diff options
Diffstat (limited to 'sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-conf-opts.patch')
| -rw-r--r-- | sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-conf-opts.patch | 213 |
1 files changed, 213 insertions, 0 deletions
diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-conf-opts.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-conf-opts.patch new file mode 100644 index 000000000..820960354 --- /dev/null +++ b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-conf-opts.patch @@ -0,0 +1,213 @@ + src/build-system/configure | 34 +++++++++++++++++++++++----------- + src/build-system/configure.ac | 33 ++++++++++++++++++++++----------- + 2 files changed, 45 insertions(+), 22 deletions(-) + +diff --git a/src/build-system/configure b/src/build-system/configure +index 82fc9ef..d31a4f2 100755 +--- a/src/build-system/configure ++++ b/src/build-system/configure +@@ -924,7 +924,7 @@ Optional Packages: + --without-distcc do not automatically use distcc if available + --without-ncbi-c do not use NCBI C Toolkit + --without-sss do not use NCBI SSS libraries +- --without-utils do not use NCBI SSS UTIL library ++ --without-sssutils do not use NCBI SSS UTIL library + --without-sssdb do not use NCBI SSS DB library + --with-included-sss use the in-tree copy of SSS + --with-z=DIR use zlib installation in DIR +@@ -2835,12 +2835,12 @@ check ncbi-public strip pch caution ccache distcc \ + ncbi-c wxwidgets wxwidgets-ucs fastcgi sss sssdb sssutils included-sss \ + geo included-geo \ + z bz2 lzo pcre gnutls openssl sybase sybase-local sybase-new \ +-ftds mysql orbacus freetype fltk opengl mesa glut glew glew-mx \ ++ftds mysql orbacus odbc freetype fltk opengl mesa glut glew glew-mx \ + bdb python jni sqlite3 icu boost boost-tag \ + sp expat sablot libxml libxslt xerces xalan oechem sge muparser hdf5 \ + gif jpeg tiff png xpm magic curl 3psw \ + local-lbsm ncbi-crypt connext \ +-serial objects dbapi app ctools gui algo internal gbench" ++serial objects dbapi app ctools gui algo internal gbench x" + + x_with_list=`echo "$x_with_list" | sed 's/\([^ ][^ ]*\)/--with-\1 --without-\1/g'` + +@@ -2864,6 +2864,7 @@ for x_arg in "$@" ; do + case "$x_arg" in + --with-extra-action= | --exec-prefix= | --with-projects= | --srcdir= \ + | --cache-file= | --build= | --host= | --target= | --with-runpath= \ ++ | --mandir= | --infodir= | --datadir= | --sysconfdir= | --localstatedir= \ + | --with-relative-runpath= | --x-includes= | --x-libraries= ) + { { echo "$as_me:$LINENO: error: $x_arg: requires value; use --help to show usage" >&5 + echo "$as_me: error: $x_arg: requires value; use --help to show usage" >&2;} +@@ -2876,6 +2877,7 @@ echo "$as_me: error: $x_arg: requires value; use --help to show usage" >&2;} + | --with-universal=* | --with-tcheck=* \ + | --cache-file=* | --build=* | --host=* | --prefix=* | --exec-prefix=* \ + | --libdir=* | --bindir=* | --includedir=* | --srcdir=* \ ++ | --mandir=* | --infodir=* | --datadir=* | --sysconfdir=* | --localstatedir=* \ + | [A-Z]*=* \ + | --with-z=* | --with-bz2=* | --with-lzo=* \ + | --with-pcre=* \ +@@ -3023,7 +3025,8 @@ echo "$as_me: error: --without-extra-action is not allowed" >&2;} + fi + + case "$with_projects" in +- "") if test -r projects; then ++ ""|yes) ++ if test -r projects; then + { echo "$as_me:$LINENO: using default projects file \"projects\"." >&5 + echo "$as_me: using default projects file \"projects\"." >&6;} + with_projects=projects +@@ -3049,6 +3052,16 @@ echo "$as_me: WARNING: default projects file \"projects\" is a dangling link." > + ;; + esac + ++if test -n "$with_projects"; then ++ case "$with_projects" in ++ /* ) abs_projects=$with_projects ;; ++ yes) abs_projects=$srcdir/projects ;; ++ * ) abs_projects=$srcdir/$with_projects ;; ++ esac ++ test -r "$abs_projects" || \ ++ as_fn_error $? "unable to read requested projects file \"$abs_projects\"." "$LINENO" 5 ++fi ++ + + #### Always define this + +@@ -32712,7 +32725,7 @@ else + sep=", " + fi + if test -n "$reason" -a "$with_internal" = "yes"; then +- if test -z "$with_projects" -o "$with_projects" = "no"; then ++ if test -z "$with_projects"; then + { { echo "$as_me:$LINENO: error: --with-internal: Cannot build INTERNAL projects: missing $reason" >&5 + echo "$as_me: error: --with-internal: Cannot build INTERNAL projects: missing $reason" >&2;} + { (exit 1); exit 1; }; } +@@ -34949,11 +34962,9 @@ if test "$with_flat_makefile" != "no"; then + else + cfm_flags='-remoteptb' + fi +- case "$with_projects" in +- yes ) cfm_flags="$cfm_flags -p projects" ;; +- no | '' ) ;; +- * ) cfm_flags="$cfm_flags -p $with_projects" ;; +- esac ++ if test -n "$with_projects"; then ++ cfm_flags="$cfm_flags -p $with_projects" ++ fi + if test "$with_configure_dialog" = yes; then + cfm_flags="$cfm_flags -cfg" + fi +@@ -34997,7 +35008,8 @@ lib) + esac + + if test -n "$with_projects"; then +- build_proj="To build selected projects: cd $builddir && make all_p" ++ build_proj="To build selected projects (as listed in \"$with_projects\"): ++ cd $builddir && make all_p" + fi + + cat << EOCONF +diff --git a/src/build-system/configure.ac b/src/build-system/configure.ac +index 7b733af..3b55bf5 100644 +--- a/src/build-system/configure.ac ++++ b/src/build-system/configure.ac +@@ -222,7 +222,7 @@ AC_ARG_WITH(ncbi-c, + AC_ARG_WITH(sss, + [ --without-sss do not use NCBI SSS libraries]) + AC_ARG_WITH(sssutils, +- [ --without-utils do not use NCBI SSS UTIL library]) ++ [ --without-sssutils do not use NCBI SSS UTIL library]) + AC_ARG_WITH(sssdb, + [ --without-sssdb do not use NCBI SSS DB library]) + AC_ARG_WITH(included-sss, +@@ -462,12 +462,12 @@ check ncbi-public strip pch caution ccache distcc \ + ncbi-c wxwidgets wxwidgets-ucs fastcgi sss sssdb sssutils included-sss \ + geo included-geo \ + z bz2 lzo pcre gnutls openssl sybase sybase-local sybase-new \ +-ftds mysql orbacus freetype fltk opengl mesa glut glew glew-mx \ ++ftds mysql orbacus odbc freetype fltk opengl mesa glut glew glew-mx \ + bdb python jni sqlite3 icu boost boost-tag \ + sp expat sablot libxml libxslt xerces xalan oechem sge muparser hdf5 \ + gif jpeg tiff png xpm magic curl 3psw \ + local-lbsm ncbi-crypt connext \ +-serial objects dbapi app ctools gui algo internal gbench" ++serial objects dbapi app ctools gui algo internal gbench x" + + changequote(, )dnl + x_with_list=`echo "$x_with_list" | sed 's/\([^ ][^ ]*\)/--with-\1 --without-\1/g'` +@@ -493,6 +493,7 @@ for x_arg in "$@" ; do + case "$x_arg" in + --with-extra-action= | --exec-prefix= | --with-projects= | --srcdir= \ + | --cache-file= | --build= | --host= | --target= | --with-runpath= \ ++ | --mandir= | --infodir= | --datadir= | --sysconfdir= | --localstatedir= \ + | --with-relative-runpath= | --x-includes= | --x-libraries= ) + AC_MSG_ERROR([$x_arg: requires value; use --help to show usage]) + ;; +@@ -503,6 +504,7 @@ for x_arg in "$@" ; do + | --with-universal=* | --with-tcheck=* \ + | --cache-file=* | --build=* | --host=* | --prefix=* | --exec-prefix=* \ + | --libdir=* | --bindir=* | --includedir=* | --srcdir=* \ ++ | --mandir=* | --infodir=* | --datadir=* | --sysconfdir=* | --localstatedir=* \ + | [[A-Z]*=*] \ + | --with-z=* | --with-bz2=* | --with-lzo=* \ + | --with-pcre=* \ +@@ -581,7 +583,8 @@ if test "$with_extra_action" = "no" ; then + fi + + case "$with_projects" in +- "") if test -r projects; then ++ ""|yes) ++ if test -r projects; then + AC_MSG_NOTICE([using default projects file "projects".]) + with_projects=projects + AC_SUBST(PROJECTS, "\$(top_srcdir)/projects") +@@ -599,6 +602,15 @@ case "$with_projects" in + * ) AC_SUBST(PROJECTS, "\$(top_srcdir)/$with_projects") ;; + esac + ++if test -n "$with_projects"; then ++ case "$with_projects" in ++ /* ) abs_projects=$with_projects ;; ++ yes) abs_projects=$srcdir/projects ;; ++ * ) abs_projects=$srcdir/$with_projects ;; ++ esac ++ test -r "$abs_projects" || \ ++ AC_MSG_ERROR([unable to read requested projects file "$abs_projects".]) ++fi + + #### Always define this + AC_DEFINE(NCBI_CXX_TOOLKIT, 1, [This is the NCBI C++ Toolkit.]) +@@ -6198,7 +6210,7 @@ else + sep=", " + fi + if test -n "$reason" -a "$with_internal" = "yes"; then +- if test -z "$with_projects" -o "$with_projects" = "no"; then ++ if test -z "$with_projects"; then + AC_MSG_ERROR([--with-internal: Cannot build INTERNAL projects: missing $reason]) + else + AC_MSG_WARN([--with-internal: Cannot build all INTERNAL projects: missing $reason]) +@@ -6807,11 +6819,9 @@ if test "$with_flat_makefile" != "no"; then + else + cfm_flags='-remoteptb' + fi +- case "$with_projects" in +- yes ) cfm_flags="$cfm_flags -p projects" ;; +- no | '' ) ;; +- * ) cfm_flags="$cfm_flags -p $with_projects" ;; +- esac ++ if test -n "$with_projects"; then ++ cfm_flags="$cfm_flags -p $with_projects" ++ fi + if test "$with_configure_dialog" = yes; then + cfm_flags="$cfm_flags -cfg" + fi +@@ -6854,7 +6864,8 @@ lib) + esac + + if test -n "$with_projects"; then +- build_proj="To build selected projects: cd $builddir && make all_p" ++ build_proj="To build selected projects (as listed in \"$with_projects\"): ++ cd $builddir && make all_p" + fi + + cat << EOCONF |