to provide hardware-supported 3D graphics to applications written in Java. <use> <flag name="cg">Enable NVidia Cg binding.</flag> </use> + <upstream> + <remote-id type="github">sgothel/jogl</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-lang/ispc/ChangeLog b/dev-lang/ispc/ChangeLog index 529d48d08..afec6c690 100644 --- a/dev-lang/ispc/ChangeLog +++ b/dev-lang/ispc/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for dev-lang/ispc -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-lang/ispc: Add github to remote-id in metadata.xml + 25 Oct 2014; Christoph Junghans <ottxor@gentoo.org> ispc-9999.ebuild: sync with gx86 diff --git a/dev-lang/ispc/metadata.xml b/dev-lang/ispc/metadata.xml index 06c3d15a6..4663d3aa7 100644 --- a/dev-lang/ispc/metadata.xml +++ b/dev-lang/ispc/metadata.xml @@ -5,4 +5,7 @@ <email>ottxor@gentoo.org</email> <name>Christoph Junghans</name> </maintainer> + <upstream> + <remote-id type="github">ispc/ispc</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-lang/terra/ChangeLog b/dev-lang/terra/ChangeLog index 32af2a21d..817b66bb0 100644 --- a/dev-lang/terra/ChangeLog +++ b/dev-lang/terra/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-lang/terra: Add github to remote-id in metadata.xml + *terra-2015.03.12 (24 Apr 2015) 24 Apr 2015; Christoph Junghans <ottxor@gentoo.org> +metadata.xml, diff --git a/dev-lang/terra/metadata.xml b/dev-lang/terra/metadata.xml index 745b9e1ce..2e41c46b1 100644 --- a/dev-lang/terra/metadata.xml +++ b/dev-lang/terra/metadata.xml @@ -1,8 +1,11 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <maintainer> - <email>ottxor@gentoo.org</email> - <name>Christoph Junghans</name> - </maintainer> + <maintainer> + <email>ottxor@gentoo.org</email> + <name>Christoph Junghans</name> + </maintainer> + <upstream> + <remote-id type="github">zdevito/terra</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-libs/utf8proc/ChangeLog b/dev-libs/utf8proc/ChangeLog index 77d9155e2..758f69e9a 100644 --- a/dev-libs/utf8proc/ChangeLog +++ b/dev-libs/utf8proc/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-libs/utf8proc: Add github to remote-id in metadata.xml + *utf8proc-1.2-r1 (25 May 2015) 25 May 2015; Justin Lecher <jlec@gentoo.org> +utf8proc-1.2-r1.ebuild, diff --git a/dev-libs/utf8proc/metadata.xml b/dev-libs/utf8proc/metadata.xml index 740304bf0..4d104ac19 100644 --- a/dev-libs/utf8proc/metadata.xml +++ b/dev-libs/utf8proc/metadata.xml @@ -11,4 +11,7 @@ (U+2212) and “Hyphen-Minus” (U+002D, ASCII Minus) all into the ASCII minus sign, to make them equal for comparisons. </longdescription> + <upstream> + <remote-id type="github">JuliaLang/utf8proc</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/RecSQL/ChangeLog b/dev-python/RecSQL/ChangeLog index ef054f357..e995523c0 100644 --- a/dev-python/RecSQL/ChangeLog +++ b/dev-python/RecSQL/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for dev-python/RecSQL -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-python/RecSQL: Add github to remote-id in metadata.xml + 06 Jan 2014; Justin Lecher <jlec@gentoo.org> RecSQL-9999.ebuild: Switch from git-2 to git-r3 diff --git a/dev-python/RecSQL/metadata.xml b/dev-python/RecSQL/metadata.xml index 098ac091a..ba2081c24 100644 --- a/dev-python/RecSQL/metadata.xml +++ b/dev-python/RecSQL/metadata.xml @@ -6,4 +6,7 @@ <email>alexxy@gentoo.org</email> <name>Alexey Shvetsov</name> </maintainer> + <upstream> + <remote-id type="github">orbeckst/RecSQL</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/pysolar/ChangeLog b/dev-python/pysolar/ChangeLog index a103d4a14..1c538ff17 100644 --- a/dev-python/pysolar/ChangeLog +++ b/dev-python/pysolar/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for dev-python/pysolar -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-python/pysolar: Add github to remote-id in metadata.xml + 23 Jul 2013; Sébastien Fabbro <bicatali@gentoo.org> -pysolar-0.4.4.ebuild, metadata.xml, pysolar-0.5.ebuild: dev-python/pysolar: Fixed syntax, removed old, keyword for prefix diff --git a/dev-python/pysolar/metadata.xml b/dev-python/pysolar/metadata.xml index 96827aac9..072ad7c77 100644 --- a/dev-python/pysolar/metadata.xml +++ b/dev-python/pysolar/metadata.xml @@ -1,15 +1,16 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci-astronomy</herd> -<longdescription lang="en"> + <herd>sci-astronomy</herd> + <longdescription lang="en"> Pysolar is a collection of Python libraries for simulating the irradiation of any point on earth by the sun. It includes code for extremely precise ephemeris calculations, and more. Pysolar can calculate the location of the sun or the shading percentage as a function of time for a row of 2-axis tracked panels. </longdescription> -<upstream> - <remote-id type="pypi">Pysolar</remote-id> -</upstream> + <upstream> + <remote-id type="pypi">Pysolar</remote-id> + <remote-id type="github">pingswept/pysolar</remote-id> + </upstream> </pkgmetadata> diff --git a/eclass/alternatives-2.eclass b/eclass/alternatives-2.eclass index 5a7eb6cc2..4fcf67295 100644 --- a/eclass/alternatives-2.eclass +++ b/eclass/alternatives-2.eclass @@ -21,17 +21,17 @@ # sure you explicitly run alternatives-2_pkg_{postinst,prerm} where appropriate. case "${EAPI:-0}" in - 0|1|2|3) + 0|1|2|3|4) die "Unsupported EAPI=${EAPI:-0} (too old) for ${ECLASS}" ;; - 4|5) + 5) ;; *) die "Unsupported EAPI=${EAPI} (unknown) for ${ECLASS}" ;; esac -DEPEND=">=app-admin/eselect-1.4.4-r100" +DEPEND=">=app-admin/eselect-1.4.4-r102" RDEPEND="${DEPEND} !app-admin/eselect-blas !app-admin/eselect-cblas @@ -56,87 +56,12 @@ ALTERNATIVES_DIR="/etc/env.d/alternatives" alternatives_for() { debug-print-function ${FUNCNAME} "${@}" - (( $# >= 5 )) && (( ($#-3)%2 == 0)) || \ - die "${FUNCNAME} requires exactly 3+N*2 arguments where N>=1" - local alternative=${1} provider=${2} importance=${3} index src target ret=0 - shift 3 + dodir /etc/env.d/alternatives - # Make sure importance is a signed integer - if [[ -n ${importance} ]] && ! [[ ${importance} =~ ^[0-9]+(\.[0-9]+)*$ ]]; then - eerror "Invalid importance (${importance}) detected" - ((ret++)) - fi - - # Create alternative provider subdirectories under ALTERNATIVES_DIR if needed - [[ -d "${ED}${ALTERNATIVES_DIR}/${alternative}/${provider}" ]] || \ - dodir "${ALTERNATIVES_DIR}/${alternative}/${provider}" - - # Keep track of provided alternatives for use in pkg_{postinst,prerm}. - # Keep a mapping between importance and provided alternatives - # and make sure the former is set to only one value. - if ! has "${alternative}:${provider}" "${ALTERNATIVES_PROVIDED[@]}"; then - # Add new provider and set its importance - index=${#ALTERNATIVES_PROVIDED[@]} - ALTERNATIVES_PROVIDED+=( "${alternative}:${provider}" ) - ALTERNATIVES_IMPORTANCE[index]=${importance} - [[ -n ${importance} ]] && \ - echo "${importance}" > "${ED}${ALTERNATIVES_DIR}/${alternative}/${provider}/_importance" - else - # Set importance for existing provider - for ((index=0;index<${#ALTERNATIVES_PROVIDED[@]};index++)); do - if [[ ${alternative}:${provider} == ${ALTERNATIVES_PROVIDED[index]} ]]; then - if [[ -n ${ALTERNATIVES_IMPORTANCE[index]} ]]; then - if [[ -n ${importance} && ${ALTERNATIVES_IMPORTANCE[index]} != ${importance} ]]; then - eerror "Differing importance (${ALTERNATIVES_IMPORTANCE[index]} != ${importance}) detected" - ((ret++)) - fi - else - ALTERNATIVES_IMPORTANCE[index]=${importance} - [[ -n ${importance} ]] && \ - echo "${importance}" > "${ED}${ALTERNATIVES_DIR}/${alternative}/${provider}/_importance" - fi - fi - done - fi + ALTERNATIVESDIR_ROOTLESS="${ED}/etc/env.d/alternatives" \ + eselect alternatives add ${@} || die - # Process source-target pairs - while (( $# >= 2 )); do - src=${1//+(\/)/\/}; target=${2//+(\/)/\/} - if [[ ${src} != /* ]]; then - eerror "Source path must be absolute, but got ${src}" - ((ret++)) - - else - local reltarget= dir=${ALTERNATIVES_DIR}/${alternative}/${provider}${src%/*} - while [[ -n ${dir} ]]; do - reltarget+=../ - dir=${dir%/*} - done - - reltarget=${reltarget%/} - [[ ${target} == /* ]] || reltarget+=${src%/*}/ - reltarget+=${target} - dodir "${ALTERNATIVES_DIR}/${alternative}/${provider}${src%/*}" - dosym "${reltarget}" "${ALTERNATIVES_DIR}/${alternative}/${provider}${src}" - - # The -e test will fail if existing symlink points to non-existing target, - # so check for -L also. - # Say ${ED}/sbin/init exists and links to /bin/systemd (which doesn't exist yet). - if [[ -e ${ED}${src} || -L ${ED}${src} ]]; then - local fulltarget=${target} - [[ ${fulltarget} != /* ]] && fulltarget=${src%/*}/${fulltarget} - if [[ -e ${ED}${fulltarget} || -L ${ED}${fulltarget} ]]; then - die "${src} defined as provider for ${fulltarget}, but both already exist in \${ED}" - else - mv "${ED}${src}" "${ED}${fulltarget}" || die - fi - fi - fi - shift 2 - done - - # Stop if there were any errors - [[ ${ret} -eq 0 ]] || die "Errors detected for ${provider}, provided for ${alternative}" + ALTERNATIVES_CREATED+=( ${1} ) } # @FUNCTION: cleanup_old_alternatives_module @@ -151,7 +76,7 @@ cleanup_old_alternatives_module() { if [[ -f "${old_module}" && $(grep 'ALTERNATIVE=' "${old_module}" | cut -d '=' -f 2) == "${alt}" ]]; then local version="$(grep 'VERSION=' "${old_module}" | grep -o '[0-9.]\+')" if [[ "${version}" == "0.1" || "${version}" == "20080924" ]]; then - echo "rm ${old_module}" + einfo "rm ${old_module}" rm "${old_module}" || eerror "rm ${old_module} failed" fi fi @@ -168,30 +93,12 @@ cleanup_old_alternatives_module() { alternatives-2_pkg_postinst() { debug-print-function ${FUNCNAME} "${@}" - local a alt provider module_version="20150521" - local EAUTO="${EROOT%/}/usr/share/eselect/modules/auto" - - for a in "${ALTERNATIVES_PROVIDED[@]}"; do - alt="${a%:*}" - provider="${a#*:}" - if [[ ! -f "${EAUTO}/${alt}.eselect" \ - || "$(grep '^VERSION=' "${EAUTO}/${alt}.eselect" | grep -o '[0-9]\+')" \ - -ne "${module_version}" ]]; then - if [[ ! -d ${EAUTO} ]]; then - install -d "${EAUTO}" || eerror "Could not create eselect modules dir" - fi - einfo "Creating alternatives eselect module for ${alt}" - cat > "${EAUTO}/${alt}.eselect" <<- EOF - # This module was automatically generated by alternatives-2.eclass - DESCRIPTION="Alternatives for ${alt}" - VERSION="${module_version}" - MAINTAINER="eselect@gentoo.org" - ESELECT_MODULE_GROUP="Alternatives" - - ALTERNATIVE="${alt}" - - inherit alternatives - EOF + local alt + + for alt in ${ALTERNATIVES_CREATED[@]}; do + if ! eselect ${alt} show > /dev/null; then + einfo "Creating Alternative for ${alt}" + eselect alternatives create ${alt} fi # Set alternative provider if there is no valid provider selected @@ -211,25 +118,20 @@ alternatives-2_pkg_postinst() { alternatives-2_pkg_prerm() { debug-print-function ${FUNCNAME} "${@}" - local a alt provider ignore ret - local EAUTO="${EROOT%/}/usr/share/eselect/modules/auto" + local alt ret # If we are uninstalling, update alternatives to valid provider [[ -n ${REPLACED_BY_VERSION} ]] || ignore="--ignore" - for a in "${ALTERNATIVES_PROVIDED[@]}"; do - alt="${a%:*}" - provider="${a#*:}" + + for alt in ${ALTERNATIVES_CREATED[@]}; do eselect "${alt}" update ${ignore} "${provider}" - ret=$? - [[ -n ${REPLACED_BY_VERSION} ]] || \ - einfo "Removing ${provider} alternative module for ${alt}, current is $(eselect ${alt} show)" + case ${ret} in 0) : ;; 2) # This was last provider for the alternative, remove eselect module einfo "Cleaning up unused alternatives module for ${alt}" - rm "${EAUTO}/${alt}.eselect" || \ - eerror "rm ${EAUTO}/${alt}.eselect failed" + eselect alternatives delete "${alt}" || eerror "Failed to remove ${alt}" ;; *) eerror "eselect ${alt} update ${provider} returned ${ret}" diff --git a/sci-biology/TransDecoder/ChangeLog b/sci-biology/TransDecoder/ChangeLog index 6fd8f5c4c..4e2164c0b 100644 --- a/sci-biology/TransDecoder/ChangeLog +++ b/sci-biology/TransDecoder/ChangeLog @@ -1,7 +1,10 @@ -# ChangeLog for sci-biology/transdecoder +# ChangeLog for sci-biology/TransDecoder # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-biology/TransDecoder: Add github to remote-id in metadata.xml + 27 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> transdecoder-2.0.1.ebuild: sci-biology/transdecoder: more ebuild cleanup diff --git a/sci-biology/TransDecoder/metadata.xml b/sci-biology/TransDecoder/metadata.xml index 2bc893037..33de46b4c 100644 --- a/sci-biology/TransDecoder/metadata.xml +++ b/sci-biology/TransDecoder/metadata.xml @@ -6,4 +6,7 @@ <email>mmokrejs@fold.natur.cuni.cz</email> <name>Martin Mokrejs</name> </maintainer> + <upstream> + <remote-id type="github">TransDecoder/TransDecoder</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/Trinotate/ChangeLog b/sci-biology/Trinotate/ChangeLog index 4ef519a5f..86519b975 100644 --- a/sci-biology/Trinotate/ChangeLog +++ b/sci-biology/Trinotate/ChangeLog @@ -2,6 +2,12 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> Trinotate-2.0.1.ebuild: + sci-biology/Trinotate: Fix whitespaces + + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-biology/Trinotate: Add github to remote-id in metadata.xml + *Trinotate-2.0.1 (30 Apr 2015) 30 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> diff --git a/sci-biology/Trinotate/Trinotate-2.0.1.ebuild b/sci-biology/Trinotate/Trinotate-2.0.1.ebuild index 8665fb403..0cf111604 100644 --- a/sci-biology/Trinotate/Trinotate-2.0.1.ebuild +++ b/sci-biology/Trinotate/Trinotate-2.0.1.ebuild @@ -35,8 +35,8 @@ RDEPEND="${DEPEND} # $HMMSEARCH_BINARY = "/path/to/hmmsearch2"; src_install(){ - perl_set_version - dobin Trinotate + perl_set_version + dobin Trinotate insinto /usr/share/"${PN}" doins -r admin java sample_data util TrinotateWeb insinto ${VENDOR_LIB}/${PN} diff --git a/sci-biology/Trinotate/metadata.xml b/sci-biology/Trinotate/metadata.xml index 2bc893037..2fa34fe9c 100644 --- a/sci-biology/Trinotate/metadata.xml +++ b/sci-biology/Trinotate/metadata.xml @@ -6,4 +6,7 @@ <email>mmokrejs@fold.natur.cuni.cz</email> <name>Martin Mokrejs</name> </maintainer> + <upstream> + <remote-id type="github">Trinotate/Trinotate</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/bcftools/ChangeLog b/sci-biology/bcftools/ChangeLog index f8f7b58ac..a53d27c16 100644 --- a/sci-biology/bcftools/ChangeLog +++ b/sci-biology/bcftools/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-biology/bcftools: Add github to remote-id in metadata.xml + *bcftools-1.2 (02 Mar 2015) 02 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> diff --git a/sci-biology/bcftools/metadata.xml b/sci-biology/bcftools/metadata.xml index 2bc893037..39c1d32fa 100644 --- a/sci-biology/bcftools/metadata.xml +++ b/sci-biology/bcftools/metadata.xml @@ -6,4 +6,7 @@ <email>mmokrejs@fold.natur.cuni.cz</email> <name>Martin Mokrejs</name> </maintainer> + <upstream> + <remote-id type="github">samtools/bcftools</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/bedtools/ChangeLog b/sci-biology/bedtools/ChangeLog index a36ef570b..e72833e57 100644 --- a/sci-biology/bedtools/ChangeLog +++ b/sci-biology/bedtools/ChangeLog @@ -2,6 +2,12 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> bedtools-2.22.1.ebuild: + sci-biology/bedtools: Bump to EAPI=5 + + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-biology/bedtools: Add github to remote-id in metadata.xml + *bedtools-2.22.1 (14 Jan 2015) 14 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> diff --git a/sci-biology/bedtools/bedtools-2.22.1.ebuild b/sci-biology/bedtools/bedtools-2.22.1.ebuild index df72ec7b3..97a20b3f7 100644 --- a/sci-biology/bedtools/bedtools-2.22.1.ebuild +++ b/sci-biology/bedtools/bedtools-2.22.1.ebuild @@ -2,7 +2,7 @@ # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI=4 +EAPI=5 inherit flag-o-matic diff --git a/sci-biology/bedtools/metadata.xml b/sci-biology/bedtools/metadata.xml index d841c4bcb..6edffa4a6 100644 --- a/sci-biology/bedtools/metadata.xml +++ b/sci-biology/bedtools/metadata.xml @@ -12,5 +12,6 @@ </longdescription> <upstream> <remote-id type="google-code">bedtools</remote-id> + <remote-id type="github">arq5x/bedtools2</remote-id> </upstream> </pkgmetadata> diff --git a/sci-biology/fastx_toolkit/ChangeLog b/sci-biology/fastx_toolkit/ChangeLog index f233c5472..931fa7947 100644 --- a/sci-biology/fastx_toolkit/ChangeLog +++ b/sci-biology/fastx_toolkit/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-biology/fastx_toolkit -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-biology/fastx_toolkit: Add github to remote-id in metadata.xml + *fastx_toolkit-0.0.14 (20 Jan 2014) 20 Jan 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> diff --git a/sci-biology/fastx_toolkit/metadata.xml b/sci-biology/fastx_toolkit/metadata.xml index 897aa2e6b..bd98b5829 100644 --- a/sci-biology/fastx_toolkit/metadata.xml +++ b/sci-biology/fastx_toolkit/metadata.xml @@ -2,4 +2,7 @@ <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <herd>sci</herd> + <upstream> + <remote-id type="github">agordon/fastx_toolkit</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/ffindex/ChangeLog b/sci-biology/ffindex/ChangeLog index c82f67079..7dfb4b433 100644 --- a/sci-biology/ffindex/ChangeLog +++ b/sci-biology/ffindex/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-biology/ffindex: Add github to remote-id in metadata.xml + 25 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> ffindex-0.9.9.3.ebuild: sci-biology/ffindex: fix SRC_URI because TransDecoder which contains this diff --git a/sci-biology/ffindex/metadata.xml b/sci-biology/ffindex/metadata.xml index 2bc893037..33de46b4c 100644 --- a/sci-biology/ffindex/metadata.xml +++ b/sci-biology/ffindex/metadata.xml @@ -6,4 +6,7 @@ <email>mmokrejs@fold.natur.cuni.cz</email> <name>Martin Mokrejs</name> </maintainer> + <upstream> + <remote-id type="github">TransDecoder/TransDecoder</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/gffutils/ChangeLog b/sci-biology/gffutils/ChangeLog index 486a807cc..c61729349 100644 --- a/sci-biology/gffutils/ChangeLog +++ b/sci-biology/gffutils/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-biology/gffutils: Add github to remote-id in metadata.xml + 13 Apr 2015; Justin Lecher <jlec@gentoo.org> gffutils-0.8.3.ebuild: sci-biology/gffutils: Streamline ebuild diff --git a/sci-biology/gffutils/metadata.xml b/sci-biology/gffutils/metadata.xml index b7551a6aa..32143ba08 100644 --- a/sci-biology/gffutils/metadata.xml +++ b/sci-biology/gffutils/metadata.xml @@ -6,4 +6,7 @@ <email>mschu.dev@gmail.com</email> <name>Michael Schubert</name> </maintainer> + <upstream> + <remote-id type="github">daler/gffutils</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/igv/ChangeLog b/sci-biology/igv/ChangeLog index 20edbaead..243b3e9d4 100644 --- a/sci-biology/igv/ChangeLog +++ b/sci-biology/igv/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-biology/igv: Add github to remote-id in metadata.xml + *igv-2.3.52 (11 May 2015) 11 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> diff --git a/sci-biology/igv/metadata.xml b/sci-biology/igv/metadata.xml index fc7c76942..ddebe6007 100644 --- a/sci-biology/igv/metadata.xml +++ b/sci-biology/igv/metadata.xml @@ -6,4 +6,7 @@ <name>Andrey Kislyuk</name> </maintainer> <herd>sci-biology</herd> + <upstream> + <remote-id type="github">broadinstitute/IGV</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/metaseq/ChangeLog b/sci-biology/metaseq/ChangeLog index a61a470db..058230ae6 100644 --- a/sci-biology/metaseq/ChangeLog +++ b/sci-biology/metaseq/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-biology/metaseq: Add github to remote-id in metadata.xml + 13 Apr 2015; Justin Lecher <jlec@gentoo.org> metaseq-0.5.3.ebuild: sci-biology/metaseq: Streamline ebuild diff --git a/sci-biology/metaseq/metadata.xml b/sci-biology/metaseq/metadata.xml index b7551a6aa..8174cbd9e 100644 --- a/sci-biology/metaseq/metadata.xml +++ b/sci-biology/metaseq/metadata.xml @@ -6,4 +6,7 @@ <email>mschu.dev@gmail.com</email> <name>Michael Schubert</name> </maintainer> + <upstream> + <remote-id type="github">daler/metaseq</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/mira/ChangeLog b/sci-biology/mira/ChangeLog new file mode 100644 index 000000000..42555055d --- /dev/null +++ b/sci-biology/mira/ChangeLog @@ -0,0 +1,130 @@ +# ChangeLog for sci-biology/mira +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/mira/ChangeLog,v 1.31 2015/04/07 14:33:30 jlec Exp $ + + 25 Jan 2015; Justin Lecher <jlec@gentoo.org> mira-4.0.2.ebuild, + +files/mira-4.0.2-cout.patch: + Build fix for newer gcc, #537564 + +*mira-4.0.2 (23 Jan 2015) + + 23 Jan 2015; Justin Lecher <jlec@gentoo.org> +mira-4.0.2.ebuild: + Version Bump, thanks Martin Mokrejš for the work + + 23 Jan 2015; Justin Lecher <jlec@gentoo.org> mira-3.9.18.ebuild: + Add workaroung for m4 dir location, #536172 + + 14 Jan 2014; Justin Lecher <jlec@gentoo.org> -mira-3.2.1.ebuild: + Drop old + + 14 Jan 2014; Agostino Sarubbo <ago@gentoo.org> mira-3.9.18.ebuild: + Stable for x86, wrt bug #497218 + + 12 Jan 2014; Pacho Ramos <pacho@gentoo.org> mira-3.9.18.ebuild: + amd64 stable, bug #497218 + + 06 Jan 2014; Justin Lecher <jlec@gentoo.org> mira-3.2.1.ebuild: + Punt base.eclass + + 06 Jan 2014; Justin Lecher <jlec@gentoo.org> -mira-3.2.1-r1.ebuild, + -mira-3.4.0.2.ebuild: + Drop old + +*mira-3.9.18 (07 Jul 2013) + + 07 Jul 2013; Justin Lecher <jlec@gentoo.org> +mira-3.9.18.ebuild: + Version Bump; fixed compilation with dev-libs/boost-1.53.0 and some libtool + versions, #450322; thanks Martin Mokrejs for all his work + + 11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml: + Drop Andrey as maintainer so that bugs get assigned to sci-biology directly + +*mira-3.4.0.2 (07 Nov 2012) + + 07 Nov 2012; Justin Lecher <jlec@gentoo.org> mira-3.2.1.ebuild, + mira-3.2.1-r1.ebuild, +mira-3.4.0.2.ebuild, + +files/mira-3.4.0.2-boost-1.50.patch: + Version Bump, #377807 + +*mira-3.2.1-r1 (07 Nov 2012) + + 07 Nov 2012; Justin Lecher <jlec@gentoo.org> mira-3.2.1.ebuild, + +mira-3.2.1-r1.ebuild, +files/mira-3.2.1-boost-1.50.patch: + Fix for boost >1.50, #425468 + + 08 Jul 2012; Justin Lecher <jlec@gentoo.org> -mira-3.0.5.ebuild, + -mira-3.2.0.ebuild: + Drop old + + 25 Jun 2012; Jeff Horelick <jdhore@gentoo.org> mira-3.2.1.ebuild: + marked x86 per bug 418439 + + 24 Jun 2012; Agostino Sarubbo <ago@gentoo.org> mira-3.2.1.ebuild: + Stable for amd64, wrt bug #418439 + + 23 Jun 2012; Kacper Kowalik <xarthisius.kk@gmail.com> mira-3.2.1.ebuild: + Don't install docs that are no longer there, thanks to David Abbott for the + patch + +*mira-3.2.1 (21 May 2011) + + 21 May 2011; Andrey Kislyuk <weaver@gentoo.org> +mira-3.2.1.ebuild: + Version bump and fix bug 367921 + + 11 Feb 2011; Markos Chandras <hwoarang@gentoo.org> mira-3.2.0.ebuild: + Stable on amd64 wrt bug #353568 + + 07 Feb 2011; Pawel Hajdan jr <phajdan.jr@gentoo.org> mira-3.2.0.ebuild: + x86 stable wrt bug #353568 + + 17 Oct 2010; Andrey Kislyuk <weaver@gentoo.org> mira-3.2.0.ebuild: + Remove doc USE flag and dependency, workaround for bug 340419 + +*mira-3.2.0 (26 Sep 2010) + + 26 Sep 2010; Andrey Kislyuk <weaver@gentoo.org> -mira-3.0.0.ebuild, + -mira-3.0.3.ebuild, +mira-3.2.0.ebuild: + Version bump, drop old + + 28 Jun 2010; Justin Lecher <jlec@gentoo.org> mira-3.0.0.ebuild, + mira-3.0.3.ebuild, mira-3.0.5.ebuild: + Prepared for prefix, #325929 + +*mira-3.0.5 (05 May 2010) + + 05 May 2010; Andrey Kislyuk <weaver@gentoo.org> +mira-3.0.5.ebuild: + Version bump + +*mira-3.0.3 (18 Mar 2010) + + 18 Mar 2010; Andrey Kislyuk <weaver@gentoo.org> -mira-3.0.2.ebuild, + +mira-3.0.3.ebuild: + Hotfix from upstream + +*mira-3.0.2 (10 Mar 2010) + + 10 Mar 2010; Andrey Kislyuk <weaver@gentoo.org> -mira-3.0.1.ebuild, + +mira-3.0.2.ebuild: + Hotfix from upstream + +*mira-3.0.1 (06 Mar 2010) + + 06 Mar 2010; Andrey Kislyuk <weaver@gentoo.org> +mira-3.0.1.ebuild: + Version bump (bugfix release) + + 25 Feb 2010; Samuli Suominen <ssuominen@gentoo.org> mira-3.0.0.ebuild, + +files/mira-3.0.0-asneeded.patch: + Fix ax_lib_expat.m4 macro to not use LDFLAGS for passing libraries wrt + #305547 by Kacper Kowalik. + + 03 Feb 2010; Andrey Kislyuk <weaver@gentoo.org> mira-3.0.0.ebuild: + add eautoreconf + + 03 Feb 2010; Andrey Kislyuk <weaver@gentoo.org> mira-3.0.0.ebuild: + Install 3rd party files + +*mira-3.0.0 (02 Feb 2010) + + 02 Feb 2010; Andrey Kislyuk <weaver@gentoo.org> +metadata.xml, + +mira-3.0.0.ebuild: + New package, ebuild written by me diff --git a/sci-biology/mira/Manifest b/sci-biology/mira/Manifest new file mode 100644 index 000000000..a095295dd --- /dev/null +++ b/sci-biology/mira/Manifest @@ -0,0 +1,2 @@ +DIST mira-4.9.5.tar.bz2 10444005 SHA256 07160f9847edcb5109fa9085109f73a18849473fc2afdcda1118faf3c5fc3d77 SHA512 f56bd9e1c6982b501534bc8c64fed0ed81f20505546d6e79b48cfed3d82780a43691e985f5be3910af55adf12a955dbf1901cb1da1f182636d5e1357d8129cf8 WHIRLPOOL be0abe4213ecbe40534bee65dba390ac3695d3763123ad93c4a32bbcded15aa2f99ef93304b8e4cdc65728f0859e2748ad828826919bf7e4fc6b8499bccbdf9c +DIST mira_3rdparty_06-07-2012.tar.bz2 31656 SHA256 53cbbb9d57e2fa51706b3f1d055621c0863091542b8851f3ce8a45850951d7d2 SHA512 4d4dbdf7ab5126f9d47160bee8bc127b6a225de8087f6b9914c754324a74d966333207c86a3f38cf0ea9f91408707e2a24086dbe1318fdfa2870b0c39bc5033b WHIRLPOOL c9946ddc032d6864a33e7a60a4d1a515262ca2204535c7d81dcc73144b4f471f766007082d1912fc4ca219a9cbb4ac5a485451c625a7ffcc1949fb8574a3f3d2 diff --git a/sci-biology/mira/files/mira-3.4.0.2-boost-1.50.patch b/sci-biology/mira/files/mira-3.4.0.2-boost-1.50.patch new file mode 100644 index 000000000..427192294 --- /dev/null +++ b/sci-biology/mira/files/mira-3.4.0.2-boost-1.50.patch @@ -0,0 +1,24 @@ + config/m4/ax_boost_regex.m4 | 4 ++-- + 1 file changed, 2 insertions(+), 2 deletions(-) + +diff --git a/config/m4/ax_boost_regex.m4 b/config/m4/ax_boost_regex.m4 +index 1ac06af..5b7be93 100644 +--- a/config/m4/ax_boost_regex.m4 ++++ b/config/m4/ax_boost_regex.m4 +@@ -78,14 +78,14 @@ AC_DEFUN([AX_BOOST_REGEX], + for libextension in `ls $BOOSTLIBDIR/libboost_regex*.so* $BOOSTLIBDIR/libboost_regex*.a* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^lib\(boost_regex.*\)\.so.*$;\1;' -e 's;^lib\(boost_regex.*\)\.a*$;\1;'` ; do + ax_lib=${libextension} + AC_CHECK_LIB($ax_lib, exit, +- [BOOST_REGEX_LIB="-l$ax_lib"; AC_SUBST(BOOST_REGEX_LIB) link_regex="yes"; break], ++ [BOOST_REGEX_LIB="-l$ax_lib -lboost_system"; AC_SUBST(BOOST_REGEX_LIB) link_regex="yes"; break], + [link_regex="no"]) + done + if test "x$link_regex" != "xyes"; then + for libextension in `ls $BOOSTLIBDIR/boost_regex*.{dll,a}* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^\(boost_regex.*\)\.dll.*$;\1;' -e 's;^\(boost_regex.*\)\.a*$;\1;'` ; do + ax_lib=${libextension} + AC_CHECK_LIB($ax_lib, exit, +- [BOOST_REGEX_LIB="-l$ax_lib"; AC_SUBST(BOOST_REGEX_LIB) link_regex="yes"; break], ++ [BOOST_REGEX_LIB="-l$ax_lib -lboost_system"; AC_SUBST(BOOST_REGEX_LIB) link_regex="yes"; break], + [link_regex="no"]) + done + fi diff --git a/sci-biology/mira/files/mira-4.9.5-cout.patch b/sci-biology/mira/files/mira-4.9.5-cout.patch new file mode 100644 index 000000000..14feb0284 --- /dev/null +++ b/sci-biology/mira/files/mira-4.9.5-cout.patch @@ -0,0 +1,16 @@ + src/progs/quirks.C | 2 ++ + 1 file changed, 2 insertions(+) + +diff --git a/src/progs/quirks.C b/src/progs/quirks.C +index 47e5ee8..060b6f3 100644 +--- a/src/progs/quirks.C ++++ b/src/progs/quirks.C +@@ -25,6 +25,8 @@ + + #include <boost/filesystem.hpp> + ++#include <iostream> ++ + // make the "tcmalloc: large alloc" messages from TCMallom disappear + // by setting the reporting environment variable to a very large value + // see: http://groups.google.com/group/google-perftools/browse_thread/thread/24a003fc35f3d470?pli=1 diff --git a/sci-biology/mira/metadata.xml b/sci-biology/mira/metadata.xml new file mode 100644 index 000000000..f17a827e3 --- /dev/null +++ b/sci-biology/mira/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/mira/mira-4.9.5.ebuild b/sci-biology/mira/mira-4.9.5.ebuild new file mode 100644 index 000000000..e643b5b79 --- /dev/null +++ b/sci-biology/mira/mira-4.9.5.ebuild @@ -0,0 +1,79 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/mira/mira-4.0.2.ebuild,v 1.2 2015/01/25 17:04:35 jlec Exp $ + +EAPI=5 + +MIRA_3RDPARTY_PV="06-07-2012" +MY_PV="${PV/_}" # convert from mira-4.0_rc2 (Gentoo ebuild filename derived) to mira-4.0rc2 (upstream fromat) + +inherit autotools eutils multilib + +DESCRIPTION="Whole Genome Shotgun and EST Sequence Assembler for Sanger, 454 and Solexa / Illumina" +HOMEPAGE="http://www.chevreux.org/projects_mira.html" +SRC_URI=" + http://sourceforge.net/projects/mira-assembler/files/MIRA/development/"${PN}"-"${MY_PV}".tar.bz2 + mirror://sourceforge/mira-assembler/mira_3rdparty_${MIRA_3RDPARTY_PV}.tar.bz2" +# http://sourceforge.net/projects/mira-assembler/files/MIRA/stable/"${PN}"-"${MY_PV}".tar.bz2 +# http://sourceforge.net/projects/mira-assembler/files/MIRA/development/${P}.tar.bz2 +# mirror://sourceforge/mira-assembler/mira_3rdparty_${MIRA_3RDPARTY_PV}.tar.bz2" + +S="${WORKDIR}"/"${PN}"-"${MY_PV}" + +SLOT="0" +LICENSE="GPL-2" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x86-macos" +IUSE="doc" + +CDEPEND=" + dev-libs/boost + dev-util/google-perftools" +DEPEND="${CDEPEND} + app-editors/vim-core + dev-libs/expat" +RDEPEND="${CDEPEND}" + +#DOCS=( AUTHORS GETTING_STARTED NEWS README HELP_WANTED +# THANKS doc/3rdparty/scaffolding_MIRA_BAMBUS.pdf ) +DOCS=( AUTHORS GETTING_STARTED NEWS README HELP_WANTED THANKS ) + +# mira 4.9.x requires C++14 standard compliant compiler, so >=gcc-4.9.1 +src_prepare() { + find -name 'configure*' -or -name 'Makefile*' | xargs sed -i 's/flex++/flex -+/' || die + epatch \ + "${FILESDIR}"/${PN}-3.4.0.2-boost-1.50.patch \ + "${FILESDIR}"/${P}-cout.patch + + sed \ + -e "s:-O[23]::g" \ + -e "s:-funroll-loops::g" \ + -i configure.ac || die + + eautoreconf +} + +src_configure() { + econf \ + --with-boost="${EPREFIX}/usr/$(get_libdir)" \ + --with-boost-libdir="${EPREFIX}/usr/$(get_libdir)" \ + --with-boost-thread=boost_thread-mt +} + +#src_compile() { +# base_src_compile +# # TODO: resolve docbook incompatibility for building docs +# if use doc; then emake -C doc clean docs || die; fi +#} + +src_install() { + default + dodoc ${DOCS[@]} + + dobin "${WORKDIR}"/3rdparty/{sff_extract,qual2ball,*.pl} + dodoc "${WORKDIR}"/3rdparty/{README.txt,midi_screen.fasta} +} + +pkg_postinst() { + einfo "Documentation is no longer built, you can find it at:" + einfo "http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html" +} diff --git a/sci-biology/pybedtools/ChangeLog b/sci-biology/pybedtools/ChangeLog index d4cc4783b..2fb878ae1 100644 --- a/sci-biology/pybedtools/ChangeLog +++ b/sci-biology/pybedtools/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-biology/pybedtools: Add github to remote-id in metadata.xml + 13 Apr 2015; Justin Lecher <jlec@gentoo.org> pybedtools-0.6.9.ebuild: sci-biology/pybedtools: Streamline ebuild diff --git a/sci-biology/pybedtools/metadata.xml b/sci-biology/pybedtools/metadata.xml index b7551a6aa..3352804f1 100644 --- a/sci-biology/pybedtools/metadata.xml +++ b/sci-biology/pybedtools/metadata.xml @@ -6,4 +6,7 @@ <email>mschu.dev@gmail.com</email> <name>Michael Schubert</name> </maintainer> + <upstream> + <remote-id type="github">daler/pybedtools</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/trinityrnaseq/ChangeLog b/sci-biology/trinityrnaseq/ChangeLog index f4ce466b7..c8d81e0c1 100644 --- a/sci-biology/trinityrnaseq/ChangeLog +++ b/sci-biology/trinityrnaseq/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-biology/trinityrnaseq: Add github to remote-id in metadata.xml + 02 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> trinityrnaseq-2.0.6.ebuild: sci-biology/trinityrnaseq: added missing quotes diff --git a/sci-biology/trinityrnaseq/metadata.xml b/sci-biology/trinityrnaseq/metadata.xml index 2bc893037..5fa67e941 100644 --- a/sci-biology/trinityrnaseq/metadata.xml +++ b/sci-biology/trinityrnaseq/metadata.xml @@ -6,4 +6,7 @@ <email>mmokrejs@fold.natur.cuni.cz</email> <name>Martin Mokrejs</name> </maintainer> + <upstream> + <remote-id type="github">trinityrnaseq/trinityrnaseq</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-chemistry/GromacsWrapper/ChangeLog b/sci-chemistry/GromacsWrapper/ChangeLog index 7e3d83cec..eba252f5a 100644 --- a/sci-chemistry/GromacsWrapper/ChangeLog +++ b/sci-chemistry/GromacsWrapper/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-chemistry/GromacsWrapper -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-chemistry/GromacsWrapper: Add github to remote-id in metadata.xml + 06 Jan 2014; Justin Lecher <jlec@gentoo.org> GromacsWrapper-9999.ebuild: Switch from git-2 to git-r3 diff --git a/sci-chemistry/GromacsWrapper/metadata.xml b/sci-chemistry/GromacsWrapper/metadata.xml index 13ef0bf5a..43390c986 100644 --- a/sci-chemistry/GromacsWrapper/metadata.xml +++ b/sci-chemistry/GromacsWrapper/metadata.xml @@ -6,4 +6,7 @@ <email>alexxy@gentoo.org</email> <name>Alexey Shvetsov</name> </maintainer> + <upstream> + <remote-id type="github">orbeckst/GromacsWrapper</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-libs/clblas/ChangeLog b/sci-libs/clblas/ChangeLog index c6ea0b48a..e6656f8f5 100644 --- a/sci-libs/clblas/ChangeLog +++ b/sci-libs/clblas/ChangeLog @@ -2,6 +2,18 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*clblas-2.4-r1 (06 Jun 2015) + + 06 Jun 2015; Marius Brehler <marbre@linux.sungazer.de> +clblas-2.4-r1.ebuild, + +files/clblas-2.4-Install-cmake-configuration-to-lib-cmake-clBLAS.patch, + -clblas-2.4.ebuild, clblas-9999.ebuild: + sci-libs/clblas: Fix installation of cmake configuration + + 06 Jun 2015; Marius Brehler <marbre@linux.sungazer.de> -clblas-2.2.ebuild, + -files/clblas-2.2-client_CMakeLists.patch, + -files/clblas-2.2-library_tools_tune_CMakeLists.patch: + sci-libs/clblas: Drop old + 05 Jun 2015; Marius Brehler <marbre@linux.sungazer.de> clblas-2.2.ebuild, clblas-2.4.ebuild, clblas-9999.ebuild: sci-libs/clblas: Cleanup ebuilds diff --git a/sci-libs/clblas/Manifest b/sci-libs/clblas/Manifest index b54efe1eb..47dd24365 100644 --- a/sci-libs/clblas/Manifest +++ b/sci-libs/clblas/Manifest @@ -1,2 +1 @@ -DIST clblas-2.2.tar.gz 794888 SHA256 0563e028485d240f8b6e6efcae61677049627b19e924dcb1ef8014065b6416df SHA512 9f094845d854130d3901d639606069050da10a33b05985757d72188b2d8ef6e7836edc105f5ad8bf2d0922eb19e9a178388260b2a9da34e2fe27dc731233ec85 WHIRLPOOL 2f81de82d584ec4f2158c1165d02221cacf3775cdb9c96617ca2e3ea1fbb7844c833e50cbd8c7b2601585771ddb81a48795dd1534200806b560954a069cf4ec1 DIST clblas-2.4.tar.gz 800848 SHA256 3e9b8e138c465df1daff0235d9c93b0005986a7257a3739aea2d4c8b60b7ed37 SHA512 ae8c1fc1bef7573b12279977fc32f9e97c9b81b9167994ca6f352587a670dcee0f486ab2b7d5191092324f5e8fc00f9a2ea29303a026a0c1201be31d384cafe7 WHIRLPOOL a97537d7390055ad608eeac66679362956db7acfa96cf1165581ff8f9adfe309b8ff8231225bd8ca6247c8f588bff24d6f648e131cec52f8e3093168a3f26f82 diff --git a/sci-libs/clblas/clblas-2.2.ebuild b/sci-libs/clblas/clblas-2.2.ebuild deleted file mode 100644 index ff407df7f..000000000 --- a/sci-libs/clblas/clblas-2.2.ebuild +++ /dev/null @@ -1,64 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -PYTHON_COMPAT=( python2_7 ) - -inherit cmake-utils python-single-r1 - -MY_PN="clBLAS" - -DESCRIPTION="A software library containing BLAS routines for OpenCL" -HOMEPAGE="https://github.com/clMathLibraries/clBLAS" -SRC_URI="https://github.com/clMathLibraries/${MY_PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz" -KEYWORDS="~amd64" -S="${WORKDIR}/${MY_PN}-${PV}/src" - -LICENSE="Apache-2.0" -SLOT="0" -IUSE="+client examples +ktest performance test" - -RDEPEND=" - >=sys-devel/gcc-4.6:* - virtual/opencl - || ( >=dev-util/amdapp-2.9 dev-util/intel-ocl-sdk ) - dev-libs/boost - performance? ( ${PYTHON_DEPS} ) - " -DEPEND="${RDEPEND}" -# test? ( -# >=dev-cpp/gtest-1.6.0 -# >=sci-libs/acml-6.1.0.3 -# )" - -# The tests only get compiled to an executable named Test, which is not recogniozed by cmake. -# Therefore src_test() won't execute any test. -RESTRICT="test" - -PATCHES=( - "${FILESDIR}/${P}"-client_CMakeLists.patch - "${FILESDIR}/${P}"-library_tools_tune_CMakeLists.patch - "${FILESDIR}"/clblas-samples_CMakeLists.patch - "${FILESDIR}"/clblas-scripts_perf_CMakeLists.patch -) - -pkg_pretend() { - if [[ ${MERGE_TYPE} != binary ]]; then - if [[ $(gcc-major-version) -lt 4 ]] || ( [[ $(gcc-major-version) -eq 4 && $(gcc-minor-version) -lt 6 ]] ) ; then - die "Compilation with gcc older than 4.6 is not supported." - fi - fi -} - -src_configure() { - local mycmakeargs=( - $(cmake-utils_use_build client CLIENT) - $(cmake-utils_use_build examples SAMPLE) - $(cmake-utils_use_build ktest KTEST) - $(cmake-utils_use_build performance PERFORMANCE) - $(cmake-utils_use_build test TEST) - ) - cmake-utils_src_configure -} diff --git a/sci-libs/clblas/clblas-2.4.ebuild b/sci-libs/clblas/clblas-2.4-r1.ebuild index 945a9a477..00133c2e3 100644 --- a/sci-libs/clblas/clblas-2.4.ebuild +++ b/sci-libs/clblas/clblas-2.4-r1.ebuild @@ -40,6 +40,7 @@ RESTRICT="test" PATCHES=( "${FILESDIR}"/clblas-samples_CMakeLists.patch "${FILESDIR}"/clblas-scripts_perf_CMakeLists.patch + "${FILESDIR}"/clblas-2.4-Install-cmake-configuration-to-lib-cmake-clBLAS.patch ) pkg_pretend() { diff --git a/sci-libs/clblas/clblas-9999.ebuild b/sci-libs/clblas/clblas-9999.ebuild index 8850929e9..bb47c0d37 100644 --- a/sci-libs/clblas/clblas-9999.ebuild +++ b/sci-libs/clblas/clblas-9999.ebuild @@ -39,6 +39,7 @@ RESTRICT="test" PATCHES=( "${FILESDIR}"/clblas-samples_CMakeLists.patch "${FILESDIR}"/clblas-scripts_perf_CMakeLists.patch + "${FILESDIR}"/clblas-2.4-Install-cmake-configuration-to-lib-cmake-clBLAS.patch ) pkg_pretend() { diff --git a/sci-libs/clblas/files/clblas-2.2-client_CMakeLists.patch b/sci-libs/clblas/files/clblas-2.2-client_CMakeLists.patch deleted file mode 100644 index 552e230e3..000000000 --- a/sci-libs/clblas/files/clblas-2.2-client_CMakeLists.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- client/CMakeLists.txt 2014-06-19 22:53:25.000000000 +0200 -+++ client/CMakeLists.txt.new 2015-03-23 16:30:39.164046584 +0100 -@@ -52,7 +52,7 @@ include_directories( - - add_executable(client ${CLIENT_SRC} ${CLIENT_HEADER}) - target_link_libraries(client ${Boost_LIBRARIES} ${OPENCL_LIBRARIES} clBLAS) --set_target_properties( client PROPERTIES RUNTIME_OUTPUT_DIRECTORY "${PROJECT_BINARY_DIR}/staging" ) -+set_target_properties( client PROPERTIES RUNTIME_OUTPUT_DIRECTORY "${PROJECT_BINARY_DIR}/staging" OUTPUT_NAME clBLAS-client ) - - add_executable(testPerfWrapper ${WRAPPER_SRC}) - target_link_libraries(testPerfWrapper ${Boost_LIBRARIES}) diff --git a/sci-libs/clblas/files/clblas-2.2-library_tools_tune_CMakeLists.patch b/sci-libs/clblas/files/clblas-2.2-library_tools_tune_CMakeLists.patch deleted file mode 100644 index 5f1f763fe..000000000 --- a/sci-libs/clblas/files/clblas-2.2-library_tools_tune_CMakeLists.patch +++ /dev/null @@ -1,14 +0,0 @@ -Install tune as clBLAS-tune. - -Patch by Marius Brehler. ---- library/tools/tune/CMakeLists.txt -+++ library/tools/tune/CMakeLists.txt -@@ -138,7 +138,7 @@ endif() - add_executable(tune ${TOOLS_SRC} ${TOOLS_EXTERNAL_SRC}) - add_dependencies(tune GENERATE_CLT) - target_link_libraries(tune ${OPENCL_LIBRARIES} ${TIME_LIBRARY} ${MATH_LIBRARY}) --set_target_properties( tune PROPERTIES RUNTIME_OUTPUT_DIRECTORY "${PROJECT_BINARY_DIR}/staging" ) -+set_target_properties( tune PROPERTIES RUNTIME_OUTPUT_DIRECTORY "${PROJECT_BINARY_DIR}/staging" OUTPUT_NAME clBLAS-tune ) - - # CPack configuration; include the executable into the package - install( TARGETS tune diff --git a/sci-libs/clblas/files/clblas-2.4-Install-cmake-configuration-to-lib-cmake-clBLAS.patch b/sci-libs/clblas/files/clblas-2.4-Install-cmake-configuration-to-lib-cmake-clBLAS.patch new file mode 100644 index 000000000..32cb7b553 --- /dev/null +++ b/sci-libs/clblas/files/clblas-2.4-Install-cmake-configuration-to-lib-cmake-clBLAS.patch @@ -0,0 +1,25 @@ +From b83750ab917b12500f9755dc4c81f99eb55bb67e Mon Sep 17 00:00:00 2001 +From: Marius Brehler <marius.brehler@tu-dortmund.de> +Date: Sat, 6 Jun 2015 10:35:32 +0200 +Subject: [PATCH] Install cmake configuration to lib/cmake/clBLAS + +--- + src/CMakeLists.txt | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt +index a23cd37..5c378dc 100644 +--- a/src/CMakeLists.txt ++++ b/src/CMakeLists.txt +@@ -300,7 +300,7 @@ endif( ) + if(WIN32) + set(destdir CMake) + else() +- set(destdir share/clBLAS) ++ set(destdir lib${SUFFIX_LIB}/cmake/clBLAS) + endif() + string(REGEX REPLACE "[^/]+" ".." reldir "${destdir}") + configure_file( +-- +2.3.6 + diff --git a/sci-libs/dealii/ChangeLog b/sci-libs/dealii/ChangeLog index b3491fe13..c900cbe52 100644 --- a/sci-libs/dealii/ChangeLog +++ b/sci-libs/dealii/ChangeLog @@ -2,6 +2,13 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> dealii-8.1.0-r2.ebuild, + dealii-8.2.1-r1.ebuild, dealii-9999.ebuild: + sci-libs/dealii: Add SLOT operators + + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-libs/dealii: Add github to remote-id in metadata.xml + *dealii-8.2.1-r1 (28 Mar 2015) 28 Mar 2015; Matthias Maier <tamiko@gentoo.org> +dealii-8.2.1-r1.ebuild, diff --git a/sci-libs/dealii/dealii-8.1.0-r2.ebuild b/sci-libs/dealii/dealii-8.1.0-r2.ebuild index e1bce5e4a..0703aa8af 100644 --- a/sci-libs/dealii/dealii-8.1.0-r2.ebuild +++ b/sci-libs/dealii/dealii-8.1.0-r2.ebuild @@ -46,7 +46,7 @@ RDEPEND="dev-libs/boost mumps? ( sci-libs/mumps[mpi] ) netcdf? ( sci-libs/netcdf-cxx:0 ) p4est? ( sci-libs/p4est[mpi] ) - parameter_gui? ( dev-qt/qtgui ) + parameter_gui? ( dev-qt/qtgui:4 ) petsc? ( sci-mathematics/petsc[mpi=] ) sparse? ( sci-libs/umfpack ) tbb? ( dev-cpp/tbb ) diff --git a/sci-libs/dealii/dealii-8.2.1-r1.ebuild b/sci-libs/dealii/dealii-8.2.1-r1.ebuild index 145cb29e6..331dd0dce 100644 --- a/sci-libs/dealii/dealii-8.2.1-r1.ebuild +++ b/sci-libs/dealii/dealii-8.2.1-r1.ebuild @@ -53,9 +53,9 @@ RDEPEND="dev-libs/boost mumps? ( sci-libs/mumps[mpi] ) muparser? ( dev-cpp/muParser ) netcdf? ( sci-libs/netcdf-cxx:0 ) - opencascade? ( sci-libs/opencascade ) + opencascade? ( sci-libs/opencascade:* ) p4est? ( sci-libs/p4est[mpi] ) - parameter_gui? ( dev-qt/qtgui ) + parameter_gui? ( dev-qt/qtgui:4 ) petsc? ( sci-mathematics/petsc[mpi=] ) sparse? ( sci-libs/umfpack ) tbb? ( dev-cpp/tbb ) diff --git a/sci-libs/dealii/dealii-9999.ebuild b/sci-libs/dealii/dealii-9999.ebuild index dc836023b..c00c3835f 100644 --- a/sci-libs/dealii/dealii-9999.ebuild +++ b/sci-libs/dealii/dealii-9999.ebuild @@ -51,9 +51,9 @@ RDEPEND="dev-libs/boost mpi? ( virtual/mpi ) muparser? ( dev-cpp/muParser ) netcdf? ( sci-libs/netcdf-cxx:0 ) - opencascade? ( sci-libs/opencascade ) + opencascade? ( sci-libs/opencascade:* ) p4est? ( sci-libs/p4est[mpi] ) - parameter_gui? ( dev-qt/qtgui ) + parameter_gui? ( dev-qt/qtgui:4 ) petsc? ( sci-mathematics/petsc[mpi=] ) sparse? ( sci-libs/umfpack ) tbb? ( dev-cpp/tbb ) diff --git a/sci-libs/dealii/metadata.xml b/sci-libs/dealii/metadata.xml index e838dc172..bce7b01bc 100644 --- a/sci-libs/dealii/metadata.xml +++ b/sci-libs/dealii/metadata.xml @@ -31,4 +31,7 @@ and extra output. If you want to get meaningful backtraces see <flag name="tbb">Add threading support with the help of the tbb library (<pkg>dev-cpp/tbb</pkg>)</flag> <flag name="trilinos">Add support for trilinos (<pkg>sci-libs/trilinos</pkg>)</flag> </use> + <upstream> + <remote-id type="github">dealii/dealii</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-libs/libsc/ChangeLog b/sci-libs/libsc/ChangeLog index db89785ac..6925e4156 100644 --- a/sci-libs/libsc/ChangeLog +++ b/sci-libs/libsc/ChangeLog @@ -1,7 +1,13 @@ # ChangeLog for sci-libs/libsc -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> libsc-1.0.ebuild: + sci-libs/libsc: Add SLOT operators + + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-libs/libsc: Add github to remote-id in metadata.xml + *libsc-1.1 (13 Oct 2014) 13 Oct 2014; Matthias Maier <tamiko@gentoo.org> +libsc-1.1.ebuild, diff --git a/sci-libs/libsc/libsc-1.0.ebuild b/sci-libs/libsc/libsc-1.0.ebuild index c0cb21288..64b597f49 100644 --- a/sci-libs/libsc/libsc-1.0.ebuild +++ b/sci-libs/libsc/libsc-1.0.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ @@ -8,19 +8,19 @@ WANT_AUTOMAKE=1.11 inherit autotools-utils toolchain-funcs eutils multilib -DESCRIPTION="The SC Library provides support for parallel scientific applications." +DESCRIPTION="Support for parallel scientific applications" HOMEPAGE="http://www.p4est.org/" SRC_URI="https://github.com/cburstedde/libsc/archive/v${PV}.tar.gz -> ${P}.tar.gz" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" LICENSE="LGPL-2.1+" SLOT="0" - +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" IUSE="debug examples mpi romio static-libs" + REQUIRED_USE="romio? ( mpi )" RDEPEND=" - dev-lang/lua + dev-lang/lua:* sys-apps/util-linux virtual/blas virtual/lapack @@ -55,8 +55,7 @@ src_configure() { src_install() { autotools-utils_src_install - if use examples - then + if use examples; then docinto examples dodoc -r example/* docompress -x /usr/share/doc/${PF}/examples diff --git a/sci-libs/libsc/metadata.xml b/sci-libs/libsc/metadata.xml index 6d4eba7c1..b145b03cb 100644 --- a/sci-libs/libsc/metadata.xml +++ b/sci-libs/libsc/metadata.xml @@ -13,4 +13,7 @@ This support library is primarily used by the p4est library. <use> <flag name="romio">Build with support for the ROMIO MPI-IO component</flag> </use> + <upstream> + <remote-id type="github">cburstedde/libsc</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-libs/openblas/ChangeLog b/sci-libs/openblas/ChangeLog index 0912ff190..e783b9d38 100644 --- a/sci-libs/openblas/ChangeLog +++ b/sci-libs/openblas/ChangeLog @@ -2,6 +2,13 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> openblas-0.2.11.ebuild, + openblas-0.2.8.ebuild, openblas-9999.ebuild: + sci-libs/openblas: Add missing eclass + + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-libs/openblas: Add github to remote-id in metadata.xml + 02 Apr 2015; Marius Brehler <marbre@linux.sungazer.de> openblas-9999.ebuild: Fix Bug 528974 diff --git a/sci-libs/openblas/metadata.xml b/sci-libs/openblas/metadata.xml index 32441d18a..6ef9b5417 100644 --- a/sci-libs/openblas/metadata.xml +++ b/sci-libs/openblas/metadata.xml @@ -10,4 +10,7 @@ <flag name="int64">Build the 64 bits integer library</flag> <flag name="dynamic">Build dynamic architecture detection at run time (for multi targets)</flag> </use> + <upstream> + <remote-id type="github">xianyi/OpenBLAS</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-libs/openblas/openblas-0.2.11.ebuild b/sci-libs/openblas/openblas-0.2.11.ebuild index 2b5f76db2..c69932e42 100644 --- a/sci-libs/openblas/openblas-0.2.11.ebuild +++ b/sci-libs/openblas/openblas-0.2.11.ebuild @@ -5,7 +5,7 @@ EAPI=5 EBASE_PROFNAME="openblas" -inherit alternatives-2 eutils fortran-2 multibuild multilib-build toolchain-funcs fortran-int64 +inherit alternatives-2 eutils multilib fortran-2 multibuild multilib-build toolchain-funcs fortran-int64 SRC_URI+="http://dev.gentoo.org/~gienah/distfiles/${PN}-0.2.11-gentoo.patch" if [[ ${PV} == "9999" ]] ; then diff --git a/sci-libs/openblas/openblas-0.2.8.ebuild b/sci-libs/openblas/openblas-0.2.8.ebuild index 96ca05b80..565215bb9 100644 --- a/sci-libs/openblas/openblas-0.2.8.ebuild +++ b/sci-libs/openblas/openblas-0.2.8.ebuild @@ -1,10 +1,10 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ EAPI=5 -inherit eutils toolchain-funcs alternatives-2 multilib fortran-2 +inherit eutils multilib toolchain-funcs alternatives-2 multilib fortran-2 DESCRIPTION="Optimized BLAS library based on GotoBLAS2" HOMEPAGE="http://xianyi.github.com/OpenBLAS/" diff --git a/sci-libs/openblas/openblas-9999.ebuild b/sci-libs/openblas/openblas-9999.ebuild index db150b020..c5166a35f 100644 --- a/sci-libs/openblas/openblas-9999.ebuild +++ b/sci-libs/openblas/openblas-9999.ebuild @@ -5,7 +5,7 @@ EAPI=5 EBASE_PROFNAME="openblas" -inherit alternatives-2 eutils fortran-2 multibuild multilib-build toolchain-funcs fortran-int64 +inherit alternatives-2 eutils multilib fortran-2 multibuild multilib-build toolchain-funcs fortran-int64 SRC_URI+="http://dev.gentoo.org/~gienah/distfiles/${PN}-0.2.11-gentoo.patch" if [[ ${PV} == "9999" ]] ; then diff --git a/sci-libs/p4est/ChangeLog b/sci-libs/p4est/ChangeLog index 61500661e..42e91d06a 100644 --- a/sci-libs/p4est/ChangeLog +++ b/sci-libs/p4est/ChangeLog @@ -1,7 +1,13 @@ # ChangeLog for sci-libs/p4est -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> p4est-1.0.ebuild: + sci-libs/p4est: Add SLOT operators + + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-libs/p4est: Add github to remote-id in metadata.xml + 13 Oct 2014; Matthias Maier <tamiko@gentoo.org> p4est-1.0.ebuild: sci-libs/p4est: Fix build dependencies diff --git a/sci-libs/p4est/metadata.xml b/sci-libs/p4est/metadata.xml index c8a9acb72..85fc0a1a7 100644 --- a/sci-libs/p4est/metadata.xml +++ b/sci-libs/p4est/metadata.xml @@ -16,4 +16,7 @@ processor cores. <flag name="vtk-binary">Enable binary vtk output. If disabled vtk files will be written in ASCII text format.</flag> <flag name="romio">Build with support for the ROMIO MPI-IO component</flag> </use> + <upstream> + <remote-id type="github">cburstedde/libsc</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-libs/p4est/p4est-1.0.ebuild b/sci-libs/p4est/p4est-1.0.ebuild index 4c6946d94..e753ed7e1 100644 --- a/sci-libs/p4est/p4est-1.0.ebuild +++ b/sci-libs/p4est/p4est-1.0.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ @@ -24,7 +24,7 @@ REQUIRED_USE="romio? ( mpi )" RDEPEND=" >=sci-libs/libsc-1.0[mpi,romio] - dev-lang/lua + dev-lang/lua:* sys-apps/util-linux virtual/blas virtual/lapack diff --git a/sci-mathematics/acl2/ChangeLog b/sci-mathematics/acl2/ChangeLog index baff65ab7..76c3446f5 100644 --- a/sci-mathematics/acl2/ChangeLog +++ b/sci-mathematics/acl2/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-mathematics/acl2: Add github to remote-id in metadata.xml + *acl2-7.0 (25 Mar 2015) 25 Mar 2015; zcj <ustcscgy@163.com> +acl2-7.0.ebuild, -acl2-6.3.ebuild, diff --git a/sci-mathematics/acl2/metadata.xml b/sci-mathematics/acl2/metadata.xml index 47ab9cabf..672cea888 100644 --- a/sci-mathematics/acl2/metadata.xml +++ b/sci-mathematics/acl2/metadata.xml @@ -1,21 +1,24 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci-mathematics</herd> - <maintainer> - <email>dongxuli2011@gmail.com</email> - <name>Dongxu Li</name> - <description>Industrial strength theorem prover</description> - </maintainer> - <longdescription> + <herd>sci-mathematics</herd> + <maintainer> + <email>dongxuli2011@gmail.com</email> + <name>Dongxu Li</name> + <description>Industrial strength theorem prover</description> + </maintainer> + <longdescription> ACL2 is both a programming language in which you can model computer systems and a tool to help you prove properties of those models. ACL2 is part of the Boyer-Moore family of provers, for which its authors have received the 2005 ACM Software System Award. </longdescription> - <use> - <flag name="books"> + <use> + <flag name="books"> build community books, the canonical collection of open-source libraries </flag> - </use> + </use> + <upstream> + <remote-id type="github">acl2/acl2</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-misc/nltk/ChangeLog b/sci-misc/nltk/ChangeLog index 613b269e1..d91ac2a39 100644 --- a/sci-misc/nltk/ChangeLog +++ b/sci-misc/nltk/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-misc/nltk -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-misc/nltk: Add github to remote-id in metadata.xml + 04 Dec 2013; Justin Lecher <jlec@gentoo.org> -nltk-2.0.1_rc1.ebuild, +nltk-2.0.4.ebuild, metadata.xml: Version Bump; Bump to distutils-r1 eclass diff --git a/sci-misc/nltk/metadata.xml b/sci-misc/nltk/metadata.xml index eefdbc160..8cf6c1d55 100644 --- a/sci-misc/nltk/metadata.xml +++ b/sci-misc/nltk/metadata.xml @@ -8,4 +8,7 @@ NLTK is collection of natural language tools written in python language. It also contains huge corpora. </longdescription> + <upstream> + <remote-id type="github">nltk/nltk</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-physics/espresso++/ChangeLog b/sci-physics/espresso++/ChangeLog index ca71bfef9..7a589edd3 100644 --- a/sci-physics/espresso++/ChangeLog +++ b/sci-physics/espresso++/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-physics/espresso++: Add github to remote-id in metadata.xml + 20 Mar 2015; Christoph Junghans <ottxor@gentoo.org> espresso++-9999.ebuild: added test feature diff --git a/sci-physics/espresso++/metadata.xml b/sci-physics/espresso++/metadata.xml index a556ddb82..25acc4649 100644 --- a/sci-physics/espresso++/metadata.xml +++ b/sci-physics/espresso++/metadata.xml @@ -6,4 +6,7 @@ <email>ottxor@gentoo.org</email> <name>Christoph Junghans</name> </maintainer> + <upstream> + <remote-id type="github">espressopp/espressopp</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-physics/looptools/ChangeLog b/sci-physics/looptools/ChangeLog index 6e5903308..407587aa5 100644 --- a/sci-physics/looptools/ChangeLog +++ b/sci-physics/looptools/ChangeLog @@ -1,7 +1,12 @@ # ChangeLog for sci-physics/looptools -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*looptools-2.12 (07 Jun 2015) + + 07 Jun 2015; Jauhien Piatlicki <jauhien@gentoo.org> +looptools-2.12.ebuild: + version bump + *looptools-2.11 (31 Aug 2014) *looptools-2.10 (31 Aug 2014) *looptools-2.9 (31 Aug 2014) diff --git a/sci-physics/looptools/Manifest b/sci-physics/looptools/Manifest index 3c4607565..f4810e3a2 100644 --- a/sci-physics/looptools/Manifest +++ b/sci-physics/looptools/Manifest @@ -1,4 +1,5 @@ DIST LoopTools-2.10.tar.gz 550654 SHA256 141ab2153006ca3f1cc01e66e1552c02bf8164b9216304ff1829370b7b5c77bb SHA512 1fc9ef5a9ced8ea08ddc5f494338fb27b55bacdd23a968ca4379e5ca63f8d74ea947fb0bb98a80dfd6dddc0db1e80d2d454433abdcfeac323b51c27432046954 WHIRLPOOL b118d3f5f13b6e23920f7680b4b1a0b1d2c4079ac78c0763e73d30e9750d14ae57cd00f889e5b7392bc2ef53f88122be4d7f52de96f999676aa4e1e603353eae DIST LoopTools-2.11.tar.gz 546351 SHA256 efe14e774fcd66bdd46bbeb8065138793e3c1f5c73594c84c116edbab74c842d SHA512 fbe6c43b857561d0e7f35acdea32c34f2430c2faf23172790ad4426c469e39cd0df413d2c3cdc080ce9c4dcfb95773b7dc70b13738341c9d0438f4445cdbf6ab WHIRLPOOL 74b30ebe59998f2217b7e5cfb6e90671193159e5e3adfb2c26fee9c6f7b4021932ea8158e191f2e538e2e6d037fc86382659a697f638dc22ea3d068dfb92340c +DIST LoopTools-2.12.tar.gz 545153 SHA256 df04d944de15ec73665edaf76f655d1db797cbc02b54baa7664ac761ecfa2f70 SHA512 70726493bd138fb80b85a46955fbe28b7f1432d9b67a100fe3ff74c2fa22232a07e461a6742745b0ead81793bb64b81cc4265d09b91fa048e7bdd32cf6956b27 WHIRLPOOL af3abaf31a4a868e0f65bdb0b21405c413c470063e4c8130e31b2a9e05a4f0e65e9999323e3cdf0b4277e48e84d767288852e984d486468abab3aaa664f66879 DIST LoopTools-2.8.tar.gz 546810 SHA256 2395518d0eac9b0883a2c249b9a5ba80df443929c520c45e60f5a4284166eb42 SHA512 32211669fd092d2d5bb38e26a6471a95df0647d9e7ea0cc4e99ff4fd7c3e3fee107f6432ed9075e3102224f0041fac6f7075b1f0a91f7744ec3890b4b36d276e WHIRLPOOL c8dff8030d7ea1bfc6b65bef3370c5acfec69fa73f223a63b7424163b81a3bdf788eb3ffecd07e9bf61a31a63138b1fd126b6442a298c8fad1f4b04b69663a47 DIST LoopTools-2.9.tar.gz 548404 SHA256 e3cdc10fdbc9fe68e56402d34c6d3abd1ec6d727db8914b0cec0119273f7aa4d SHA512 3a46c94a5ff72079c930d7ec2076b0f5278e897130383fdd656173218840f04e03ebb9fdef362af36a207a71a87c038fec6e008a231ef259120073760aa05534 WHIRLPOOL 50591b6aa4e7e624282ad2102c78060cd421c6f5b7abd293bb18b2ca6844857bdcdbafab8e33c86ff4bd464f1245ba0cd13978800ac4786411a658ffd947cc38 diff --git a/sci-physics/looptools/looptools-2.12.ebuild b/sci-physics/looptools/looptools-2.12.ebuild new file mode 100644 index 000000000..66a959c4a --- /dev/null +++ b/sci-physics/looptools/looptools-2.12.ebuild @@ -0,0 +1,39 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit eutils fortran-2 multilib + +MYP=LoopTools-${PV} + +DESCRIPTION="Tools for evaluation of scalar and tensor one-loop integrals" +HOMEPAGE="http://www.feynarts.de/looptools" +SRC_URI="http://www.feynarts.de/looptools/${MYP}.tar.gz" + +LICENSE="LGPL-3" + +SLOT="0/${PV}" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="doc static-libs" + +DEPEND="virtual/fortran" +RDEPEND="${DEPEND}" + +S="${WORKDIR}/${MYP}" + +src_prepare() { + epatch "${FILESDIR}"/${PN}-2.10-makefile.patch + export VER="${PV}" + # necessary fix for prefix + sed -i "s/lib\$(LIBDIRSUFFIX)/$(get_libdir)/" makefile.in || die +} + +src_install() { + default + # another one of these package building archive with pic + # no: ooptools is not a typo + use static-libs || rm "${ED}"/usr/$(get_libdir)/libooptools.a + use doc && dodoc manual/*.pdf +} diff --git a/sci-visualization/mayavi/ChangeLog b/sci-visualization/mayavi/ChangeLog index f0c228bda..588ac41ad 100644 --- a/sci-visualization/mayavi/ChangeLog +++ b/sci-visualization/mayavi/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: Exp $ + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-visualization/mayavi: Add github to remote-id in metadata.xml + 18 Feb 2015; Justin Lecher <jlec@gentoo.org> mayavi-4.4.0.ebuild, metadata.xml: sci-visualization/mayavi: fix SLOT operators diff --git a/sci-visualization/mayavi/metadata.xml b/sci-visualization/mayavi/metadata.xml index a76fa19f9..023851c52 100644 --- a/sci-visualization/mayavi/metadata.xml +++ b/sci-visualization/mayavi/metadata.xml @@ -21,4 +21,7 @@ used as an Envisage plug-in which allows it to be embedded in other Envisage based applications natively. </longdescription> + <upstream> + <remote-id type="github">enthought/mayavi</remote-id> + </upstream> </pkgmetadata> diff --git a/sys-cluster/htcondor/ChangeLog b/sys-cluster/htcondor/ChangeLog index 7215000f4..959952f85 100644 --- a/sys-cluster/htcondor/ChangeLog +++ b/sys-cluster/htcondor/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sys-cluster/htcondor: Add github to remote-id in metadata.xml + 18 Feb 2015; Justin Lecher <jlec@gentoo.org> htcondor-8.0.0.ebuild, htcondor-8.3.2.ebuild: sys-cluster/htcondor: fix SLOT operators diff --git a/sys-cluster/htcondor/metadata.xml b/sys-cluster/htcondor/metadata.xml index 6485807ae..7767e2fac 100644 --- a/sys-cluster/htcondor/metadata.xml +++ b/sys-cluster/htcondor/metadata.xml @@ -26,4 +26,7 @@ <flag name="minimal">Don't support standard universe jobs</flag> <flag name="X">Enable the HTCondor Keyboard Daemon to monitor logged in X users for activity</flag> </use> + <upstream> + <remote-id type="github">htcondor/htcondor</remote-id> + </upstream> </pkgmetadata> |