diff options
Diffstat (limited to 'sci-biology/hmmer/files')
| -rw-r--r-- | sci-biology/hmmer/files/hmmer-3.0-fix_tests.patch | 23 | ||||
| -rw-r--r-- | sci-biology/hmmer/files/hmmer-3.0-perl-5.16-2.patch | 132 |
2 files changed, 0 insertions, 155 deletions
diff --git a/sci-biology/hmmer/files/hmmer-3.0-fix_tests.patch b/sci-biology/hmmer/files/hmmer-3.0-fix_tests.patch deleted file mode 100644 index 983827b0bd46..000000000000 --- a/sci-biology/hmmer/files/hmmer-3.0-fix_tests.patch +++ /dev/null @@ -1,23 +0,0 @@ ---- easel/Makefile.in -+++ easel/Makefile.in -@@ -26,8 +26,7 @@ - LDFLAGS = @LDFLAGS@ - SIMDFLAGS= @SIMD_CFLAGS@ - CPPFLAGS = @CPPFLAGS@ --LIBGSL = @LIBGSL@ --LIBS = @LIBS@ @PTHREAD_LIBS@ -+LIBS = @LIBS@ @LIBGSL@ @PTHREAD_LIBS@ - - # Other tools - # -@@ -252,8 +251,8 @@ - else \ - DFILE=${srcdir}/esl_$${BASENAME}.c ;\ - fi;\ -- echo ${CC} ${CFLAGS} ${SIMDFLAGS} ${DEFS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm;\ -- ${CC} ${CFLAGS} ${SIMDFLAGS} ${DEFS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm -+ echo ${CC} ${CFLAGS} ${SIMDFLAGS} ${DEFS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS};\ -+ ${CC} ${CFLAGS} ${SIMDFLAGS} ${DEFS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS} - - - # install: installs libeasel.a in ${libdir}/ diff --git a/sci-biology/hmmer/files/hmmer-3.0-perl-5.16-2.patch b/sci-biology/hmmer/files/hmmer-3.0-perl-5.16-2.patch deleted file mode 100644 index 19d38c8e32ed..000000000000 --- a/sci-biology/hmmer/files/hmmer-3.0-perl-5.16-2.patch +++ /dev/null @@ -1,132 +0,0 @@ - easel/devkit/autodoc | 4 ++-- - easel/devkit/esl-dependencies | 4 ++-- - easel/devkit/sqc | 7 +++---- - easel/testsuite/coverage_report.pl | 4 ++-- - easel/testsuite/driver_report.pl | 4 ++-- - easel/testsuite/valgrind_report.pl | 4 ++-- - profmark/rocplot.pl | 4 ++-- - 7 files changed, 15 insertions(+), 16 deletions(-) - -diff --git a/easel/devkit/autodoc b/easel/devkit/autodoc -index 16bda4d..f5c5efc 100755 ---- a/easel/devkit/autodoc -+++ b/easel/devkit/autodoc -@@ -49,8 +49,8 @@ - # - # SRE, Tue Nov 30 19:43:47 2004 - --require "getopts.pl"; --&Getopts('n:t'); -+use Getopt::Std; -+getopts('n:t'); - $cfile = shift; - - if ($opt_t) { $show_api_table = 1; } -diff --git a/easel/devkit/esl-dependencies b/easel/devkit/esl-dependencies -index a4dc126..b61fa7a 100755 ---- a/easel/devkit/esl-dependencies -+++ b/easel/devkit/esl-dependencies -@@ -13,8 +13,8 @@ - # SRE, Mon Jun 11 11:15:31 2007 - # SVN $Id$ - --require "getopts.pl" --&Getopts('1afr'); -+use Getopt::Std; -+getopts('1afr'); - - if ($opt_1) { $show_summary_table = 1; } - if ($opt_a) { $list_augfiles = 1; } -diff --git a/easel/devkit/sqc b/easel/devkit/sqc -index af3adf6..0cdb458 100755 ---- a/easel/devkit/sqc -+++ b/easel/devkit/sqc -@@ -205,12 +205,11 @@ - # SRE, Tue Aug 6 11:16:39 2002 - # SVN $Id: sqc 1796 2007-01-03 22:36:44Z eddys $ - --require "getopts.pl"; --require "importenv.pl"; -+use Getopt::Std; - - # Parse our command line - # --&Getopts('v'); -+getopts('v'); - if ($opt_v) { $verbose = 1; } - - -@@ -609,7 +608,7 @@ sub check_valgrind_status - # - sub tempname { - my ($dir, $name, $suffix); -- if ($TMPDIR) { $dir = $TMPDIR."/"; } else {$dir = "";} -+ if ($ENV{TMPDIR}) { $dir = $ENV{TMPDIR}."/"; } else {$dir = "";} - - foreach $suffix ("aa".."zz") { - $name = "$dir"."esltmp".$suffix.$$; -diff --git a/easel/testsuite/coverage_report.pl b/easel/testsuite/coverage_report.pl -old mode 100755 -new mode 100644 -index 9c77791..024ed34 ---- a/easel/testsuite/coverage_report.pl -+++ b/easel/testsuite/coverage_report.pl -@@ -16,9 +16,9 @@ - # - # SRE, Thu Mar 1 19:22:57 2007 (Janelia) - # SVN $Id: coverage_report.pl 231 2008-03-25 14:43:57Z eddys $ --require "getopts.pl"; -+use Getopt::Std; - $have_sloccount = 1; --&Getopts('cs'); -+getopts('cs'); - if ($opt_c) { $do_recompile = 1; } - if ($opt_s) { $have_sloccount = 0; } - -diff --git a/easel/testsuite/driver_report.pl b/easel/testsuite/driver_report.pl -index 757854d..a9a8902 100755 ---- a/easel/testsuite/driver_report.pl -+++ b/easel/testsuite/driver_report.pl -@@ -25,8 +25,8 @@ - # SRE, Fri Mar 2 10:01:44 2007 (Janelia) - # SVN $Id: driver_report.pl 326 2009-02-28 15:49:07Z eddys $ - --require "getopts.pl"; --&Getopts('c'); -+use Getopt::Std; -+getopts('c'); - if ($opt_c) { $do_recompile = 1; } - - if ($ENV{'CC'} ne "") { $CC = $ENV{'CC'}; } else { $CC = "gcc"; } -diff --git a/easel/testsuite/valgrind_report.pl b/easel/testsuite/valgrind_report.pl -old mode 100755 -new mode 100644 -index 186a392..07026a0 ---- a/easel/testsuite/valgrind_report.pl -+++ b/easel/testsuite/valgrind_report.pl -@@ -10,8 +10,8 @@ - # - # SRE, Fri Mar 2 08:37:48 2007 [Janelia] - # SVN $Id: valgrind_report.pl 231 2008-03-25 14:43:57Z eddys $ --require "getopts.pl"; --&Getopts('c'); -+use Getopt::Std; -+getopts('c'); - if ($opt_c) { $do_recompile = 1; } - - if ($ENV{'CC'} ne "") { $CC = $ENV{'CC'}; } else { $CC = "gcc"; } -diff --git a/profmark/rocplot.pl b/profmark/rocplot.pl -index d4c0f67..4e8175a 100755 ---- a/profmark/rocplot.pl -+++ b/profmark/rocplot.pl -@@ -2,8 +2,8 @@ - - $nsearches = 1567; - --require "getopts.pl"; --&Getopts('n:X:x:'); -+use Getopt::Std -+getopts('n:X:x:'); - - if ($opt_n) { $nsearches = $opt_n; } - if ($opt_X) { |