[med-svn] [Git][med-team/paml][master] 9 commits: hardening.patch: fortify source and fix crossbuilds.
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Sat Dec 24 14:30:29 GMT 2022
Étienne Mollier pushed to branch master at Debian Med / paml
Commits:
7770af77 by Étienne Mollier at 2022-12-24T13:10:44+01:00
hardening.patch: fortify source and fix crossbuilds.
- - - - -
2d6f1551 by Étienne Mollier at 2022-12-24T13:11:34+01:00
add_clean_target.patch: refresh.
- - - - -
cf24c16a by Étienne Mollier at 2022-12-24T13:11:50+01:00
d/t/run-unit-test: only run Test 4 on !amd64.
This fixes autopkgtest timing out on a number of slow CI hosts.
Closes: #1026913
- - - - -
7a321117 by Étienne Mollier at 2022-12-24T13:13:10+01:00
initialise changelog.
- - - - -
2a35ce79 by Étienne Mollier at 2022-12-24T13:13:52+01:00
routine-update: Standards-Version: 4.6.2
- - - - -
5d3226a5 by Étienne Mollier at 2022-12-24T13:13:52+01:00
routine-update: debhelper-compat 13
- - - - -
4e1422d5 by Étienne Mollier at 2022-12-24T13:14:05+01:00
Apply multi-arch hints.
+ paml-doc: Add Multi-Arch: foreign.
Changes-By: apply-multiarch-hints
- - - - -
e11b66ef by Étienne Mollier at 2022-12-24T13:14:10+01:00
routine-update: watch file standard 4
- - - - -
08c44059 by Étienne Mollier at 2022-12-24T15:29:42+01:00
routine-update: Ready to upload to unstable
- - - - -
6 changed files:
- debian/changelog
- debian/control
- debian/patches/add_clean_target.patch
- debian/patches/hardening.patch
- debian/tests/run-unit-test
- debian/watch
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,16 @@
+paml (4.9j+dfsg-4) unstable; urgency=medium
+
+ * Team upload.
+ * hardening.patch: fortify source and fix crossbuilds.
+ * add_clean_target.patch: refresh.
+ * d/t/run-unit-test: only run Test 4 on !amd64. (Closes: #1026913)
+ * Standards-Version: 4.6.2 (routine-update)
+ * paml-doc: Add Multi-Arch: foreign.
+ * debhelper-compat 13 (routine-update)
+ * watch file standard 4 (routine-update)
+
+ -- Étienne Mollier <emollier at debian.org> Sat, 24 Dec 2022 13:14:11 +0100
+
paml (4.9j+dfsg-3) unstable; urgency=medium
* Team upload.
=====================================
debian/control
=====================================
@@ -5,8 +5,8 @@ Uploaders: Pjotr Prins <pjotr.debian at thebird.nl>,
Andreas Tille <tille at debian.org>
Section: science
Priority: optional
-Build-Depends: debhelper-compat (= 12)
-Standards-Version: 4.5.0
+Build-Depends: debhelper-compat (= 13)
+Standards-Version: 4.6.2
Vcs-Browser: https://salsa.debian.org/med-team/paml
Vcs-Git: https://salsa.debian.org/med-team/paml.git
Homepage: http://abacus.gene.ucl.ac.uk/software/paml.html
@@ -27,6 +27,7 @@ Package: paml-doc
Architecture: all
Section: doc
Depends: ${misc:Depends}
+Multi-Arch: foreign
Description: Documentation for PAML
PAML is a package of programs for phylogenetic analyses of DNA or
protein sequences using maximum likelihood. PAML is not good for tree
=====================================
debian/patches/add_clean_target.patch
=====================================
@@ -2,13 +2,13 @@ Description: Add clean target to upstream Makefile
Author: Andreas Tille <tille at debian.org>
Last-Update Mon, 02 May 2016 15:37:17 +0200
---- a/src/Makefile
-+++ b/src/Makefile
-@@ -25,3 +25,7 @@ yn00: yn00.c tools.c paml.h
- $(CC) $(CFLAGS) -o $@ yn00.c tools.c $(LIBS)
+--- paml.orig/src/Makefile
++++ paml/src/Makefile
+@@ -25,3 +25,7 @@
+ $(CC) $(CPPFLAGS) $(CFLAGS) -o $@ yn00.c tools.c $(LIBS)
chi2 : chi2.c
- $(CC) $(CFLAGS) -o $@ chi2.c $(LIBS)
+ $(CC) $(CPPFLAGS) $(CFLAGS) -o $@ chi2.c $(LIBS)
+
+clean:
+ rm -f $(PRGS) infinitesites
-+
++.PHONY: clean
=====================================
debian/patches/hardening.patch
=====================================
@@ -2,18 +2,45 @@ Description: Enable propagation of hardening flags
Author: Andreas Tille <tille at debian.org>
Date: Tue, 15 May 2012 11:10:59 +0200
---- a/src/Makefile
-+++ b/src/Makefile
-@@ -1,10 +1,10 @@
+--- paml.orig/src/Makefile
++++ paml/src/Makefile
+@@ -1,27 +1,27 @@
PRGS = baseml codeml basemlg mcmctree pamp evolver yn00 chi2
- CC = cc # cc, gcc, cl
+-CC = cc # cc, gcc, cl
++CC ?= cc # cc, gcc, cl
-CFLAGS = -O3
+CFLAGS += -O3
#CFLAGS = -fast
-LIBS = -lm # -lM
-+LIBS = -lm $(LDFLAGS) # -lM
++LIBS = $(LDFLAGS) -lm # -lM
all : $(PRGS)
+ baseml : baseml.c tools.c treesub.c treespace.c paml.h
+- $(CC) $(CFLAGS) -o $@ baseml.c tools.c $(LIBS)
++ $(CC) $(CPPFLAGS) $(CFLAGS) -o $@ baseml.c tools.c $(LIBS)
+ basemlg : basemlg.c tools.c treesub.c treespace.c paml.h
+- $(CC) $(CFLAGS) -o $@ basemlg.c tools.c $(LIBS)
++ $(CC) $(CPPFLAGS) $(CFLAGS) -o $@ basemlg.c tools.c $(LIBS)
+ codeml : codeml.c tools.c treesub.c treespace.c paml.h
+- $(CC) $(CFLAGS) -o $@ codeml.c tools.c $(LIBS)
++ $(CC) $(CPPFLAGS) $(CFLAGS) -o $@ codeml.c tools.c $(LIBS)
+ evolver : evolver.c tools.c treesub.c treespace.c paml.h
+- $(CC) $(CFLAGS) -o $@ evolver.c tools.c $(LIBS)
++ $(CC) $(CPPFLAGS) $(CFLAGS) -o $@ evolver.c tools.c $(LIBS)
+ pamp : pamp.c tools.c treesub.c treespace.c paml.h
+- $(CC) $(CFLAGS) -o $@ pamp.c tools.c $(LIBS)
++ $(CC) $(CPPFLAGS) $(CFLAGS) -o $@ pamp.c tools.c $(LIBS)
+ mcmctree : mcmctree.c tools.c treesub.c treespace.c paml.h
+- $(CC) $(CFLAGS) -o $@ mcmctree.c tools.c $(LIBS)
+- $(CC) $(CFLAGS) -o infinitesites -D INFINITESITES mcmctree.c tools.c $(LIBS)
++ $(CC) $(CPPFLAGS) $(CFLAGS) -o $@ mcmctree.c tools.c $(LIBS)
++ $(CC) $(CPPFLAGS) $(CFLAGS) -o infinitesites -D INFINITESITES mcmctree.c tools.c $(LIBS)
+ yn00: yn00.c tools.c paml.h
+- $(CC) $(CFLAGS) -o $@ yn00.c tools.c $(LIBS)
++ $(CC) $(CPPFLAGS) $(CFLAGS) -o $@ yn00.c tools.c $(LIBS)
+ chi2 : chi2.c
+- $(CC) $(CFLAGS) -o $@ chi2.c $(LIBS)
++ $(CC) $(CPPFLAGS) $(CFLAGS) -o $@ chi2.c $(LIBS)
=====================================
debian/tests/run-unit-test
=====================================
@@ -16,24 +16,28 @@ cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}"
cd "${AUTOPKGTEST_TMP}"
-echo -e "\e[93m\e[1mTest 1\e[0m"
-cd HIVNSsites
-codeml
-cd ..
-echo -e "\e[92m\e[1mPassed\e[0m"
-echo
+# These tests take too much time on non-amd64 platforms.
+if [ "$(uname -m)" = "x86_64" ]
+then
+ echo -e "\e[93m\e[1mTest 1\e[0m"
+ cd HIVNSsites
+ codeml
+ cd ..
+ echo -e "\e[92m\e[1mPassed\e[0m"
+ echo
-echo -e "\e[93m\e[1mTest 2\e[0m"
-cd lysin
-codeml
-echo -e "\e[92m\e[1mPassed\e[0m"
-echo
+ echo -e "\e[93m\e[1mTest 2\e[0m"
+ cd lysin
+ codeml
+ echo -e "\e[92m\e[1mPassed\e[0m"
+ echo
-echo -e "\e[93m\e[1mTest 3\e[0m"
-codeml codemlYangSwanson2002.ctl
-cd ..
-echo -e "\e[92m\e[1mPassed\e[0m"
-echo
+ echo -e "\e[93m\e[1mTest 3\e[0m"
+ codeml codemlYangSwanson2002.ctl
+ cd ..
+ echo -e "\e[92m\e[1mPassed\e[0m"
+ echo
+fi
echo -e "\e[93m\e[1mTest 4\e[0m"
cd lysozyme
@@ -41,40 +45,43 @@ codeml
echo -e "\e[92m\e[1mPassed\e[0m"
echo
-echo -e "\e[93m\e[1mTest 5\e[0m"
-codeml lysozymeSmall.ctl
-echo -e "\e[92m\e[1mPassed\e[0m"
-echo
-
-echo -e "\e[93m\e[1mTest 6\e[0m"
-codeml lysozymeLarge.ctl
-cd ..
-echo -e "\e[92m\e[1mPassed\e[0m"
-echo
+# These tests take too much time on non-amd64 platforms.
+if [ "$(uname -m)" = "x86_64" ]
+then
+ echo -e "\e[93m\e[1mTest 5\e[0m"
+ codeml lysozymeSmall.ctl
+ echo -e "\e[92m\e[1mPassed\e[0m"
+ echo
-echo -e "\e[93m\e[1mTest 7\e[0m"
-cd MouseLemurs
-baseml
-cd ..
-echo -e "\e[92m\e[1mPassed\e[0m"
-echo
+ echo -e "\e[93m\e[1mTest 6\e[0m"
+ codeml lysozymeLarge.ctl
+ cd ..
+ echo -e "\e[92m\e[1mPassed\e[0m"
+ echo
-echo -e "\e[93m\e[1mTest 8\e[0m"
-cd mtCDNA
-codeml codeml.AAcodon.ctl
-cd ..
-echo -e "\e[92m\e[1mPassed\e[0m"
-echo
+ echo -e "\e[93m\e[1mTest 7\e[0m"
+ cd MouseLemurs
+ baseml
+ cd ..
+ echo -e "\e[92m\e[1mPassed\e[0m"
+ echo
-echo -e "\e[93m\e[1mTest 9\e[0m"
-cd mtCDNAape
-codeml
-echo -e "\e[92m\e[1mPassed\e[0m"
-echo
+ echo -e "\e[93m\e[1mTest 8\e[0m"
+ cd mtCDNA
+ codeml codeml.AAcodon.ctl
+ cd ..
+ echo -e "\e[92m\e[1mPassed\e[0m"
+ echo
-echo -e "\e[93m\e[1mTest 10\e[0m"
-codeml codeml.HC.ctl
-cd ..
-echo -e "\e[92m\e[1mPassed\e[0m"
-echo
+ echo -e "\e[93m\e[1mTest 9\e[0m"
+ cd mtCDNAape
+ codeml
+ echo -e "\e[92m\e[1mPassed\e[0m"
+ echo
+ echo -e "\e[93m\e[1mTest 10\e[0m"
+ codeml codeml.HC.ctl
+ cd ..
+ echo -e "\e[92m\e[1mPassed\e[0m"
+ echo
+fi
=====================================
debian/watch
=====================================
@@ -1,3 +1,3 @@
-version=3
+version=4
opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,repack,compression=xz" \
http://abacus.gene.ucl.ac.uk/software/paml.html paml([0-9a-z.]+)\.(?:tgz|tbz|txz|(?:tar\.(?:gz|bz2|xz))|zip)
View it on GitLab: https://salsa.debian.org/med-team/paml/-/compare/a6406999699111db8a5d84e79191f66d805522a3...08c44059474c874022bdd1061feb0a04162d4e2e
--
View it on GitLab: https://salsa.debian.org/med-team/paml/-/compare/a6406999699111db8a5d84e79191f66d805522a3...08c44059474c874022bdd1061feb0a04162d4e2e
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