[EMBOSS] fix compile issue on i686, missing deps, plplot, tfm
Tom Callaway
spot at fedoraproject.org
Wed Nov 10 19:23:41 UTC 2010
commit 2c274f6702701f31f0817c287154a0fb327e745d
Author: Tom "spot" Callaway <tcallawa at redhat.com>
Date: Wed Nov 10 14:23:38 2010 -0500
fix compile issue on i686, missing deps, plplot, tfm
EMBOSS-6.3.1-fix-amd64-check.patch | 14 ++++
EMBOSS-6.3.1-fix-doc-finding.patch | 67 -------------------
EMBOSS-6.3.1-new-fix-doc-finding.patch | 109 ++++++++++++++++++++++++++++++++
EMBOSS-6.3.1-system-zlib.patch | 92 +++++++++++++++++++++++++++
EMBOSS.spec | 45 +++++++++----
5 files changed, 246 insertions(+), 81 deletions(-)
---
diff --git a/EMBOSS-6.3.1-fix-amd64-check.patch b/EMBOSS-6.3.1-fix-amd64-check.patch
new file mode 100644
index 0000000..e43e4cc
--- /dev/null
+++ b/EMBOSS-6.3.1-fix-amd64-check.patch
@@ -0,0 +1,14 @@
+diff -up EMBOSS-6.3.1/m4/amd64.m4.BAD EMBOSS-6.3.1/m4/amd64.m4
+--- EMBOSS-6.3.1/m4/amd64.m4.BAD 2010-11-10 11:13:27.153159001 -0500
++++ EMBOSS-6.3.1/m4/amd64.m4 2010-11-10 11:14:21.722159000 -0500
+@@ -12,8 +12,8 @@ AC_DEFUN([CHECK_AMD64],
+ [AC_MSG_CHECKING([if Linux x86_64])
+
+
+-if test "`uname -a | grep Linux`"; then
+- if test "`uname -a | grep x86_64`"; then
++if test "`uname -o | grep Linux`"; then
++ if test "`uname -m | grep x86_64`"; then
+ CFLAGS="${CFLAGS} -D__amd64__"
+ AC_MSG_RESULT(yes)
+ else
diff --git a/EMBOSS-6.3.1-new-fix-doc-finding.patch b/EMBOSS-6.3.1-new-fix-doc-finding.patch
new file mode 100644
index 0000000..ed9d443
--- /dev/null
+++ b/EMBOSS-6.3.1-new-fix-doc-finding.patch
@@ -0,0 +1,109 @@
+diff -up EMBOSS-6.3.1/emboss/tfm.c.fix-doc-finding EMBOSS-6.3.1/emboss/tfm.c
+--- EMBOSS-6.3.1/emboss/tfm.c.fix-doc-finding 2010-04-13 10:25:56.000000000 -0400
++++ EMBOSS-6.3.1/emboss/tfm.c 2010-11-10 13:53:05.957159000 -0500
+@@ -143,13 +143,15 @@ static void tfm_FindAppDocRoot(const AjP
+ AjPStr roottmp = NULL;
+ AjPStr tmpstr = NULL;
+ AjPStr embassy = NULL;
+-
++ AjPStr doctest = NULL;
++
+ AjBool is_windows = ajFalse;
+ #ifdef WIN32
+ is_windows = ajTrue;
+ #endif
+
+ docrootinst = ajStrNew();
++ doctest = ajStrNew();
+ roottmp = ajStrNew();
+ tmpstr = ajStrNew();
+
+@@ -163,11 +165,25 @@ static void tfm_FindAppDocRoot(const AjP
+ /* look at EMBOSS doc files */
+
+ /* try to open the installed doc directory */
+- if(ajStrGetLen(roottmp))
+- ajStrAssignS(docroot, roottmp);
+- else
++ if(ajStrGetLen(roottmp))
++ {
++ /*
++ ** Check for old-style EMBOSS_DOCROOT and adjust accordingly
++ */
++ ajFmtPrintS(&doctest,"%S%cprograms%ctext",roottmp,SLASH_CHAR,
++ SLASH_CHAR);
++ ajStrAssignS(&docrootinst,roottmp);
++ ajDirnameFix(&docrootinst);
++
++ if(!ajDirnameFixExists(&doctest))
++ {
++ ajDirnameUp(&docrootinst);
++ ajDirnameUp(&docrootinst);
++ }
++ }
++ else
+ {
+- ajStrAssignS(&docrootinst, ajNamValueInstalldir());
++ ajStrAssignS(&docrootinst, ajNamValueInstalldir());
+ ajDirnameFix(&docrootinst);
+
+ if(is_windows)
+@@ -184,28 +200,28 @@ static void tfm_FindAppDocRoot(const AjP
+ else
+ ajFmtPrintAppS(&docrootinst, "share%sEMBOSS%sdoc%s",
+ SLASH_STRING,SLASH_STRING,SLASH_STRING);
++ }
+
+-
+- if(html)
+- {
+- if(ajStrGetLen(embassy))
++ if(html)
++ {
++ if(ajStrGetLen(embassy))
+ ajFmtPrintS(docroot,"%Shtml%sembassy%s%S%s",
+ docrootinst,SLASH_STRING,SLASH_STRING,
+ embassy, SLASH_STRING);
+- else
+- {
+- if(is_windows)
+- ajFmtPrintS(docroot,"%Sprograms%shtml%s",
+- docrootinst,SLASH_STRING,SLASH_STRING);
+- else
+- ajFmtPrintS(docroot,"%Sprograms%shtml%s",
+- docrootinst,SLASH_STRING,SLASH_STRING);
+- }
+- }
+ else
++ {
++ if(is_windows)
++ ajFmtPrintS(docroot,"%Sprograms%shtml%s",
++ docrootinst,SLASH_STRING,SLASH_STRING);
++ else
++ ajFmtPrintS(docroot,"%Sprograms%shtml%s",
++ docrootinst,SLASH_STRING,SLASH_STRING);
++ }
++ }
++ else
+ ajFmtPrintS(docroot,"%Sprograms%stext%s",docrootinst,SLASH_STRING,
+ SLASH_STRING);
+- }
++
+ ajDirnameFix(docroot);
+ ajDebug("installed docroot '%S'\n", *docroot);
+
+@@ -248,6 +264,7 @@ static void tfm_FindAppDocRoot(const AjP
+
+ ajStrDel(&roottmp);
+ ajStrDel(&docrootinst);
++ ajStrDel(&doctest);
+ ajStrDel(&tmpstr);
+
+ return;
+@@ -348,4 +365,4 @@ static void tfm_FixImages(AjPStr *line,
+ ajStrDel(&pre);
+
+ return;
+-}
++}
+\ No newline at end of file
diff --git a/EMBOSS-6.3.1-system-zlib.patch b/EMBOSS-6.3.1-system-zlib.patch
new file mode 100644
index 0000000..a50a2a3
--- /dev/null
+++ b/EMBOSS-6.3.1-system-zlib.patch
@@ -0,0 +1,92 @@
+diff -up EMBOSS-6.3.1/configure.in.system-zlib EMBOSS-6.3.1/configure.in
+--- EMBOSS-6.3.1/configure.in.system-zlib 2010-11-10 08:49:30.735682003 -0500
++++ EMBOSS-6.3.1/configure.in 2010-11-10 08:49:30.745682003 -0500
+@@ -425,6 +425,7 @@ if test "${enable_systemlibs}" = "yes" ;
+ have_systemlibs=yes
+ AC_CHECK_LIB(pcre, pcre_compile)
+ AC_CHECK_LIB(expat, XML_ParserCreate)
++ AC_CHECK_LIB(z, compress)
+ fi
+ AM_CONDITIONAL(ESYSTEMLIBS, test "$have_systemlibs" = "yes")
+ AC_SUBST(ESYSTEMLIBS)
+@@ -661,7 +662,7 @@ CHECK_THREADS
+
+
+ AC_OUTPUT([plplot/Makefile plplot/lib/Makefile nucleus/Makefile ajax/Makefile
+-ajax/zlib/Makefile ajax/core/Makefile
++ajax/core/Makefile
+ ajax/graphics/Makefile ajax/ensembl/Makefile ajax/ajaxdb/Makefile
+ ajax/acd/Makefile
+ emboss/Makefile emboss/acd/Makefile test/Makefile test/data/Makefile
+diff -up EMBOSS-6.3.1/configure.system-zlib EMBOSS-6.3.1/configure
+--- EMBOSS-6.3.1/configure.system-zlib 2010-11-10 08:50:26.740682011 -0500
++++ EMBOSS-6.3.1/configure 2010-11-10 08:50:58.823682003 -0500
+@@ -14991,6 +14991,51 @@ _ACEOF
+
+ fi
+
++ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for compress in -lz" >&5
++$as_echo_n "checking for compress in -lz... " >&6; }
++if test "${ac_cv_lib_z_compress+set}" = set; then :
++ $as_echo_n "(cached) " >&6
++else
++ ac_check_lib_save_LIBS=$LIBS
++LIBS="-lz $LIBS"
++cat confdefs.h - <<_ACEOF >conftest.$ac_ext
++/* end confdefs.h. */
++
++/* Override any GCC internal prototype to avoid an error.
++ Use char because int might match the return type of a GCC
++ builtin and then its argument prototype would still apply. */
++#ifdef __cplusplus
++extern "C"
++#endif
++char compress ();
++int
++main ()
++{
++return compress ();
++ ;
++ return 0;
++}
++_ACEOF
++if ac_fn_c_try_link "$LINENO"; then :
++ ac_cv_lib_z_compress=yes
++else
++ ac_cv_lib_z_compress=no
++fi
++rm -f core conftest.err conftest.$ac_objext \
++ conftest$ac_exeext conftest.$ac_ext
++LIBS=$ac_check_lib_save_LIBS
++fi
++{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_z_compress" >&5
++$as_echo "$ac_cv_lib_z_compress" >&6; }
++if test "x$ac_cv_lib_z_compress" = x""yes; then :
++ cat >>confdefs.h <<_ACEOF
++#define HAVE_LIBZ 1
++_ACEOF
++
++ LIBS="-lz $LIBS"
++
++fi
++
+ fi
+ if test "$have_systemlibs" = "yes"; then
+ ESYSTEMLIBS_TRUE=
+@@ -15344,7 +15389,7 @@ fi
+
+
+
+-ac_config_files="$ac_config_files plplot/Makefile plplot/lib/Makefile nucleus/Makefile ajax/Makefile ajax/zlib/Makefile ajax/core/Makefile ajax/graphics/Makefile ajax/ensembl/Makefile ajax/ajaxdb/Makefile ajax/acd/Makefile emboss/Makefile emboss/acd/Makefile test/Makefile test/data/Makefile test/embl/Makefile test/genbank/Makefile test/pir/Makefile test/swiss/Makefile test/swnew/Makefile test/testdb/Makefile emboss/data/Makefile emboss/data/AAINDEX/Makefile emboss/data/CODONS/Makefile emboss/data/REBASE/Makefile emboss/data/JASPAR_CORE/Makefile emboss/data/JASPAR_FAM/Makefile emboss/data/JASPAR_PHYLOFACTS/Makefile emboss/data/JASPAR_CNE/Makefile emboss/data/JASPAR_POLII/Makefile emboss/data/JASPAR_SPLICE/Makefile emboss/data/JASPAR_PBM/Makefile emboss/data/JASPAR_PBM_HLH/Makefile emboss/data/JASPAR_PBM_HOMEO/Makefile emboss/data/PRINTS/Makefile emboss/data/PROSITE/Makefile doc/Makefile doc/manuals/Makefile doc/tutorials/Makefile doc/programs/Makefile doc/programs/html/Makef
ile doc/programs/text/Makefile jemboss/Makefile jemboss/images/Makefile jemboss/lib/Makefile jemboss/lib/axis/Makefile jemboss/resources/Makefile jemboss/utils/Makefile Makefile"
++ac_config_files="$ac_config_files plplot/Makefile plplot/lib/Makefile nucleus/Makefile ajax/Makefile ajax/core/Makefile ajax/graphics/Makefile ajax/ensembl/Makefile ajax/ajaxdb/Makefile ajax/acd/Makefile emboss/Makefile emboss/acd/Makefile test/Makefile test/data/Makefile test/embl/Makefile test/genbank/Makefile test/pir/Makefile test/swiss/Makefile test/swnew/Makefile test/testdb/Makefile emboss/data/Makefile emboss/data/AAINDEX/Makefile emboss/data/CODONS/Makefile emboss/data/REBASE/Makefile emboss/data/JASPAR_CORE/Makefile emboss/data/JASPAR_FAM/Makefile emboss/data/JASPAR_PHYLOFACTS/Makefile emboss/data/JASPAR_CNE/Makefile emboss/data/JASPAR_POLII/Makefile emboss/data/JASPAR_SPLICE/Makefile emboss/data/JASPAR_PBM/Makefile emboss/data/JASPAR_PBM_HLH/Makefile emboss/data/JASPAR_PBM_HOMEO/Makefile emboss/data/PRINTS/Makefile emboss/data/PROSITE/Makefile doc/Makefile doc/manuals/Makefile doc/tutorials/Makefile doc/programs/Makefile doc/programs/html/Makefile doc/programs/te
xt/Makefile jemboss/Makefile jemboss/images/Makefile jemboss/lib/Makefile jemboss/lib/axis/Makefile jemboss/resources/Makefile jemboss/utils/Makefile Makefile"
+
+ cat >confcache <<\_ACEOF
+ # This file is a shell script that caches the results of configure
+@@ -16402,7 +16447,6 @@ do
+ "plplot/lib/Makefile") CONFIG_FILES="$CONFIG_FILES plplot/lib/Makefile" ;;
+ "nucleus/Makefile") CONFIG_FILES="$CONFIG_FILES nucleus/Makefile" ;;
+ "ajax/Makefile") CONFIG_FILES="$CONFIG_FILES ajax/Makefile" ;;
+- "ajax/zlib/Makefile") CONFIG_FILES="$CONFIG_FILES ajax/zlib/Makefile" ;;
+ "ajax/core/Makefile") CONFIG_FILES="$CONFIG_FILES ajax/core/Makefile" ;;
+ "ajax/graphics/Makefile") CONFIG_FILES="$CONFIG_FILES ajax/graphics/Makefile" ;;
+ "ajax/ensembl/Makefile") CONFIG_FILES="$CONFIG_FILES ajax/ensembl/Makefile" ;;
diff --git a/EMBOSS.spec b/EMBOSS.spec
index c6572b9..cdc564f 100644
--- a/EMBOSS.spec
+++ b/EMBOSS.spec
@@ -18,7 +18,7 @@
Name: EMBOSS
Version: 6.3.1
-Release: 6%{?dist}
+Release: 7%{?dist}
Summary: The European Molecular Biology Open Software Suite
Group: Applications/Engineering
@@ -42,18 +42,23 @@ Patch0: ftp://emboss.open-bio.org/pub/EMBOSS/fixes/patches/patch-1-4.gz
# Use system-wide pcre. Sent upstream.
Patch1: EMBOSS-6.3.1-system-pcre.patch
# Use system-wide plplot
-Patch3: EMBOSS-6.3.1-system-plplot.patch
+# Patch3: EMBOSS-6.3.1-system-plplot.patch
# Use system-wide expat
Patch4: EMBOSS-6.3.1-system-expat.patch
+# Use system-wide zlib
+Patch5: EMBOSS-6.3.1-system-zlib.patch
+# Fix x86_64 check to be finer grained, eliminate koji false positive
+# Sent upstream 2010-11-10
+Patch6: EMBOSS-6.3.1-fix-amd64-check.patch
#Fedora-specific. Not sent upstream.
-Patch5: %{name}-fedora.patch
-Patch6: EMBOSS-6.3.1-prevent-autotooling.patch
-Patch7: EMBOSS-6.3.1-system-hack.patch
+Patch7: %{name}-fedora.patch
+Patch8: EMBOSS-6.3.1-system-hack.patch
# Sent upstream on 2010-10-27
# Cleaner version generated on 2010-11-04
-Patch8: EMBOSS-6.3.1-fix-doc-finding.patch
+# Upstream's final version received on 2010-11-10
+Patch9: EMBOSS-6.3.1-new-fix-doc-finding.patch
BuildRoot: %{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n)
@@ -61,9 +66,12 @@ BuildRequires: gd-devel
BuildRequires: pam-devel
BuildRequires: pcre-devel
BuildRequires: zlib-devel
-BuildRequires: plplot-devel
+# BuildRequires: plplot-devel
BuildRequires: expat-devel
BuildRequires: libharu-devel
+BuildRequires: postgresql-devel
+BuildRequires: mysql-devel
+BuildRequires: libtool, autoconf
%if %{with jemboss}
BuildRequires: ant
BuildRequires: desktop-file-utils
@@ -138,15 +146,16 @@ http://www.hgmp.mrc.ac.uk/Software/EMBOSS/Jemboss/
%setup -q
%patch0 -p1
%patch1 -p1 -b .system-pcre
-%patch3 -p1 -b .system-plplot
+# %%patch3 -p1 -b .system-plplot
%patch4 -p1 -b .system-expat
-%patch5 -p0 -b .fedora
-%patch6 -p1 -b .autobarf
-%patch7 -p1 -b .system
-%patch8 -p1 -b .fix-doc-finding
+%patch5 -p1 -b .system-zlib
+%patch6 -p1 -b .fix-amd64-check
-# Remove bundled plplot, expat, pcre and zlib to make sure that system versions are used
-rm -rf plplot/
+%patch7 -p0 -b .fedora
+%patch8 -p1 -b .system
+%patch9 -p1 -b .fix-doc-finding
+
+# Remove bundled expat, pcre and zlib to make sure that system versions are used
rm -rf ajax/{expat,pcre,zlib}
#install the patch readme
@@ -183,6 +192,8 @@ done
export PATH=$PATH:%{_java}/bin/
%endif
+autoreconf -i
+
%configure \
--disable-static \
--with-x \
@@ -302,6 +313,12 @@ rm -rf $RPM_BUILD_ROOT
%changelog
+* Tue Nov 9 2010 Tom "spot" Callaway <tcallawa at redhat.com> - 6.3.1-7
+- use bundled plplot (EMBOSS depends on fork)
+- add BR for postgresql-devel and mysql-devel
+- use autotools to generate updated configure/Makefiles
+- fix amd64 check to be finer grained, eliminate koji false positive
+
* Thu Nov 4 2010 Tom "spot" Callaway <tcallawa at redhat.com> - 6.3.1-6
- more intricate fix doc finding patch for 6.3.1
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