[med-svn] [Git][med-team/phast][master] 5 commits: d/rules: use $(MAKE) to avoid interference with the jobserver.

Sun Jan 5 19:35:10 GMT 2025


Étienne Mollier pushed to branch master at Debian Med / phast


Commits:
c0c1d46f by Étienne Mollier at 2025-01-05T19:59:09+01:00
d/rules: use $(MAKE) to avoid interference with the jobserver.

- - - - -
12a90d59 by Étienne Mollier at 2025-01-05T20:24:55+01:00
make.patch: new: fix build parallelism issues.

Several makefiles collide on editing the libphast.a, so this patch
blocks the parallelism on that target.

Closes: #1091563

- - - - -
0b4cd98e by Étienne Mollier at 2025-01-05T20:27:43+01:00
gcc-14.patch: declare forwarding unneeded.

- - - - -
d05055de by Étienne Mollier at 2025-01-05T20:28:21+01:00
d/patches/*: normalize the last-update timestamp.

- - - - -
98d74582 by Étienne Mollier at 2025-01-05T20:34:32+01:00
d/changelog: ready for upload to unstable.

- - - - -


10 changed files:

- debian/changelog
- debian/patches/do_not_install_to_opt.patch
- debian/patches/gcc-14.patch
- debian/patches/hardening.patch
- + debian/patches/make.patch
- debian/patches/pcre2.patch
- debian/patches/series
- debian/patches/use_debian_packaged_help2man.patch
- debian/patches/use_debian_packaged_libpcre.patch
- debian/rules


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,14 @@
+phast (1.7+dfsg-2) unstable; urgency=medium
+
+  * d/rules: use $(MAKE) to avoid interference with the jobserver.
+  * make.patch: new: fix build parallelism issues.
+    Several makefiles collide on editing the libphast.a, so this patch
+    blocks the parallelism on that target. (Closes: #1091563)
+  * gcc-14.patch: declare forwarding unneeded.
+  * d/patches/*: normalize the last-update timestamp.
+
+ -- Étienne Mollier <emollier at debian.org>  Sun, 05 Jan 2025 20:28:50 +0100
+
 phast (1.7+dfsg-1) unstable; urgency=medium
 
   * New upstream version


=====================================
debian/patches/do_not_install_to_opt.patch
=====================================
@@ -1,5 +1,5 @@
 Author: Andreas Tille <tille at debian.org>
-Last-Update: Fri, 27 May 2016 18:06:35 +0200
+Last-Update: 2016-05-27
 Description: Packages should not install anything to /opt
 
 --- a/src/Makefile


=====================================
debian/patches/gcc-14.patch
=====================================
@@ -5,10 +5,12 @@ Description: fix multiple issues gone fatal with gcc 14.
  modified signature of str_re_new, as otherwise the code would have to
  include a huge amount of type casts for each and every call of
  str_re_new.
-
+ .
+ Upstream followed a different path to resolve the problem in upcoming
+ phast versions, so forwarding this patch has become irrelevant.
 Author: Étienne Mollier <emollier at debian.org>
 Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1075383
-Forwarded: no
+Forwarded: not-needed
 Last-Update: 2024-07-31
 ---
 This patch header follows DEP-3: http://dep.debian.net/deps/dep3/


=====================================
debian/patches/hardening.patch
=====================================
@@ -1,5 +1,5 @@
 Author: Andreas Tille <tille at debian.org>
-Last-Update: Fri, 27 May 2016 18:06:35 +0200
+Last-Update: 2016-05-27
 Description: Propagate hardening options
 
 --- a/src/make-include.mk


=====================================
debian/patches/make.patch
=====================================
@@ -0,0 +1,87 @@
+Description: force sequential access to libphast.a.
+ When building phast using make's parallel capabilities, the build
+ almost always fails because the many subdirectories of src/lib/*/ are
+ trying to add objects to the libphast.a static library at the same
+ time, resulting in corruption and weird error messages like:
+ .
+ 	gcc  -L/<<PKGBUILDDIR>>/src/dless/../../lib  -o /<<PKGBUILDDIR>>/src/dless/../../bin/dless dless.o phast_bd_phylo_hmm.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now 
+ 	/usr/bin/ld: /<<PKGBUILDDIR>>/src/dless/../../lib/libphast.a: error adding symbols: malformed archive
+ 	collect2: error: ld returned 1 exit status
+ .
+ Placing .NOTPARALLEL pseudo targets at strategic locations looks to
+ reliably resolve the problem while preserving otherwise some level of
+ parallelism where the library is not involved.  Checkout the GNU Make
+ manual's chapter about [Disabling Parallel Execution] for further
+ details.
+ .
+ [Disabling Parallel Execution]: https://www.gnu.org/software/make/manual/html_node/Parallel-Disable.html
+Author: Étienne Mollier <emollier at debian.org>
+Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1091563
+Forwarded: https://github.com/CshlSiepelLab/phast/pull/80
+Last-Update: 2025-01-05
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- phast.orig/src/lib/base/Makefile
++++ phast/src/lib/base/Makefile
+@@ -17,3 +17,5 @@
+ 
+ clean:
+ 	rm -f *.o 
++
++.NOTPARALLEL:
+--- phast.orig/src/lib/feature/Makefile
++++ phast/src/lib/feature/Makefile
+@@ -17,3 +17,5 @@
+ 
+ clean:
+ 	rm -f *.o 
++
++.NOTPARALLEL:
+--- phast.orig/src/lib/hmm/Makefile
++++ phast/src/lib/hmm/Makefile
+@@ -17,3 +17,5 @@
+ 
+ clean:
+ 	rm -f *.o 
++
++.NOTPARALLEL:
+--- phast.orig/src/lib/motif/Makefile
++++ phast/src/lib/motif/Makefile
+@@ -17,3 +17,5 @@
+ 
+ clean:
+ 	rm -f *.o 
++
++.NOTPARALLEL:
+--- phast.orig/src/lib/msa/Makefile
++++ phast/src/lib/msa/Makefile
+@@ -17,3 +17,5 @@
+ 
+ clean:
+ 	rm -f *.o 
++
++.NOTPARALLEL:
+--- phast.orig/src/lib/phylo/Makefile
++++ phast/src/lib/phylo/Makefile
+@@ -17,3 +17,5 @@
+ 
+ clean:
+ 	rm -f *.o 
++
++.NOTPARALLEL:
+--- phast.orig/src/lib/phylo_hmm/Makefile
++++ phast/src/lib/phylo_hmm/Makefile
+@@ -17,3 +17,5 @@
+ 
+ clean:
+ 	rm -f *.o 
++
++.NOTPARALLEL:
+--- phast.orig/src/lib/rphast/Makefile
++++ phast/src/lib/rphast/Makefile
+@@ -14,3 +14,5 @@
+ 
+ clean:
+ 	rm -f *.o 
++
++.NOTPARALLEL:


=====================================
debian/patches/pcre2.patch
=====================================
@@ -1,7 +1,7 @@
 Description: Port from pcre3 to pcre2
 Bug-Debian: https://bugs.debian.org/1000000
 Author: Andreas Tille <tille at debian.org>
-Last-Update: Fri, 19 Nov 2021 13:12:51 +0100
+Last-Update: 2021-11-19
 Forwarded: https://github.com/CshlSiepelLab/phast/issues/49
 
 --- a/include/phast/stringsplus.h


=====================================
debian/patches/series
=====================================
@@ -5,3 +5,4 @@ use_debian_packaged_help2man.patch
 hardening.patch
 pcre2.patch
 gcc-14.patch
+make.patch


=====================================
debian/patches/use_debian_packaged_help2man.patch
=====================================
@@ -1,5 +1,5 @@
 Author: Andreas Tille <tille at debian.org>
-Last-Update: Fri, 27 May 2016 18:06:35 +0200
+Last-Update: 2016-05-27
 Description: Debian packaged help2man creates better results
 
 --- a/src/Makefile


=====================================
debian/patches/use_debian_packaged_libpcre.patch
=====================================
@@ -1,5 +1,5 @@
 Author: Andreas Tille <tille at debian.org>
-Last-Update: Fri, 27 May 2016 18:06:35 +0200
+Last-Update: 2016-05-27
 Description: Use Debian packaged libpcre
 
 --- a/src/make-include.mk


=====================================
debian/rules
=====================================
@@ -1,7 +1,5 @@
 #!/usr/bin/make -f
 
-# DH_VERBOSE := 1
-
 export DEB_BUILD_MAINT_OPTIONS = hardening=+all
 
 %:
@@ -9,11 +7,11 @@ export DEB_BUILD_MAINT_OPTIONS = hardening=+all
 
 override_dh_auto_clean:
 	dh_auto_clean
-	cd src && make clean
+	cd src && $(MAKE) clean
 
 override_dh_auto_test:
 ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
-	cd test && PATH=$(CURDIR)/bin:$(PATH) make msa_view
+	cd test && PATH=$(CURDIR)/bin:$(PATH) $(MAKE) msa_view
 endif
 
 override_dh_installexamples:



View it on GitLab: https://salsa.debian.org/med-team/phast/-/compare/7ba14524e3549180e977ce78a4f533c0fdf748f7...98d74582645053919732ce518555e84408cbce7d

-- 
View it on GitLab: https://salsa.debian.org/med-team/phast/-/compare/7ba14524e3549180e977ce78a4f533c0fdf748f7...98d74582645053919732ce518555e84408cbce7d
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