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author | Robin H. Johnson <robbat2@gentoo.org> | 2015-08-08 13:49:04 -0700 |
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committer | Robin H. Johnson <robbat2@gentoo.org> | 2015-08-08 17:38:18 -0700 |
commit | 56bd759df1d0c750a065b8c845e93d5dfa6b549d (patch) | |
tree | 3f91093cdb475e565ae857f1c5a7fd339e2d781e /sci-biology/primer3/files | |
download | gentoo-56bd759df1d0c750a065b8c845e93d5dfa6b549d.tar.gz gentoo-56bd759df1d0c750a065b8c845e93d5dfa6b549d.tar.bz2 gentoo-56bd759df1d0c750a065b8c845e93d5dfa6b549d.zip |
proj/gentoo: Initial commit
This commit represents a new era for Gentoo:
Storing the gentoo-x86 tree in Git, as converted from CVS.
This commit is the start of the NEW history.
Any historical data is intended to be grafted onto this point.
Creation process:
1. Take final CVS checkout snapshot
2. Remove ALL ChangeLog* files
3. Transform all Manifests to thin
4. Remove empty Manifests
5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$
5.1. Do not touch files with -kb/-ko keyword flags.
Signed-off-by: Robin H. Johnson <robbat2@gentoo.org>
X-Thanks: Alec Warner <antarus@gentoo.org> - did the GSoC 2006 migration tests
X-Thanks: Robin H. Johnson <robbat2@gentoo.org> - infra guy, herding this project
X-Thanks: Nguyen Thai Ngoc Duy <pclouds@gentoo.org> - Former Gentoo developer, wrote Git features for the migration
X-Thanks: Brian Harring <ferringb@gentoo.org> - wrote much python to improve cvs2svn
X-Thanks: Rich Freeman <rich0@gentoo.org> - validation scripts
X-Thanks: Patrick Lauer <patrick@gentoo.org> - Gentoo dev, running new 2014 work in migration
X-Thanks: Michał Górny <mgorny@gentoo.org> - scripts, QA, nagging
X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed
Diffstat (limited to 'sci-biology/primer3/files')
-rw-r--r-- | sci-biology/primer3/files/primer3-1.1.4-ldflags.patch | 25 | ||||
-rw-r--r-- | sci-biology/primer3/files/primer3-2.3.4-buildsystem.patch | 148 |
2 files changed, 173 insertions, 0 deletions
diff --git a/sci-biology/primer3/files/primer3-1.1.4-ldflags.patch b/sci-biology/primer3/files/primer3-1.1.4-ldflags.patch new file mode 100644 index 000000000000..66a5a52d4e8e --- /dev/null +++ b/sci-biology/primer3/files/primer3-1.1.4-ldflags.patch @@ -0,0 +1,25 @@ +Respect LDFLAGS + +http://bugs.gentoo.org/show_bug.cgi?id=335225 + +--- src/Makefile ++++ src/Makefile +@@ -103,10 +103,10 @@ + $(CC) $(LDFLAGS) -o $@ ntdpal_main.o dpal.o
+
+ oligotm: oligotm_main.c oligotm.h $(OLIGOTM_LIB)
+- $(CC) $(CFLAGS) -o $@ oligotm_main.c $(OLIGOTM_LIB) $(LIBOPTS) $(LDLIBS)
++ $(CC) $(LDFLAGS) $(CFLAGS) -o $@ oligotm_main.c $(OLIGOTM_LIB) $(LIBOPTS) $(LDLIBS)
+
+ long_seq_tm_test: long_seq_tm_test_main.c oligotm.o
+- $(CC) $(CFLAGS) -o $@ long_seq_tm_test_main.c oligotm.o $(LIBOPTS) $(LDLIBS)
++ $(CC) $(LDFLAGS) $(CFLAGS) -o $@ long_seq_tm_test_main.c oligotm.o $(LIBOPTS) $(LDLIBS)
+
+ boulder_input.o: boulder_input.c boulder_input.h primer3.h primer3_release.h dpal.h
+ $(CC) -c $(CFLAGS) $(P_DEFINES) -o $@ boulder_input.c
+@@ -136,4 +136,4 @@ + primer_test: test
+
+ test: $(PRIMER_EXE) ntdpal
+- cd ../test; make test
++ $(MAKE) -C ../test test
diff --git a/sci-biology/primer3/files/primer3-2.3.4-buildsystem.patch b/sci-biology/primer3/files/primer3-2.3.4-buildsystem.patch new file mode 100644 index 000000000000..cf47b35af502 --- /dev/null +++ b/sci-biology/primer3/files/primer3-2.3.4-buildsystem.patch @@ -0,0 +1,148 @@ + src/Makefile | 61 ++++++++++++++++++++++++++++++------------------------------ + 1 file changed, 31 insertions(+), 30 deletions(-) + +diff --git a/src/Makefile b/src/Makefile +index 607ab45..a88adf4 100644 +--- a/src/Makefile ++++ b/src/Makefile +@@ -52,15 +52,16 @@ TESTOPTS= + WINMAKE=mingw32-make + + LDLIBS = -lm +-AR = ar +-CC = gcc +-CPP = g++ +-O_OPTS = -O2 +-CC_OPTS = -g -Wall -D__USE_FIXED_PROTOTYPES__ +-P_DEFINES = ++AR ?= ar ++CC ?= gcc ++CXX ?= g++ ++O_OPTS ?= ++CC_OPTS ?= -Wall -D__USE_FIXED_PROTOTYPES__ ++P_DEFINES ?= + +-CFLAGS = $(CC_OPTS) $(O_OPTS) +-LDFLAGS = -g ++CFLAGS += $(CC_OPTS) $(O_OPTS) ++CXXFLAGS += $(CC_OPTS) $(O_OPTS) ++LDFLAGS += + # Note, for profiling, use + # make O_OPTS='-pg -O0' LDFLAGS='-g -pg' + +@@ -92,7 +93,7 @@ LIBPRIMER3 = libprimer3.a + LIBPRIMER3_DYN = libprimer3.so.1.0.0 + LIBRARIES = $(LIBPRIMER3) $(LIBDPAL) $(LIBTHAL) $(LIBOLIGOTM) + DYNLIBS = $(LIBPRIMER3_DYN) $(LIBDPAL_DYN) $(LIBTHAL_DYN) $(LIBOLIGOTM_DYN) +-RANLIB = ranlib ++RANLIB ?= ranlib + + PRIMER_OBJECTS1=primer3_boulder_main.o\ + format_output.o\ +@@ -127,85 +128,85 @@ $(LIBOLIGOTM): oligotm.o + $(RANLIB) $@ + + $(LIBOLIGOTM_LIB): oligotm.o +- $(CC) -shared -W1,-soname,liboligotm.so.1 -o $(LIBOLIGOTM_DYN) oligotm.o ++ $(CC) $(LDFLAGS) -shared -W1,-soname,liboligotm.so.1 -o $(LIBOLIGOTM_DYN) oligotm.o + + $(LIBDPAL): dpal_primer.o + $(AR) rv $@ dpal_primer.o + $(RANLIB) $@ + + $(LIBDPAL_DYN): dpal_primer.o +- $(CC) -shared -W1,-soname,libdpal.so.1 -o $(LIBDPAL_DYN_LIB) dpal_primer.o ++ $(CC) $(LDFLAGS) -shared -W1,-soname,libdpal.so.1 -o $(LIBDPAL_DYN_LIB) dpal_primer.o + + $(LIBTHAL): thal_primer.o + $(AR) rv $@ thal_primer.o + $(RANLIB) $@ + + $(LIBTHAL_DYN): thal_primer.o +- $(CC) -shared -W1,-soname,libthal.so.1 -o $(LIBTHAL_DYN_LIB) thal_primer.o ++ $(CC) $(LDFLAGS) -shared -W1,-soname,libthal.so.1 -o $(LIBTHAL_DYN_LIB) thal_primer.o + + $(LIBPRIMER3): libprimer3.o p3_seq_lib.o + $(AR) rv $@ libprimer3.o p3_seq_lib.o + $(RANLIB) $@ + + $(LIBPRIMER3_DYN): libprimer3.o p3_seq_lib.o +- $(CC) -shared -W1,-soname,liprimer3.so.1 -o $(LIBPRIMER3_DYN) libprimer3.o p3_seq_lib.o ++ $(CC) $(LDFLAGS) -shared -W1,-soname,liprimer3.so.1 -o $(LIBPRIMER3_DYN) libprimer3.o p3_seq_lib.o + + $(PRIMER_EXE): $(PRIMER_OBJECTS) +- $(CPP) $(LDFLAGS) -o $@ $(PRIMER_OBJECTS) $(LIBOPTS) $(LDLIBS) ++ $(CXX) $(LDFLAGS) -o $@ $(PRIMER_OBJECTS) $(LIBOPTS) $(LDLIBS) + + libprimer3.o: libprimer3.c libprimer3.h p3_seq_lib.h dpal.h thal.h oligotm.h +- $(CPP) -c $(CFLAGS) -Wno-deprecated $(P_DEFINES) -o $@ libprimer3.c ++ $(CXX) -c $(CXXFLAGS) -Wno-deprecated $(P_DEFINES) -o $@ libprimer3.c + + $(NTDPAL_EXE): ntdpal_main.o dpal.o +- $(CPP) $(LDFLAGS) -o $@ ntdpal_main.o dpal.o ++ $(CXX) $(LDFLAGS) -o $@ ntdpal_main.o dpal.o + + $(NTTHAL_EXE): thal_main.o thal.o +- $(CPP) $(LDFLAGS) -o $@ thal_main.o thal.o $(LDLIBS) ++ $(CXX) $(LDFLAGS) -o $@ thal_main.o thal.o $(LDLIBS) + + $(OLIGOTM_EXE): oligotm_main.c oligotm.h $(LIBOLIGOTM) +- $(CPP) $(CFLAGS) -o $@ oligotm_main.c $(LIBOLIGOTM) $(LIBOPTS) $(LDLIBS) ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ oligotm_main.c $(LIBOLIGOTM) $(LIBOPTS) $(LDLIBS) + + $(LONG_SEQ_EXE): long_seq_tm_test_main.c oligotm.o +- $(CPP) $(CFLAGS) -o $@ long_seq_tm_test_main.c oligotm.o $(LIBOPTS) $(LDLIBS) ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ long_seq_tm_test_main.c oligotm.o $(LIBOPTS) $(LDLIBS) + + read_boulder.o: read_boulder.c read_boulder.h libprimer3.h dpal.h thal.h p3_seq_lib.h +- $(CPP) -c $(CFLAGS) $(P_DEFINES) -o $@ read_boulder.c ++ $(CXX) -c $(CXXFLAGS) $(P_DEFINES) -o $@ read_boulder.c + + print_boulder.o: print_boulder.c print_boulder.h libprimer3.h p3_seq_lib.h +- $(CPP) -c $(CFLAGS) $(P_DEFINES) -o $@ print_boulder.c ++ $(CXX) -c $(CXXFLAGS) $(P_DEFINES) -o $@ print_boulder.c + + dpal.o: dpal.c dpal.h +- $(CPP) -c $(CFLAGS) -o $@ dpal.c ++ $(CXX) -c $(CXXFLAGS) -o $@ dpal.c + + # We use '-ffloat-store' on windows to prevent undesirable + # precision which may lead to differences in floating point results. + thal.o: thal.c thal.h +- $(CPP) -c $(CFLAGS) -ffloat-store -o $@ thal.c ++ $(CXX) -c $(CXXFLAGS) -ffloat-store -o $@ thal.c + + p3_seq_lib.o: p3_seq_lib.c p3_seq_lib.h libprimer3.h +- $(CPP) -c $(CFLAGS) -o $@ p3_seq_lib.c ++ $(CXX) -c $(CXXFLAGS) -o $@ p3_seq_lib.c + + dpal_primer.o: dpal.c dpal.h +- $(CPP) -c $(CFLAGS) $(P_DEFINES) -o $@ dpal.c ++ $(CXX) -c $(CXXFLAGS) $(P_DEFINES) -o $@ dpal.c + + thal_primer.o: thal.c thal.h +- $(CPP) -c $(CFLAGS) -ffloat-store $(P_DEFINES) -o $@ thal.c ++ $(CXX) -c $(CXXFLAGS) -ffloat-store $(P_DEFINES) -o $@ thal.c + + format_output.o: format_output.c format_output.h libprimer3.h dpal.h thal.h p3_seq_lib.h +- $(CPP) -c $(CFLAGS) $(P_DEFINES) -o $@ format_output.c ++ $(CXX) -c $(CXXFLAGS) $(P_DEFINES) -o $@ format_output.c + + ntdpal_main.o: ntdpal_main.c dpal.h +- $(CPP) -c $(CC_OPTS) -o $@ ntdpal_main.c ++ $(CXX) -c $(CXXFLAGS) -o $@ ntdpal_main.c + + thal_main.o: thal_main.c thal.h +- $(CPP) -c $(CFLAGS) -o $@ thal_main.c ++ $(CXX) -c $(CXXFLAGS) -o $@ thal_main.c + # We use CC_OPTS above rather than CFLAGS because + # gcc 2.7.2 crashes while compiling ntdpal_main.c with -O2 + + oligotm.o: oligotm.c oligotm.h + + primer3_boulder_main.o: primer3_boulder_main.c libprimer3.h dpal.h thal.h oligotm.h format_output.h print_boulder.h read_boulder.h +- $(CPP) -c $(CFLAGS) $(P_DEFINES) primer3_boulder_main.c ++ $(CXX) -c $(CXXFLAGS) $(P_DEFINES) primer3_boulder_main.c + + primer_test: test + |