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commit: d9704bbb3086a2847673b25a93d179f240dc7037 |
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Author: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org> |
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AuthorDate: Sat Jan 15 11:03:39 2022 +0000 |
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Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org> |
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CommitDate: Sat Jan 15 11:03:39 2022 +0000 |
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URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=d9704bbb |
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|
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profiles/updates: move sra_sdk to sra-tools |
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|
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Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org> |
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|
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profiles/updates/1Q-2022 | 1 + |
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sci-biology/sra_sdk/files/libs_sra_Makefile.patch | 77 ---------------------- |
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sci-biology/sra_sdk/files/sra_sdk-destdir.patch | 76 --------------------- |
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.../sra_sdk/files/tools_vdb-vcopy_Makefile.patch | 12 ---- |
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sci-biology/sra_sdk/metadata.xml | 12 ---- |
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sci-biology/sra_sdk/sra_sdk-2.10.9.ebuild | 76 --------------------- |
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6 files changed, 1 insertion(+), 253 deletions(-) |
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|
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diff --git a/profiles/updates/1Q-2022 b/profiles/updates/1Q-2022 |
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new file mode 100644 |
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index 000000000..e905430ca |
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--- /dev/null |
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+++ b/profiles/updates/1Q-2022 |
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@@ -0,0 +1 @@ |
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+sci-biology/sra_sdk sci-biology/sra-tools |
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|
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diff --git a/sci-biology/sra_sdk/files/libs_sra_Makefile.patch b/sci-biology/sra_sdk/files/libs_sra_Makefile.patch |
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deleted file mode 100644 |
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index 44acc42b0..000000000 |
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--- a/sci-biology/sra_sdk/files/libs_sra_Makefile.patch |
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+++ /dev/null |
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@@ -1,77 +0,0 @@ |
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-diff -u -w sra_sdk-2.1.9/work/sra_sdk-2.1.9/libs/sra/Makefile sra_sdk-2.1.9/work/sra_sdk-2.1.9/libs/sra/Makefile |
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---- sra_sdk-2.1.9/work/sra_sdk-2.1.9/libs/sra/Makefile 2011-12-02 21:30:12.000000000 +0100 |
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-+++ sra_sdk-2.1.9/work/sra_sdk-2.1.9/libs/sra/Makefile 2012-02-06 18:38:45.000000000 +0100 |
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-@@ -100,7 +100,7 @@ |
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- $(addsuffix .$(LOBX),$(SRAPATH_SRC)) |
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- |
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- $(LIBDIR)/libsrapath.$(LIBX): $(SRAPATH_OBJ) |
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-- $(LD) --slib -o $@ $^ |
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-+ $(LD) --slib -o $(DESTDIR)$@ $^ |
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- |
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- libsrapath.vers.h: |
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- @ true |
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-@@ -138,10 +138,10 @@ |
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- -dklib |
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- |
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- $(LIBDIR)/libsra-schema.$(SHLX): $(SRA_SCHEMA_OBJ) |
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-- $(LD) --dlib --vers $(SRCDIR) -o $@ $^ $(SRA_SCHEMA_LIB) |
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-+ $(LD) --dlib --vers $(SRCDIR) -o $(DESTDIR)$@ $^ $(SRA_SCHEMA_LIB) |
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- |
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- $(LIBDIR)/libwsra-schema.$(SHLX): $(WSRA_SCHEMA_OBJ) |
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-- $(LD) --dlib --vers $(SRCDIR) -o $@ $^ $(WSRA_SCHEMA_LIB) |
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-+ $(LD) --dlib --vers $(SRCDIR) -o $(DESTDIR)$@ $^ $(WSRA_SCHEMA_LIB) |
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- |
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- SRASCHEMA_SRC = \ |
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- sraschema-stub |
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-@@ -168,10 +168,10 @@ |
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- $(addsuffix .$(LOBX),$(WSRASCHEMA_SRC)) |
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- |
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- $(LIBDIR)/libsraschema.$(LIBX): $(SRASCHEMA_OBJ) $(SRASCHEMA_DEPS) |
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-- $(LD) --slib -o $@ $(SRASCHEMA_OBJ) $(SRA_SCHEMA_LIB) |
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-+ $(LD) --slib -o $(DESTDIR)$@ $(SRASCHEMA_OBJ) $(SRA_SCHEMA_LIB) |
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- |
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- $(LIBDIR)/libwsraschema.$(LIBX): $(WSRASCHEMA_OBJ) $(WSRASCHEMA_DEPS) |
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-- $(LD) --slib -o $@ $(WSRASCHEMA_OBJ) $(WSRA_SCHEMA_LIB) |
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-+ $(LD) --slib -o $(DESTDIR)$@ $(WSRASCHEMA_OBJ) $(WSRA_SCHEMA_LIB) |
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- |
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- libsraschema_tag: |
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- @ $(TOP)/build/tag-module.sh $(MODULE) libsraschema $(SRASCHEMA_OBJ) |
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-@@ -205,10 +205,10 @@ |
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- -dklib |
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- |
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- $(LIBDIR)/libsradb.$(SHLX): $(SRADB_OBJ) |
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-- $(LD) --dlib --vers $(SRCDIR) -o $@ $^ $(SRADB_LIB) |
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-+ $(LD) --dlib --vers $(SRCDIR) -o $(DESTDIR)$@ $^ $(SRADB_LIB) |
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- |
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- $(LIBDIR)/libsradb.$(LIBX): $(SRADB_OBJ) |
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-- $(LD) --slib --vers $(SRCDIR) -o $@ $^ $(SRADB_LIB) |
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-+ $(LD) --slib --vers $(SRCDIR) -o $(DESTDIR)$@ $^ $(SRADB_LIB) |
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- |
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- libsradb_tag: $(SRADB_TAGS) |
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- @ $(TOP)/build/tag-module.sh $(MODULE) libsradb $(SRADB_OBJ) |
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-@@ -236,10 +236,10 @@ |
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- -dklib |
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- |
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- $(LIBDIR)/libwsradb.$(SHLX): $(WSRADB_OBJ) |
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-- $(LD) --dlib --vers $(SRCDIR) -o $@ $^ $(WSRADB_LIB) |
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-+ $(LD) --dlib --vers $(SRCDIR) -o $(DESTDIR)$@ $^ $(WSRADB_LIB) |
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- |
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- $(LIBDIR)/libwsradb.$(LIBX): $(WSRADB_OBJ) |
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-- $(LD) --slib --vers $(SRCDIR) -o $@ $^ $(WSRADB_LIB) |
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-+ $(LD) --slib --vers $(SRCDIR) -o $(DESTDIR)$@ $^ $(WSRADB_LIB) |
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- |
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- libwsradb_tag: $(WSRADB_TAGS) |
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- @ $(TOP)/build/tag-module.sh $(MODULE) libwsradb $(WSRADB_OBJ) |
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-@@ -266,10 +266,10 @@ |
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- -dklib |
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- |
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- $(LIBDIR)/libsrareader.$(SHLX): $(SRAREADER_OBJ) |
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-- $(LD) --dlib --vers $(SRCDIR) -o $@ $^ $(SRAREADER_LIB) |
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-+ $(LD) --dlib --vers $(SRCDIR) -o $(DESTDIR)$@ $^ $(SRAREADER_LIB) |
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- |
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- $(LIBDIR)/libsrareader.$(LIBX): $(SRAREADER_OBJ) |
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-- $(LD) --slib --vers $(SRCDIR) -o $@ $^ $(SRAREADER_LIB) |
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-+ $(LD) --slib --vers $(SRCDIR) -o $(DESTDIR)$@ $^ $(SRAREADER_LIB) |
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- |
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- libsrareader_tag: |
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- @ $(TOP)/build/tag-module.sh $(MODULE) libsrareader $(SRAREADER_OBJ) |
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|
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diff --git a/sci-biology/sra_sdk/files/sra_sdk-destdir.patch b/sci-biology/sra_sdk/files/sra_sdk-destdir.patch |
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deleted file mode 100644 |
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index bf66c6e46..000000000 |
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--- a/sci-biology/sra_sdk/files/sra_sdk-destdir.patch |
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+++ /dev/null |
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@@ -1,76 +0,0 @@ |
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-diff -r -u -w sra_sdk-2.1.9/work/sra_sdk-2.1.9/build/Makefile.env sra_sdk-2.1.9-/work/sra_sdk-2.1.9/build/Makefile.env |
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---- sra_sdk-2.1.9/work/sra_sdk-2.1.9/build/Makefile.env 2011-08-31 21:46:21.000000000 +0200 |
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-+++ sra_sdk-2.1.9-/work/sra_sdk-2.1.9/build/Makefile.env 2012-02-06 02:02:38.000000000 +0100 |
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-@@ -141,7 +141,7 @@ |
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- |
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- # create all required output directories |
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- makedirs: |
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-- @ mkdir -p $(addprefix $(TARGDIR)/,$(SUBDIRS) obj/$(MODULE)) $(NCBIDIR) |
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-+ @ mkdir -p $(addprefix $(TARGDIR)/,$(SUBDIRS) obj/$(MODULE)) $(DESTDIR)/$(NCBIDIR) |
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- |
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- ifeq (win,$(OS)) |
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- |
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-diff -r -u -w sra_sdk-2.1.9/work/sra_sdk-2.1.9/build/ld.linux.gcc.sh sra_sdk-2.1.9-/work/sra_sdk-2.1.9/build/ld.linux.gcc.sh |
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---- sra_sdk-2.1.9/work/sra_sdk-2.1.9/build/ld.linux.gcc.sh 2010-12-28 22:46:39.000000000 +0100 |
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-+++ sra_sdk-2.1.9-/work/sra_sdk-2.1.9/build/ld.linux.gcc.sh 2012-02-06 02:23:07.000000000 +0100 |
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-@@ -38,10 +38,10 @@ |
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- # versioned output |
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- if [ "$VERS" = "" ] |
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- then |
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-- DLIB_CMD="$DLIB_CMD -o $TARG" |
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-- EXE_CMD="$EXE_CMD -o $TARG" |
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-+ DLIB_CMD="$DLIB_CMD -o $DESTDIR$TARG" |
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-+ EXE_CMD="$EXE_CMD -o $TARG" |
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- else |
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- set-vers $(echo $VERS | tr '.' ' ') |
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-- DLIB_CMD="$DLIB_CMD -o $OUTDIR/$NAME$DBGAP.so.$VERS -Wl,-soname,$NAME.so.$MAJ" |
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-- EXE_CMD="$EXE_CMD -o $OUTDIR/$NAME$DBGAP.$VERS" |
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-+ DLIB_CMD="$DLIB_CMD -o $DESTDIR$OUTDIR/$NAME$DBGAP.so.$VERS -Wl,-soname,$NAME.so.$MAJ" |
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-+ EXE_CMD="$EXE_CMD -o $DESTDIR$OUTDIR/$NAME$DBGAP.$VERS" |
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- fi |
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-diff -r -u -w sra_sdk-2.1.9/work/sra_sdk-2.1.9/build/ld.linux.ln.sh sra_sdk-2.1.9-/work/sra_sdk-2.1.9/build/ld.linux.ln.sh |
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---- sra_sdk-2.1.9/work/sra_sdk-2.1.9/build/ld.linux.ln.sh 2010-12-28 22:46:39.000000000 +0100 |
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-+++ sra_sdk-2.1.9-/work/sra_sdk-2.1.9/build/ld.linux.ln.sh 2012-02-06 02:34:46.000000000 +0100 |
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-@@ -52,12 +52,12 @@ |
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- |
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- set-vers $(echo $VERS | tr '.' ' ') |
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- |
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--cd "$OUTDIR" || exit 5 |
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-+cd $DESTDIR$OUTDIR || exit 5 |
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- |
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- # create link |
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- create-link () |
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- { |
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-- rm -f "$2" |
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-+ rm -f $DESTDIR"$2" |
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- local CMD="ln -s $1 $2" |
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- echo $CMD |
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- $CMD |
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---- sra_sdk-2.1.9/work/sra_sdk-2.1.9/build/ld.linux.slib.sh 2012-02-06 04:05:16.000000000 +0100 |
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-+++ sra_sdk-2.1.9-/work/sra_sdk-2.1.9/build/ld.linux.slib.sh 2012-02-06 04:05:29.000000000 +0100 |
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-@@ -77,7 +77,7 @@ |
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- CMD="$CMD $TARG" |
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- else |
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- set-vers $(echo $VERS | tr '.' ' ') |
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-- CMD="$CMD $OUTDIR/$NAME$DBGAP.a.$VERS" |
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-+ CMD="$CMD $DESTDIR/$OUTDIR/$NAME$DBGAP.a.$VERS" |
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- fi |
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- |
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- # tack on object files |
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---- sra_sdk-2.1.9/work/sra_sdk-2.1.9/build/Makefile.gcc.ori 2012-02-06 04:24:39.000000000 +0100 |
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-+++ sra_sdk-2.1.9/work/sra_sdk-2.1.9/build/Makefile.gcc 2012-02-06 04:22:57.000000000 +0100 |
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-@@ -36,12 +36,12 @@ |
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- LD = @ $(TOP)/build/ld.sh $(OS) $(ARCH) gcc \ |
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- --build $(BUILD) --ldflags "$(LDFLAGS)" $(STATIC) \ |
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- $(STATICSYSLIBS) $(CHECKSUM) --objx $(OBJX) --shlx $(SHLX) --libx $(LIBX) \ |
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-- -MD --srcdir $(SRCDIR) --bindir $(BINDIR) -L$(LIBDIR):$(ILIBDIR) |
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-+ -MD --srcdir $(SRCDIR) --bindir $(BINDIR) -L$(DESTDIR)$(LIBDIR):$(ILIBDIR) |
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- |
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- LP = @ $(TOP)/build/ld.sh $(OS) $(ARCH) g++ \ |
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- --build $(BUILD) --ldflags "$(LDFLAGS)" $(STATIC) \ |
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- $(STATICSYSLIBS) $(CHECKSUM) --objx $(OBJX) --shlx $(SHLX) --libx $(LIBX) \ |
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-- -MD --srcdir $(SRCDIR) --bindir $(BINDIR) -L$(LIBDIR):$(ILIBDIR) |
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-+ -MD --srcdir $(SRCDIR) --bindir $(BINDIR) -L$(DESTDIR)$(LIBDIR):$(ILIBDIR) |
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- |
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- # tool options |
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- WARN = -Wall -Wno-variadic-macros # -Wconversion |
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|
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diff --git a/sci-biology/sra_sdk/files/tools_vdb-vcopy_Makefile.patch b/sci-biology/sra_sdk/files/tools_vdb-vcopy_Makefile.patch |
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deleted file mode 100644 |
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index 738d67cbd..000000000 |
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--- a/sci-biology/sra_sdk/files/tools_vdb-vcopy_Makefile.patch |
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+++ /dev/null |
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@@ -1,12 +0,0 @@ |
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-diff -u -w sra_sdk-2.1.9/work/sra_sdk-2.1.9/tools/vdb-copy/Makefile sra_sdk-2.1.9/work/sra_sdk-2.1.9/tools/vdb-copy/Makefile |
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---- sra_sdk-2.1.9/work/sra_sdk-2.1.9/tools/vdb-copy/Makefile 2011-12-02 22:00:36.000000000 +0100 |
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-+++ sra_sdk-2.1.9/work/sra_sdk-2.1.9/tools/vdb-copy/Makefile 2012-02-06 18:39:05.000000000 +0100 |
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-@@ -89,7 +89,7 @@ |
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- $(BINDIR)/vdb-copy: $(NCBIDIR)/vdb-copy.kfg |
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- |
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- $(NCBIDIR)/vdb-copy.kfg: $(SRCDIR)/vdb-copy.kfg |
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-- cp $^ $@ |
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-+ cp $^ $(DESTDIR)$@ |
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- |
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- VDB_COPY_SRC = \ |
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- num-gen \ |
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|
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diff --git a/sci-biology/sra_sdk/metadata.xml b/sci-biology/sra_sdk/metadata.xml |
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deleted file mode 100644 |
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index 138cb7705..000000000 |
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--- a/sci-biology/sra_sdk/metadata.xml |
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+++ /dev/null |
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@@ -1,12 +0,0 @@ |
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-<?xml version="1.0" encoding="UTF-8"?> |
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-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> |
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-<pkgmetadata> |
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- <maintainer type="person"> |
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- <email>mmokrejs@×××××××××××××××.cz</email> |
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- <name>Martin Mokrejs</name> |
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- </maintainer> |
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- <maintainer type="project"> |
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- <email>sci-biology@g.o</email> |
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- <name>Gentoo Biology Project</name> |
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- </maintainer> |
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-</pkgmetadata> |
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|
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diff --git a/sci-biology/sra_sdk/sra_sdk-2.10.9.ebuild b/sci-biology/sra_sdk/sra_sdk-2.10.9.ebuild |
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deleted file mode 100644 |
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index ef1c8a5d6..000000000 |
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--- a/sci-biology/sra_sdk/sra_sdk-2.10.9.ebuild |
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+++ /dev/null |
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@@ -1,76 +0,0 @@ |
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-# Copyright 1999-2021 Gentoo Authors |
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-# Distributed under the terms of the GNU General Public License v2 |
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- |
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-EAPI=7 |
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- |
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-DESCRIPTION="NCBI Sequence Read Archive (SRA) sratoolkit" |
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-HOMEPAGE="https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi https://github.com/ncbi/sra-tools" |
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-SRC_URI="https://github.com/ncbi/sra-tools/archive/${PV}.tar.gz -> ${P}.tar.gz" |
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- |
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-LICENSE="public-domain" |
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-SLOT="0" |
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-# missing dep ngs-sdk |
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-KEYWORDS="" |
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- |
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-DEPEND=" |
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- app-shells/bash:* |
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- sys-libs/zlib |
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- app-arch/bzip2 |
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- dev-libs/libxml2:2=" |
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-RDEPEND="${DEPEND}" |
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- |
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-S="${WORKDIR}/sra-tools-${PV}" |
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- |
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-src_configure() { |
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- # this is some non-standard configure script |
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- ./configure || die |
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-} |
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- |
267 |
-src_compile(){ |
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- emake OUTDIR="${WORKDIR}"/objdir out |
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- emake dynamic |
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- emake release |
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- default |
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-} |
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- |
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-src_install(){ |
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- rm -rf /var/tmp/portage/sci-biology/"${P}"/image/var |
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- # BUG: at the moment every binary is installed three times, e.g.: |
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- # -rwxr-xr-x 1 root root 1797720 Sep 23 01:31 abi-dump |
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- # -rwxr-xr-x 1 root root 1797720 Sep 23 01:31 abi-dump.2 |
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- # -rwxr-xr-x 1 root root 1797720 Sep 23 01:31 abi-dump.2.1.6 |
280 |
- if use amd64; then |
281 |
- builddir="x86_64" |
282 |
- elif use x86; then |
283 |
- builddir="i386" |
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- fi |
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- dodir /usr/bin /usr/lib/ncbi /usr/ncbi/schema |
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- |
287 |
- OBJDIR="${WORKDIR}"/objdir/linux/gcc/dyn/"${builddir}"/rel |
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- |
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- # BUG: neither 'doins -r' nor cp --preserve=all work |
290 |
- #insinto /usr/bin |
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- #doins -r "${WORKDIR}"/objdir/linux/rel/gcc/"${builddir}"/bin/* |
292 |
- for f in "${OBJDIR}"/bin/*; do cp --preserve=all "$f" "${D}"/usr/bin/ || die "$f copying failed" ; done |
293 |
- |
294 |
- # install the main libs and the ncbi/vdb-copy.kfg file |
295 |
- insinto /usr/lib/ncbi |
296 |
- doins "${OBJDIR}"/lib/ncbi/* |
297 |
- |
298 |
- # zap the subdirectory so that copying below does not fail |
299 |
- rm -rf "${OBJDIR}"/lib/ncbi || die |
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- |
301 |
- # BUG: neither the dolib nor cp --preserve=all work |
302 |
- #insinto /usr/lib64 |
303 |
- #dolib "${WORKDIR}"/objdir/linux/rel/gcc/"${builddir}"/lib/* |
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- mkdir -p "${D}"/usr/lib64 |
305 |
- for f in "${OBJDIR}"/lib/*; do cp --preserve=all "$f" "${D}"/usr/lib64/ || die "$f copying failed" ; done |
306 |
- |
307 |
- insinto /usr/ncbi/schema |
308 |
- doins \ |
309 |
- "${W}"/interfaces/align/*.vschema \ |
310 |
- "${W}"/interfaces/sra/*.vschema \ |
311 |
- "${W}"/interfaces/vdb/*.vschema \ |
312 |
- "${W}"/interfaces/ncbi/*.vschema \ |
313 |
- "${W}"/interfaces/insdc/*.vschema |
314 |
-} |