[med-svn] [Git][med-team/ncbi-tools6][master] 5 commits: Start work on ncbi-tools6 6.1.20170106+dfsg2-6.
Aaron M. Ucko (@ucko)
gitlab at salsa.debian.org
Mon May 26 20:46:05 BST 2025
Aaron M. Ucko pushed to branch master at Debian Med / ncbi-tools6
Commits:
322057d2 by Aaron M. Ucko at 2025-05-26T15:03:24-04:00
Start work on ncbi-tools6 6.1.20170106+dfsg2-6.
- - - - -
1a82b58b by Aaron M. Ucko at 2025-05-26T15:35:34-04:00
[#1105544] Fix or work around build-order assumptions
.. caught by make --shuffle=reverse.
* debian/rules: Explicitly invoke copy targets before compilation.
* make/makeall.unx: Build *.glo directly; GCC's on board with it, and
the current logic breaks when corresponding *.o files don't yet exist.
* make/makenet.unx: Explicitly build all static libraries encompassed
by nocopy or given as extra goals before any shared libraries.
- - - - -
2ce6ef58 by Aaron M. Ucko at 2025-05-26T15:38:01-04:00
debian/copyright: Substitute a URL for the FSF's postal address.
See #1080497.
- - - - -
feb52beb by Aaron M. Ucko at 2025-05-26T15:38:48-04:00
Standards-Version: 4.7.2 (routine-update)
- - - - -
0041f9d7 by Aaron M. Ucko at 2025-05-26T15:40:42-04:00
Finalize ncbi-tools6 6.1.20170106+dfsg2-6 for unstable.
- - - - -
7 changed files:
- debian/changelog
- debian/control
- debian/copyright
- debian/patches/debian-changes
- debian/rules
- make/makeall.unx
- make/makenet.unx
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,18 @@
+ncbi-tools6 (6.1.20170106+dfsg2-6) unstable; urgency=medium
+
+ * Fix or work around build-order assumptions caught by
+ make --shuffle=reverse. (Closes: #1105544.)
+ - debian/rules: Explicitly invoke copy targets before compilation.
+ - make/makeall.unx: Build *.glo directly; GCC's on board with it, and
+ the current logic breaks when corresponding *.o files don't yet exist.
+ - make/makenet.unx: Explicitly build all static libraries encompassed
+ by nocopy or given as extra goals before any shared libraries.
+ * debian/copyright: Substitute a URL for the FSF's postal address.
+ (See #1080497.)
+ * Standards-Version: 4.7.2 (routine-update)
+
+ -- Aaron M. Ucko <ucko at debian.org> Mon, 26 May 2025 15:40:41 -0400
+
ncbi-tools6 (6.1.20170106+dfsg2-5) unstable; urgency=medium
* debian/tests/control: Unconditionally skip network-based tests. They
=====================================
debian/control
=====================================
@@ -13,7 +13,7 @@ Build-Depends-Arch: csh | c-shell,
libxmu-dev
Build-Depends-Indep: icoutils,
imagemagick
-Standards-Version: 4.7.0
+Standards-Version: 4.7.2
Vcs-Browser: https://salsa.debian.org/med-team/ncbi-tools6
Vcs-Git: https://salsa.debian.org/med-team/ncbi-tools6.git
Homepage: https://www.ncbi.nlm.nih.gov/IEB/ToolBox/
=====================================
debian/copyright
=====================================
@@ -221,10 +221,8 @@ License: GPL-2+
PURPOSE. See the GNU General Public License for more
details.
.
- You should have received a copy of the GNU General Public
- License along with this package; if not, write to the Free
- Software Foundation, Inc., 51 Franklin St, Fifth Floor,
- Boston, MA 02110-1301 USA
+ You should have received a copy of the GNU General Public License
+ along with this package; if not, see https://www.gnu.org/licenses/.
.
On Debian systems, the full text of the GNU General Public
License version 2 can be found in the file
=====================================
debian/patches/debian-changes
=====================================
@@ -677,7 +677,21 @@ Combined patches from git.
.NO_PARALLEL: copy $(ULIB4) $(ULIB30)
-@@ -656,10 +656,12 @@ shlib.sol :
+@@ -512,12 +512,8 @@ clean :
+ .c.o :
+ $(CC) $(CFLAGS) $<
+
+-# this is ugly, because Solaris cc won't allow compile directly to .glo file
+ .c.glo :
+- mv $*.o $*.tmp
+- $(CC) $(CFLAGS) -D_OPENGL $<
+- mv $*.o $*.glo
+- mv $*.tmp $*.o
++ $(CC) $(CFLAGS) -D_OPENGL $< -o $@
+
+ ## Special case
+ ##
+@@ -656,10 +652,12 @@ shlib.sol :
cd ../shlib; make -f $(MAKESHLIB) `ls *.a | sed "s/\.a/.so/"` NCBI_OTHERLIBS=$(OTHERLIBS)
rm -f ../shlib/*.a
@@ -694,7 +708,7 @@ Combined patches from git.
shlib.sgi :
-mkdir ../shlib
-@@ -792,7 +794,7 @@ copy :
+@@ -792,7 +790,7 @@ copy :
cp -fp ../algo/blast/core/*.h ../include/algo/blast/core
- mkdir -p ../include/algo/blast/composition_adjustment
$(SRCCOPY) ../algo/blast/composition_adjustment/*.c .
@@ -760,7 +774,27 @@ Combined patches from git.
OBJDDV = ddvmain.o
OBJUDV = udvmain.o
-@@ -445,10 +447,12 @@ shlib.sol :
+@@ -388,9 +390,10 @@ ln-if-absent: ../make/ln-if-absent
+ rm -f ln-if-absent
+ ln -s ../make/ln-if-absent .
+
+-nocopy : sources $(BLIB6) $(BLIB7) $(BLIB8) $(BLIB9) \
++nocopy = sources $(BLIB6) $(BLIB7) $(BLIB8) $(BLIB9) \
+ $(DLIB31) $(DLIB33) $(NCBI_SHLIBS) $(CLIENTS) $(VIB) \
+ $(DLIB42) $(DLIB43) $(DLIB44)
++nocopy : $(nocopy)
+
+ sources : $(ALL_SRC)
+
+@@ -417,6 +420,7 @@ clean :
+ ## use subordinate makefile for building shared libraries
+ ##
+ shlib : shlib.$(LCL)
++shlib.$(LCL) : $(filter %.a,$(nocopy) $(MAKECMDGOALS))
+
+ ## Special rules to allow shared libs to be built more than once within
+ ## a given 'make' invocation
+@@ -445,10 +449,12 @@ shlib.sol :
cd ../shlib; make -f $(MAKESHLIB) `ls *.a | sed "s/\.a/.so/"` NCBI_OTHERLIBS=$(OTHERLIBS)
rm -f ../shlib/*.a
@@ -777,7 +811,7 @@ Combined patches from git.
shlib.sgi :
-mkdir ../shlib
-@@ -518,7 +522,7 @@ copy :
+@@ -518,7 +524,7 @@ copy :
$(SRCCOPY) ../network/vibnet/*.h ../include
$(SRCCOPY) ../cdromlib/*.h ../include
-$(SRCCOPY) ../network/wwwblast/Src/*.c .
@@ -786,7 +820,7 @@ Combined patches from git.
$(SRCCOPY) ../cdromlib/accentr.c .
$(SRCCOPY) ../cdromlib/accutils.c .
-$(SRCCOPY) ../sequin/*.* .
-@@ -952,6 +956,11 @@ accvdb.o : accvdb.c
+@@ -952,6 +958,11 @@ accvdb.o : accvdb.c
##
@@ -798,7 +832,7 @@ Combined patches from git.
ddv : $(OBJDDV)
$(CC) -o ddv $(LDFLAGS) $(OBJDDV) $(LIB41) $(LIB31) $(LIB20) $(LIB61) $(LIB60) $(LIB22) $(LIB45) \
$(LIB8) $(LIB7) $(NETCLILIB) $(LIB3) $(LIB4) $(LIB23) \
-@@ -1097,8 +1106,8 @@ asnval_dbx_psf.o : asnval.c
+@@ -1097,8 +1108,8 @@ asnval_dbx_psf.o : asnval.c
# asndisc program (asndisc)
asndisc : asndisc.c
$(CC) -g -o asndisc $(LDFLAGS) asndisc.c $(THREAD_OBJ) $(LIB41) \
@@ -809,7 +843,7 @@ Combined patches from git.
# asndisc_psf, uses PUBSEQBioseqFetchEnable instead of PubSeqFetchEnable
# should be used only internally within NCBI.
-@@ -1150,17 +1159,19 @@ diffshift : diffshift.c
+@@ -1150,17 +1161,19 @@ diffshift : diffshift.c
# gbseqget program (gbseqget)
gbseqget : gbseqget.c
$(CC) -g -o gbseqget $(LDFLAGS) gbseqget.c $(LIB41) $(NETCLILIB) \
@@ -832,7 +866,7 @@ Combined patches from git.
# trna2sap program (trna2sap)
trna2sap : trna2sap.c
-@@ -1181,7 +1192,8 @@ testent2 : testent2.c
+@@ -1181,7 +1194,8 @@ testent2 : testent2.c
entrez2 : entrez2.c
$(CC) -g -o entrez2 $(LDFLAGS) entrez2.c $(LIB41) $(LIB6) $(LIB20) \
$(LIB61) $(LIB60) $(LIB22) $(LIB23) $(LIBCOMPADJ) \
@@ -842,7 +876,7 @@ Combined patches from git.
$(VIB_POST_LINK) entrez2
# demo program (spidey)
-@@ -1285,7 +1297,7 @@ bl2seq : bl2seq.c
+@@ -1285,7 +1299,7 @@ bl2seq : bl2seq.c
taxblast: taxblast_main.c $(BLIB41) $(BLIB40)
$(CC) -g -o taxblast $(LDFLAGS) taxblast_main.c \
$(LIB61) $(LIB60) $(LIB36) $(LIB41) $(LIB40) $(LIB23) $(LIBCOMPADJ) \
=====================================
debian/rules
=====================================
@@ -80,10 +80,12 @@ override_dh_auto_build-arch:
cd build && ln -s ../make/*.unx .
ln -s ../make/ln-if-absent build
mv build/makeall.unx build/makefile
+ $(MAKE_IN_BUILD) copy $(COMMON_FLAGS)
$(MAKE_IN_BUILD) all $(COMMON_FLAGS) $(USESHLIB) \
CFLAGS1="-c $(CFLAGS_PIC) $(PNG_INCLUDE)" \
LIB4=libvibrant.a LIB20=libncbidesk.a LIB28=libvibgif.a \
LIB30=libncbicn3d.a LIB45=libddvlib.a $(OGL_LIBVARS)
+ $(MAKE_IN_BUILD) -f makenet.unx copy
$(MAKE_IN_BUILD) -f makenet.unx $(COMMON_FLAGS) $(USESHLIB) \
CFLAGS1="-c $(CFLAGS_PIC)" \
LDFLAGS="$(filter-out -fPIE -pie,$(LDFLAGS))" \
=====================================
make/makeall.unx
=====================================
@@ -512,12 +512,8 @@ clean :
.c.o :
$(CC) $(CFLAGS) $<
-# this is ugly, because Solaris cc won't allow compile directly to .glo file
.c.glo :
- mv $*.o $*.tmp
- $(CC) $(CFLAGS) -D_OPENGL $<
- mv $*.o $*.glo
- mv $*.tmp $*.o
+ $(CC) $(CFLAGS) -D_OPENGL $< -o $@
## Special case
##
=====================================
make/makenet.unx
=====================================
@@ -390,9 +390,10 @@ ln-if-absent: ../make/ln-if-absent
rm -f ln-if-absent
ln -s ../make/ln-if-absent .
-nocopy : sources $(BLIB6) $(BLIB7) $(BLIB8) $(BLIB9) \
+nocopy = sources $(BLIB6) $(BLIB7) $(BLIB8) $(BLIB9) \
$(DLIB31) $(DLIB33) $(NCBI_SHLIBS) $(CLIENTS) $(VIB) \
$(DLIB42) $(DLIB43) $(DLIB44)
+nocopy : $(nocopy)
sources : $(ALL_SRC)
@@ -419,6 +420,7 @@ clean :
## use subordinate makefile for building shared libraries
##
shlib : shlib.$(LCL)
+shlib.$(LCL) : $(filter %.a,$(nocopy) $(MAKECMDGOALS))
## Special rules to allow shared libs to be built more than once within
## a given 'make' invocation
View it on GitLab: https://salsa.debian.org/med-team/ncbi-tools6/-/compare/9c6181097e66cd6037461245cadeab31301d520a...0041f9d77d0748c3233a70fbdf7863f0393da463
--
View it on GitLab: https://salsa.debian.org/med-team/ncbi-tools6/-/compare/9c6181097e66cd6037461245cadeab31301d520a...0041f9d77d0748c3233a70fbdf7863f0393da463
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