[med-svn] [Git][med-team/kent-core][master] 5 commits: routine-update: New upstream version
Andreas Tille (@tille)
gitlab at salsa.debian.org
Thu Apr 13 14:26:58 BST 2023
Andreas Tille pushed to branch master at Debian Med / kent-core
Commits:
18dea4e1 by Andreas Tille at 2023-04-13T15:08:39+02:00
routine-update: New upstream version
- - - - -
8699b258 by Andreas Tille at 2023-04-13T15:08:40+02:00
New upstream version 447-test2
- - - - -
bc1c51eb by Andreas Tille at 2023-04-13T15:09:51+02:00
Update upstream source from tag 'upstream/447-test2'
Update to upstream version '447-test2'
with Debian dir 820e6f6008c724a9b9a7e1dc564c1772971bddaa
- - - - -
98bc4325 by Andreas Tille at 2023-04-13T15:10:06+02:00
Set upstream metadata fields: Repository.
Changes-By: lintian-brush
Fixes: lintian: upstream-metadata-missing-repository
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-repository.html
- - - - -
7fa31eb8 by Andreas Tille at 2023-04-13T15:26:38+02:00
Fix linking libssl
- - - - -
7 changed files:
- debian/changelog
- − debian/patches/fix_makefile.patch
- + debian/patches/link_ssl.patch
- − debian/patches/no_webBlat.patch
- debian/patches/series
- debian/upstream/metadata
- src/makefile
Changes:
=====================================
debian/changelog
=====================================
@@ -1,5 +1,5 @@
-kent-core (447-test-1) UNRELEASED; urgency=medium
+kent-core (447-test2-1) UNRELEASED; urgency=medium
* Initial release (Closes: #???)
- -- Andreas Tille <tille at debian.org> Thu, 13 Apr 2023 14:29:30 +0200
+ -- Andreas Tille <tille at debian.org> Thu, 13 Apr 2023 15:10:23 +0200
=====================================
debian/patches/fix_makefile.patch deleted
=====================================
@@ -1,144 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Fri, 31 Mar 2023 07:34:06 +0200
-Description: The makefiles contain code that references directories
- with code that is not MIT licensed and thus only in the
- original project and not in kent-core.
- This patch verifies whether the dirs exist or not.
-
---- a/src/makefile
-+++ b/src/makefile
-@@ -16,7 +16,9 @@ update:
- topLibs:
- @./checkUmask.sh
- @MACHTYPE=${MACHTYPE} ./machTest.sh
-+ifneq ($(wildcard lib/*),)
- cd lib && ${MAKE}
-+endif
- ifneq ($(wildcard jkOwnLib/*),)
- cd jkOwnLib && ${MAKE}
- endif
-@@ -29,9 +31,13 @@ optLib:
- hgLib:
- ifneq ($(wildcard hg/makefile),)
- @./hg/sqlEnvTest.sh
-+ifneq ($(wildcard hg/lib/*),)
- cd hg/lib && ${MAKE}
-+endif
-+ifneq ($(wildcard hg/cgilib/*),)
- cd hg/cgilib && ${MAKE}
- endif
-+endif
-
- libs: topLibs hgLib optLib
-
-@@ -62,20 +68,20 @@ check-beta:
- git branch | egrep '\* v[0-9]+_branch' > /dev/null
-
- blatSuite: topLibs hgLib
-- cd blat && ${MAKE}
-- cd gfClient && ${MAKE}
-- cd gfServer && ${MAKE}
-- cd webBlat && ${MAKE}
-- cd hg/pslPretty && ${MAKE}
-- cd hg/pslReps && ${MAKE}
-- cd hg/pslSort && ${MAKE}
-- cd utils/nibFrag && ${MAKE}
-- cd utils/faToNib && ${MAKE}
-- cd utils/faToTwoBit && ${MAKE}
-- cd utils/twoBitToFa && ${MAKE}
-- cd utils/twoBitInfo && ${MAKE}
-- cd isPcr && ${MAKE}
-- cd blatz && ${MAKE}
-+ (if [ -d blat ] ; then cd blat && ${MAKE} ; fi)
-+ (if [ -d gfClient ] ; then cd gfClient && ${MAKE} ; fi)
-+ (if [ -d gfServer ] ; then cd gfServer && ${MAKE} ; fi)
-+ (if [ -d webBlat ] ; then cd webBlat && ${MAKE} ; fi)
-+ (if [ -d hg/pslPretty ] ; then cd hg/pslPretty && ${MAKE} ; fi)
-+ (if [ -d hg/pslReps ] ; then cd hg/pslReps && ${MAKE} ; fi)
-+ (if [ -d hg/pslSort ] ; then cd hg/pslSort && ${MAKE} ; fi)
-+ (if [ -d utils/nibFrag ] ; then cd utils/nibFrag && ${MAKE} ; fi)
-+ (if [ -d utils/faToNib ] ; then cd utils/faToNib && ${MAKE} ; fi)
-+ (if [ -d utils/faToTwoBit ] ; then cd utils/faToTwoBit && ${MAKE} ; fi)
-+ (if [ -d utils/twoBitToFa ] ; then cd utils/twoBitToFa && ${MAKE} ; fi)
-+ (if [ -d utils/twoBitInfo ] ; then cd utils/twoBitInfo && ${MAKE} ; fi)
-+ (if [ -d isPcr ] ; then cd isPcr && ${MAKE} ; fi)
-+ (if [ -d blatz ] ; then cd blatz && ${MAKE} ; fi)
-
- # all of these application makefiles have been updated to include use
- # of DESTDIR and BINDIR
-@@ -108,7 +114,9 @@ clean:
- fi ;\
- done
- cd parasol && ${MAKE} clean
-+ifneq ($(wildcard lib/*),)
- cd lib && ${MAKE} clean
-+endif
- cd hg && ${MAKE} clean
- cd hg && ${MAKE} clean_utils
- ifneq ($(wildcard jkOwnLib/*),)
---- a/src/hg/makefile
-+++ b/src/hg/makefile
-@@ -228,8 +228,12 @@ APPS = $(UTIL_DIRS) $(UTILS_APPLIST)
- all:: cgi utils
-
- hgLib:
-+ifneq ($(wildcard lib/*),)
- cd lib && ${MAKE}
-+endif
-+ifneq ($(wildcard lib/*),)
- cd cgilib && ${MAKE}
-+endif
-
- userApps: $(UTILS_APPLIST:%=%.userApp)
- cd altSplice/lib && $(MAKE)
-@@ -256,9 +260,9 @@ compile: ${BROWSER_BINS:%=%.compile} ${B
-
- cgi: ${BROWSER_BINS:%=%.bins} ${BROWSER_LOADERS:%=%.cgi} ${ENCODE_FILES:%=%.cgi}
- %.bins: hgLib
-- cd $* && echo $* && $(MAKE)
-+ if [ -d $* ] ; then cd $* && echo $* && $(MAKE) ; fi
- %.cgi: hgLib
-- cd $* && echo $* && $(MAKE) cgi
-+ if [ -d $* ] ; then cd $* && echo $* && $(MAKE) cgi ; fi
-
- # alpha: Destination for the binaries is /usr/local/apache/cgi-bin/
-
-@@ -279,22 +283,24 @@ install: ${BROWSER_BINS:%=%.install} ${B
- cd $* && echo $* && $(MAKE) install
-
- clean::
-+ifneq ($(wildcard lib/*),)
- cd lib && ${MAKE} clean
-+endif
- @for D in ${BROWSER_BINS} ${BROWSER_LOADERS}; do \
-- (cd $${D} && ${MAKE} clean;) \
-+ (if [ -d $${D} ] ; then cd $${D} && ${MAKE} clean; fi) \
- done
- touch non-empty-rm.o
- - find . -name \*.o -print | xargs rm
-
- clean_utils::
- @for D in ${UTIL_DIRS}; do \
-- (cd $${D} && ${MAKE} clean;) \
-+ (if [ -d $${D} ] ; then cd $${D} && ${MAKE} clean; fi) \
- done
-
- clean:: ${TEST_DIRS:%=%.clean}
-
- %.clean:
-- cd $* && ${MAKE} clean
-+ if [ -d $* ] ; then cd $* && ${MAKE} clean ; fi
-
- testAll: $(APPS:%=%.testAll)
-
---- a/src/inc/common.mk
-+++ b/src/inc/common.mk
-@@ -156,7 +156,7 @@ else
- L+=/opt/local/lib/libssl.a
- else
- ifneq ($(wildcard /usr/lib/x86_64-linux-gnu/libssl.a),)
-- L+=/usr/lib/x86_64-linux-gnu/libssl.a
-+ L+=-lssl
- else
- ifneq ($(wildcard /usr/local/opt/openssl/lib/libssl.a),)
- L+=/usr/local/opt/openssl/lib/libssl.a
=====================================
debian/patches/link_ssl.patch
=====================================
@@ -0,0 +1,15 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Thu, 13 Apr 2023 15:10:23 +0200
+Description: Fix linking libssl
+
+--- a/src/inc/common.mk
++++ b/src/inc/common.mk
+@@ -156,7 +156,7 @@ else
+ L+=/opt/local/lib/libssl.a
+ else
+ ifneq ($(wildcard /usr/lib/x86_64-linux-gnu/libssl.a),)
+- L+=/usr/lib/x86_64-linux-gnu/libssl.a
++ L+=-lssl
+ else
+ ifneq ($(wildcard /usr/local/opt/openssl/lib/libssl.a),)
+ L+=/usr/local/opt/openssl/lib/libssl.a
=====================================
debian/patches/no_webBlat.patch deleted
=====================================
@@ -1,25 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Fri, 31 Mar 2023 07:34:06 +0200
-Description: To build webBlat the library jkOwnLib.a needs to be built
- first. However, the code for this library is not yet
- MIT licensed and thus not contained in this tarball.
- This patch is checking for the existence of the lib.
-
---- a/src/webBlat/makefile
-+++ b/src/webBlat/makefile
-@@ -7,6 +7,7 @@ MYLIBS = ${MYLIBDIR}/jkOwnLib.a ${MYLIB
-
- O = webBlat.o
-
-+ifneq ($(wildcard ${MYLIBDIR}/jkOwnLib.a),)
- webBlat: $O ${MYLIBS}
- ${CC} ${COPT} -o webBlat $O ${MYLIBS} ${L}
- ${STRIP} webBlat${EXE}
-@@ -22,6 +23,7 @@ installUcsc: webBlat
- installAlpha: webBlat
- cp webBlat /usr/local/apache/cgi-bin
- cp webBlat.cfg /usr/local/apache/cgi-bin
-+endif
-
- clean:
- rm -f $O webBlat
=====================================
debian/patches/series
=====================================
@@ -1,2 +1 @@
-#fix_makefile.patch
-#no_webBlat.patch
+link_ssl.patch
=====================================
debian/upstream/metadata
=====================================
@@ -19,4 +19,5 @@ Registry:
Entry: SCR_011919
- Name: bio.tools
Entry: blat
+Repository: https://github.com/ucscGenomeBrowser/kent-core.git
Repository-Browse: https://github.com/ucscGenomeBrowser/kent-core
=====================================
src/makefile
=====================================
@@ -30,8 +30,10 @@ hgLib:
ifneq ($(wildcard hg/makefile),)
@./hg/sqlEnvTest.sh
cd hg/lib && ${MAKE}
+ifneq ($(wildcard hg/cgilib/makefile),)
cd hg/cgilib && ${MAKE}
endif
+endif
libs: topLibs hgLib optLib
View it on GitLab: https://salsa.debian.org/med-team/kent-core/-/compare/bde36be930fff0106a97c70f0f471c21f9bf864c...7fa31eb8fd392183200c90f48ffa3b9a9ef85ab6
--
View it on GitLab: https://salsa.debian.org/med-team/kent-core/-/compare/bde36be930fff0106a97c70f0f471c21f9bf864c...7fa31eb8fd392183200c90f48ffa3b9a9ef85ab6
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