Re: No relro when building from inside a Git package ?
Hi, On Fri, 22 Nov 2013, Andreas Tille wrote: $ gbp-clone ssh://git.debian.org/git/debian-med/htslib.git $ cd htslib (debian/unstable) $ git branch * debian/unstable develop pristine-tar (debian/unstable) $ git-buildpackage (debian/unstable) $ lintian -I --pedantic ../build-area/htslib_0.2.0~rc4-1_amd64.changes The mere fact that the generated files are in ../build-area/ means that you're using --git-export-dir (via ~/.gbp.conf) and thus you are building in a directory that doesn't have the .git dir. It's an export (with git archive) that is unpacked in ../build-area/package/ that you use as build directory. Cheers, -- Raphaël Hertzog ◈ Debian Developer Discover the Debian Administrator's Handbook: → http://debian-handbook.info/get/ -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20131122081044.ga8...@x230-buxy.home.ouaza.com
Re: No relro when building from inside a Git package ?
Hi, On Fri, Nov 22, 2013 at 09:10:44AM +0100, Raphael Hertzog wrote: Hi, On Fri, 22 Nov 2013, Andreas Tille wrote: $ gbp-clone ssh://git.debian.org/git/debian-med/htslib.git $ cd htslib (debian/unstable) $ git branch * debian/unstable develop pristine-tar (debian/unstable) $ git-buildpackage (debian/unstable) $ lintian -I --pedantic ../build-area/htslib_0.2.0~rc4-1_amd64.changes The mere fact that the generated files are in ../build-area/ means that you're using --git-export-dir (via ~/.gbp.conf) and thus you are building in a directory that doesn't have the .git dir. It's an export (with git archive) that is unpacked in ../build-area/package/ that you use as build directory. Well, that's correct. So trying again: $ cd .. $ ln -s build-area/htslib_0.2.0~rc4.orig.tar.gz $ cd htslib (debian/unstable) $ pdebuild (debian/unstable) $ lintian -I --pedantic ../htslib_0.2.0~rc4-1_amd64.changes $ lintian -I --pedantic ../htslib_0.2.0~rc4-1_amd64.changes I: htslib source: quilt-patch-using-template-description debian-changes W: htslib source: newer-standards-version 3.9.5 (current is 3.9.4) P: libhts-dev: no-upstream-changelog W: libhts-dev: manpage-has-errors-from-man usr/share/man/man5/vcf.5.gz file `standard input', around line 15: P: htslib-test: no-upstream-changelog P: libhts0: no-upstream-changelog E: libhts0: symbols-file-contains-current-version-with-debian-revision on symbol cram_index_build@Base W: libhts0: symbols-file-contains-debian-revision on symbol bam_mplp_init_overlaps@Base and 1 others So no changes when just using pdebuild in the git directory - `-Wl,-z,relro` is correctly specified (buildlog attached as well). Sorry, can not confirm the observation from Charles Andreas. -- http://fam-tille.de htslib_0.2.0~rc4-1_amd64.build.with-.git-dir.bz2 Description: Binary data
Re: No relro when building from inside a Git package ?
Le Fri, Nov 22, 2013 at 09:31:25AM +0100, Andreas Tille a écrit : On Fri, Nov 22, 2013 at 09:10:44AM +0100, Raphael Hertzog wrote: On Fri, 22 Nov 2013, Andreas Tille wrote: $ gbp-clone ssh://git.debian.org/git/debian-med/htslib.git $ cd htslib (debian/unstable) $ git branch * debian/unstable develop pristine-tar (debian/unstable) $ git-buildpackage (debian/unstable) $ lintian -I --pedantic ../build-area/htslib_0.2.0~rc4-1_amd64.changes The mere fact that the generated files are in ../build-area/ means that you're using --git-export-dir (via ~/.gbp.conf) and thus you are building in a directory that doesn't have the .git dir. It's an export (with git archive) that is unpacked in ../build-area/package/ that you use as build directory. Well, that's correct. So trying again: $ cd .. $ ln -s build-area/htslib_0.2.0~rc4.orig.tar.gz $ cd htslib (debian/unstable) $ pdebuild Hi Andreas, I suspect that pdebuild is also using either an export or an unpacked source package. I think that if you use dpkg-buildpackage directly, you will reproduce the problem. Cheers, -- Charles -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20131122090851.gi16...@falafel.plessy.net
Re: No relro when building from inside a Git package ?
Hi, On Fri, Nov 22, 2013 at 06:08:51PM +0900, Charles Plessy wrote: Le Fri, Nov 22, 2013 at 09:31:25AM +0100, Andreas Tille a écrit : On Fri, Nov 22, 2013 at 09:10:44AM +0100, Raphael Hertzog wrote: On Fri, 22 Nov 2013, Andreas Tille wrote: $ gbp-clone ssh://git.debian.org/git/debian-med/htslib.git $ cd htslib (debian/unstable) $ git branch * debian/unstable develop pristine-tar (debian/unstable) $ git-buildpackage (debian/unstable) $ lintian -I --pedantic ../build-area/htslib_0.2.0~rc4-1_amd64.changes The mere fact that the generated files are in ../build-area/ means that you're using --git-export-dir (via ~/.gbp.conf) and thus you are building in a directory that doesn't have the .git dir. It's an export (with git archive) that is unpacked in ../build-area/package/ that you use as build directory. Well, that's correct. So trying again: $ cd .. $ ln -s build-area/htslib_0.2.0~rc4.orig.tar.gz $ cd htslib (debian/unstable) $ pdebuild Hi Andreas, I suspect that pdebuild is also using either an export or an unpacked source package. I think that if you use dpkg-buildpackage directly, you will reproduce the problem. OK, now I've got it using debuild. While I can not see any suspicious difference inside the build log I can confirm the effect that with debuild the hardening-no-relro warning occures (even if `-Wl,-z,relro` is properly specified - a lack of this option is the usual cause of this problem). I can confirm this for an up to date testing and unstable system. I noticed as well that the file size of the binary in question is smaller in the later cases (with hardening-no-relro problem) as if I build using pbuilder. I further observed that it only happens if the dir is named .git. I tried mv .git .tig cat debian/source/include-binaries EOT .tig/index .tig/objects/pack/pack-0c4620137efe646d9d99b9b2b09b861e364bc678.idx .tig/objects/pack/pack-0c4620137efe646d9d99b9b2b09b861e364bc678.pack EOT debuild and the problem vanishes (the lintian warning vanishes and the file size is larger again == same as when using pdebuild). So lacking better advise I can only say: - just use pbuilder (simply closing the eyes for the issue) - evil grinuse svn instead of git/evil grin Now its time for you Git experts to solve this riddle. I'm out. Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20131122102742.gj11...@an3as.eu
Re: No relro when building from inside a Git package ?
On Fri, 22 Nov 2013, Andreas Tille wrote: I further observed that it only happens if the dir is named .git. I tried mv .git .tig cat debian/source/include-binaries EOT .tig/index .tig/objects/pack/pack-0c4620137efe646d9d99b9b2b09b861e364bc678.idx .tig/objects/pack/pack-0c4620137efe646d9d99b9b2b09b861e364bc678.pack EOT debuild and the problem vanishes (the lintian warning vanishes and the file size is larger again == same as when using pdebuild). So lacking better advise I can only say: - just use pbuilder (simply closing the eyes for the issue) - evil grinuse svn instead of git/evil grin Now its time for you Git experts to solve this riddle. I'm out. Maybe something is doing git clean -f -x or worse, git reset --hard just before the build run, and clobbering important build tooling configured early in the build prepare process? This would account for the changed behaviour when .git is present and valid... If this is an idiotic automatically clean using git misfeature somewhere, it might not show up in a regular build log because git output is being supressed. strace should show the culprit easily... -- One disk to rule them all, One disk to find them. One disk to bring them all and in the darkness grind them. In the Land of Redmond where the shadows lie. -- The Silicon Valley Tarot Henrique Holschuh -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20131122115109.gc27...@khazad-dum.debian.net
Re: No relro when building from inside a Git package ?
Hi Charles, On Thu, Nov 21, 2013 at 09:37:14AM +0900, Charles Plessy wrote: here it is (attached). Could the problem be a side effect of the test suite ? While I do no see why the test should be different depending from the existence of a .git directory or not, I'd consider it suspicious that the library is rebuilded when running the test. IMHO this should not happen. I also see below that -Wl,-z,relro is missing in the gcc -shared -Wl,-soname,libhts.so.0 ... call below which explains the lintian warning. Seems this is also a duplicated call since it there is no such call in your +++ without-.git log. Kind regards Andreas. PS: Alioth is back online and I might have a look later this day if you would commit there. Cheers, -- Charles --- with-.git 2013-11-21 09:32:14.244499056 +0900 +++ without-.git 2013-11-21 09:34:12.908497923 +0900 @@ -150,15 +150,6 @@ dh_auto_test make -j1 test make[2]: Entering directory `/tmp/htslib' -echo '#define HTS_VERSION debian/0.2.0_rc3-1-38-g9469458' version.h -gcc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o hts.o hts.c -ar -rc libhts.a kfunc.o knetfile.o kstring.o bgzf.o faidx.o hfile.o hfile_net.o hts.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/md5.o cram/open_trace_file.o cram/pooled_alloc.o cram/sam_header.o cram/string_alloc.o cram/thread_pool.o cram/vlen.o cram/zfio.o -ranlib libhts.a -gcc -pthread -o test/fieldarith test/fieldarith.o libhts.a -lz -gcc -o test/hfile test/hfile.o libhts.a -lz -gcc -pthread -o test/test_view test/test_view.o libhts.a -lz -gcc -pthread -o test/test-vcf-api test/test-vcf-api.o libhts.a -lz -gcc -pthread -o test/test-vcf-sweep test/test-vcf-sweep.o libhts.a -lz test/fieldarith test/fieldarith.sam test/hfile cd test ./test_view.pl @@ -456,11 +447,11 @@ Failures 0 cd test ./test.pl test_vcf_api: - /tmp/htslib/test/test-vcf-api /tmp/Vvj_N60T4W/test-vcf-api.bcf + /tmp/htslib/test/test-vcf-api /tmp/cUKPv4vctM/test-vcf-api.bcf .. ok test_vcf_sweep: - /tmp/htslib/test/test-vcf-sweep /tmp/Vvj_N60T4W/test-vcf-api.bcf + /tmp/htslib/test/test-vcf-sweep /tmp/cUKPv4vctM/test-vcf-api.bcf .. ok @@ -495,10 +486,6 @@ make -j1 install DESTDIR=/tmp/htslib/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr PACKAGE_VERSION=0.2.0\~rc4-1 make[2]: Entering directory `/tmp/htslib' mkdir -p /tmp/htslib/debian/tmp/usr/include/htslib /tmp/htslib/debian/tmp/usr/lib /tmp/htslib/debian/tmp/usr/share/man/man5 -echo '#define HTS_VERSION 0.2.0~rc4-1' version.h -gcc -g -Wall -O2 -I. -DSAMTOOLS=1 -fpic -c -o hts.pico hts.c -gcc -shared -Wl,-soname,libhts.so.0 -o libhts.so kfunc.pico knetfile.pico kstring.pico bgzf.pico faidx.pico hfile.pico hfile_net.pico hts.pico sam.pico synced_bcf_reader.pico vcf_sweep.pico tbx.pico vcf.pico vcfutils.pico cram/cram_codecs.pico cram/cram_decode.pico cram/cram_encode.pico cram/cram_index.pico cram/cram_io.pico cram/cram_samtools.pico cram/cram_stats.pico cram/files.pico cram/mFILE.pico cram/md5.pico cram/open_trace_file.pico cram/pooled_alloc.pico cram/sam_header.pico cram/string_alloc.pico cram/thread_pool.pico cram/vlen.pico cram/zfio.pico -lz -ln -sf libhts.so libhts.so.0 install -p -m 644 libhts.so /tmp/htslib/debian/tmp/usr/lib/libhts.so.0.2.0~rc4-1 ln -sf libhts.so.0.2.0~rc4-1 /tmp/htslib/debian/tmp/usr/lib/libhts.so ln -sf libhts.so.0.2.0~rc4-1 /tmp/htslib/debian/tmp/usr/lib/libhts.so.0 @@ -660,7 +647,7 @@ dpkg-gensymbols: warning: some new symbols appeared in the symbols file: see diff output below dpkg-gensymbols: warning: debian/libhts0/DEBIAN/symbols doesn't match completely debian/libhts0.symbols --- debian/libhts0.symbols (libhts0_0.2.0~rc4-1_amd64) -+++ dpkg-gensymbolskXM3kh2013-11-21 09:32:00.312499189 +0900 dpkg-gensymbols4DQT532013-11-21 09:34:08.056497969 +0900 @@ -230,6 +230,7 @@ cram_huffman_encode_int0@Base 0.2.0~rc3 cram_huffman_encode_int@Base 0.2.0~rc3 @@ -675,12 +662,12 @@ rm -f debian/htslib-test/DEBIAN/shlibs dh_shlibdeps dpkg-shlibdeps -Tdebian/libhts0.substvars debian/libhts0/usr/lib/x86_64-linux-gnu/libhts.so.0.2.0\~rc4-1 -dpkg-shlibdeps: warning: symbol exp used by debian/libhts0/usr/lib/x86_64-linux-gnu/libhts.so.0.2.0~rc4-1 found in none of the libraries -dpkg-shlibdeps: warning: symbol pthread_join used by debian/libhts0/usr/lib/x86_64-linux-gnu/libhts.so.0.2.0~rc4-1 found in none of the libraries -dpkg-shlibdeps: warning: symbol pthread_kill used by debian/libhts0/usr/lib/x86_64-linux-gnu/libhts.so.0.2.0~rc4-1 found in none of the libraries dpkg-shlibdeps: warning: symbol pthread_create used by debian/libhts0/usr/lib/x86_64-linux-gnu/libhts.so.0.2.0~rc4-1 found in none of the libraries
Re: No relro when building from inside a Git package ?
Le Thu, Nov 21, 2013 at 09:00:48AM +0100, Andreas Tille a écrit : PS: Alioth is back online and I might have a look later this day if you would commit there. Thanks a lot ! gbp clone git.debian.org:/git/debian-med/htslib.git Cheers, -- Charles -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20131121082926.gf16...@falafel.plessy.net
Re: No relro when building from inside a Git package ?
Hi Charles, On Thu, Nov 21, 2013 at 05:29:26PM +0900, Charles Plessy wrote: Le Thu, Nov 21, 2013 at 09:00:48AM +0100, Andreas Tille a écrit : PS: Alioth is back online and I might have a look later this day if you would commit there. Thanks a lot ! gbp clone git.debian.org:/git/debian-med/htslib.git When doing `git-buildpackage` (which for sure includes the .git dir) I can not see the effect you are describing. The only thing lintian (and I) are more concerned about is: E: libhts0: symbols-file-contains-current-version-with-debian-revision on symbol cram_index_build@Base W: libhts0: symbols-file-contains-debian-revision on symbol bam_mplp_init_overlaps@Base and 1 others I personally would simply drop the symbols file since it seems to introduce more harm than good. Am I missing something? Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20131121102624.gc7...@an3as.eu
Re: No relro when building from inside a Git package ?
Hi Charles, On Fri, Nov 22, 2013 at 02:23:33PM +0900, Charles Plessy wrote: Le Thu, Nov 21, 2013 at 11:26:24AM +0100, Andreas Tille a écrit : On Thu, Nov 21, 2013 at 05:29:26PM +0900, Charles Plessy wrote: gbp clone git.debian.org:/git/debian-med/htslib.git When doing `git-buildpackage` (which for sure includes the .git dir) I can not see the effect you are describing. The only thing lintian (and I) are more concerned about is: E: libhts0: symbols-file-contains-current-version-with-debian-revision on symbol cram_index_build@Base W: libhts0: symbols-file-contains-debian-revision on symbol bam_mplp_init_overlaps@Base and 1 others I personally would simply drop the symbols file since it seems to introduce more harm than good. Hi Andreas, this is strange, in my case, from a fresh clone, and when building with git buildpackage -us -uc, I see the hardening-no-relro tag. $ lintian -I --pedantic ../htslib_0.2.0~rc4-1_amd64.changes I: htslib source: quilt-patch-using-template-description debian-changes W: htslib source: newer-standards-version 3.9.5 (current is 3.9.4) W: libhts0: hardening-no-relro usr/lib/x86_64-linux-gnu/libhts.so.0.2.0~rc4-1 P: libhts0: no-upstream-changelog E: libhts0: symbols-file-contains-current-version-with-debian-revision on symbol cram_index_build@Base W: libhts0: symbols-file-contains-debian-revision on symbol bam_mplp_init_overlaps@Base and 1 others P: libhts-dev: no-upstream-changelog W: libhts-dev: manpage-has-errors-from-man usr/share/man/man5/vcf.5.gz file `standard input', around line 15: P: htslib-test: no-upstream-changelog $ gbp-clone ssh://git.debian.org/git/debian-med/htslib.git $ cd htslib (debian/unstable) $ git branch * debian/unstable develop pristine-tar (debian/unstable) $ git-buildpackage (debian/unstable) $ lintian -I --pedantic ../build-area/htslib_0.2.0~rc4-1_amd64.changes I: htslib source: quilt-patch-using-template-description debian-changes W: htslib source: newer-standards-version 3.9.5 (current is 3.9.4) P: libhts0: no-upstream-changelog E: libhts0: symbols-file-contains-current-version-with-debian-revision on symbol cram_index_build@Base W: libhts0: symbols-file-contains-debian-revision on symbol bam_mplp_init_overlaps@Base and 1 others P: htslib-test: no-upstream-changelog P: libhts-dev: no-upstream-changelog W: libhts-dev: manpage-has-errors-from-man usr/share/man/man5/vcf.5.gz file `standard input', around line 15: The attached build log clearly contains '-Wl,-z,relro' where it needs to be. For the tags related to the symbols file, this is because the package is work in progress. I pull upsteam commits as they go and only update the version number when upstream makes new tags, therefore Debian revisions contain changes to the library's symbols. Given that the API is not yet stable, I understand that the symbols file is not yet useful, but I prefer having it in the package now so that I do not forget to add it when I start to upload packages built on the htslib-dev package. I personally would choose some kinf of changelog entry: TODO: create symbols file to get rid of this noise ... but I now understand your motivation. Kind regards Andreas. -- http://fam-tille.de htslib_0.2.0~rc4-1_amd64.build.bz2 Description: Binary data
Re: No relro when building from inside a Git package ?
Le Thu, Nov 21, 2013 at 11:26:24AM +0100, Andreas Tille a écrit : On Thu, Nov 21, 2013 at 05:29:26PM +0900, Charles Plessy wrote: gbp clone git.debian.org:/git/debian-med/htslib.git When doing `git-buildpackage` (which for sure includes the .git dir) I can not see the effect you are describing. The only thing lintian (and I) are more concerned about is: E: libhts0: symbols-file-contains-current-version-with-debian-revision on symbol cram_index_build@Base W: libhts0: symbols-file-contains-debian-revision on symbol bam_mplp_init_overlaps@Base and 1 others I personally would simply drop the symbols file since it seems to introduce more harm than good. Hi Andreas, this is strange, in my case, from a fresh clone, and when building with git buildpackage -us -uc, I see the hardening-no-relro tag. $ lintian -I --pedantic ../htslib_0.2.0~rc4-1_amd64.changes I: htslib source: quilt-patch-using-template-description debian-changes W: htslib source: newer-standards-version 3.9.5 (current is 3.9.4) W: libhts0: hardening-no-relro usr/lib/x86_64-linux-gnu/libhts.so.0.2.0~rc4-1 P: libhts0: no-upstream-changelog E: libhts0: symbols-file-contains-current-version-with-debian-revision on symbol cram_index_build@Base W: libhts0: symbols-file-contains-debian-revision on symbol bam_mplp_init_overlaps@Base and 1 others P: libhts-dev: no-upstream-changelog W: libhts-dev: manpage-has-errors-from-man usr/share/man/man5/vcf.5.gz file `standard input', around line 15: P: htslib-test: no-upstream-changelog For the tags related to the symbols file, this is because the package is work in progress. I pull upsteam commits as they go and only update the version number when upstream makes new tags, therefore Debian revisions contain changes to the library's symbols. Given that the API is not yet stable, I understand that the symbols file is not yet useful, but I prefer having it in the package now so that I do not forget to add it when I start to upload packages built on the htslib-dev package. Cheers, -- Charles -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20131122052333.gh16...@falafel.plessy.net
Re: No relro when building from inside a Git package ?
Hi Charles, without having checked out the repository and diving into it: Can you post a diff of the two build logs? Kind regards Andreas. On Wed, Nov 20, 2013 at 02:44:39PM +0900, Charles Plessy wrote: Dear all, I am experience a strange variation when building package from a Git repository or from the same source with the .git directory deleted. In the first case I have the Lintian warning 'libhts0: hardening-no-relro usr/lib/x86_64-linux-gnu/libhts.so.0.2.0~rc4-1', but not in the second case. The only git-dependant code that I found is to create a package version, but I override it in debian/rules by the Debian package's version. In Makefile: ifneq $(wildcard .git) original_version := $(PACKAGE_VERSION) PACKAGE_VERSION := $(shell git describe --always --dirty) In debian/rules: override_dh_auto_build: dh_auto_build -- \ CFLAGS=$$(dpkg-buildflags --get CFLAGS) \ CPPFLAGS=-I. -DSAMTOOLS=1 $$(dpkg-buildflags --get CPPFLAGS) \ LDFLAGS=$$(dpkg-buildflags --get LDFLAGS) \ PACKAGE_VERSION=$(DEB_VERSION) override_dh_auto_install: dh_auto_install -- prefix=/usr PACKAGE_VERSION=$(DEB_VERSION) (Digression: I do this because after tagging a debian revision, for instance 'debian/0.2.0_rc3-1', the package will fail to build from the Git repository since the tag becomes used for the soversion of the library, and the slash is mistaken as a directory separator. Is there a smart solution to this problem ?) You can get the source with 'gbp clone https://github.com/Debian/htslib'. Does anybody see why the hardening-no-relro is triggered when building in presence of the .git directory ? Cheers, -- Charles Plessy Debian Med packaging team, http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20131120054439.gb16...@falafel.plessy.net -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20131120212429.gc7...@an3as.eu
Re: No relro when building from inside a Git package ?
Le Wed, Nov 20, 2013 at 10:24:29PM +0100, Andreas Tille a écrit : without having checked out the repository and diving into it: Can you post a diff of the two build logs? Hi Andreas, here it is (attached). Could the problem be a side effect of the test suite ? Cheers, -- Charles --- with-.git 2013-11-21 09:32:14.244499056 +0900 +++ without-.git2013-11-21 09:34:12.908497923 +0900 @@ -150,15 +150,6 @@ dh_auto_test make -j1 test make[2]: Entering directory `/tmp/htslib' -echo '#define HTS_VERSION debian/0.2.0_rc3-1-38-g9469458' version.h -gcc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o hts.o hts.c -ar -rc libhts.a kfunc.o knetfile.o kstring.o bgzf.o faidx.o hfile.o hfile_net.o hts.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/md5.o cram/open_trace_file.o cram/pooled_alloc.o cram/sam_header.o cram/string_alloc.o cram/thread_pool.o cram/vlen.o cram/zfio.o -ranlib libhts.a -gcc -pthread -o test/fieldarith test/fieldarith.o libhts.a -lz -gcc -o test/hfile test/hfile.o libhts.a -lz -gcc -pthread -o test/test_view test/test_view.o libhts.a -lz -gcc -pthread -o test/test-vcf-api test/test-vcf-api.o libhts.a -lz -gcc -pthread -o test/test-vcf-sweep test/test-vcf-sweep.o libhts.a -lz test/fieldarith test/fieldarith.sam test/hfile cd test ./test_view.pl @@ -456,11 +447,11 @@ Failures 0 cd test ./test.pl test_vcf_api: - /tmp/htslib/test/test-vcf-api /tmp/Vvj_N60T4W/test-vcf-api.bcf + /tmp/htslib/test/test-vcf-api /tmp/cUKPv4vctM/test-vcf-api.bcf .. ok test_vcf_sweep: - /tmp/htslib/test/test-vcf-sweep /tmp/Vvj_N60T4W/test-vcf-api.bcf + /tmp/htslib/test/test-vcf-sweep /tmp/cUKPv4vctM/test-vcf-api.bcf .. ok @@ -495,10 +486,6 @@ make -j1 install DESTDIR=/tmp/htslib/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr PACKAGE_VERSION=0.2.0\~rc4-1 make[2]: Entering directory `/tmp/htslib' mkdir -p /tmp/htslib/debian/tmp/usr/include/htslib /tmp/htslib/debian/tmp/usr/lib /tmp/htslib/debian/tmp/usr/share/man/man5 -echo '#define HTS_VERSION 0.2.0~rc4-1' version.h -gcc -g -Wall -O2 -I. -DSAMTOOLS=1 -fpic -c -o hts.pico hts.c -gcc -shared -Wl,-soname,libhts.so.0 -o libhts.so kfunc.pico knetfile.pico kstring.pico bgzf.pico faidx.pico hfile.pico hfile_net.pico hts.pico sam.pico synced_bcf_reader.pico vcf_sweep.pico tbx.pico vcf.pico vcfutils.pico cram/cram_codecs.pico cram/cram_decode.pico cram/cram_encode.pico cram/cram_index.pico cram/cram_io.pico cram/cram_samtools.pico cram/cram_stats.pico cram/files.pico cram/mFILE.pico cram/md5.pico cram/open_trace_file.pico cram/pooled_alloc.pico cram/sam_header.pico cram/string_alloc.pico cram/thread_pool.pico cram/vlen.pico cram/zfio.pico -lz -ln -sf libhts.so libhts.so.0 install -p -m 644 libhts.so /tmp/htslib/debian/tmp/usr/lib/libhts.so.0.2.0~rc4-1 ln -sf libhts.so.0.2.0~rc4-1 /tmp/htslib/debian/tmp/usr/lib/libhts.so ln -sf libhts.so.0.2.0~rc4-1 /tmp/htslib/debian/tmp/usr/lib/libhts.so.0 @@ -660,7 +647,7 @@ dpkg-gensymbols: warning: some new symbols appeared in the symbols file: see diff output below dpkg-gensymbols: warning: debian/libhts0/DEBIAN/symbols doesn't match completely debian/libhts0.symbols --- debian/libhts0.symbols (libhts0_0.2.0~rc4-1_amd64) -+++ dpkg-gensymbolskXM3kh 2013-11-21 09:32:00.312499189 +0900 dpkg-gensymbols4DQT53 2013-11-21 09:34:08.056497969 +0900 @@ -230,6 +230,7 @@ cram_huffman_encode_int0@Base 0.2.0~rc3 cram_huffman_encode_int@Base 0.2.0~rc3 @@ -675,12 +662,12 @@ rm -f debian/htslib-test/DEBIAN/shlibs dh_shlibdeps dpkg-shlibdeps -Tdebian/libhts0.substvars debian/libhts0/usr/lib/x86_64-linux-gnu/libhts.so.0.2.0\~rc4-1 -dpkg-shlibdeps: warning: symbol exp used by debian/libhts0/usr/lib/x86_64-linux-gnu/libhts.so.0.2.0~rc4-1 found in none of the libraries -dpkg-shlibdeps: warning: symbol pthread_join used by debian/libhts0/usr/lib/x86_64-linux-gnu/libhts.so.0.2.0~rc4-1 found in none of the libraries -dpkg-shlibdeps: warning: symbol pthread_kill used by debian/libhts0/usr/lib/x86_64-linux-gnu/libhts.so.0.2.0~rc4-1 found in none of the libraries dpkg-shlibdeps: warning: symbol pthread_create used by debian/libhts0/usr/lib/x86_64-linux-gnu/libhts.so.0.2.0~rc4-1 found in none of the libraries +dpkg-shlibdeps: warning: symbol exp used by debian/libhts0/usr/lib/x86_64-linux-gnu/libhts.so.0.2.0~rc4-1 found in none of the libraries dpkg-shlibdeps: warning: symbol lgamma used by debian/libhts0/usr/lib/x86_64-linux-gnu/libhts.so.0.2.0~rc4-1 found in none of the libraries +dpkg-shlibdeps: warning: symbol pthread_kill used by debian/libhts0/usr/lib/x86_64-linux-gnu/libhts.so.0.2.0~rc4-1 found in none of the libraries dpkg-shlibdeps: warning: symbol log used by debian/libhts0/usr/lib/x86_64-linux-gnu/libhts.so.0.2.0~rc4-1 found in none
No relro when building from inside a Git package ?
Dear all, I am experience a strange variation when building package from a Git repository or from the same source with the .git directory deleted. In the first case I have the Lintian warning 'libhts0: hardening-no-relro usr/lib/x86_64-linux-gnu/libhts.so.0.2.0~rc4-1', but not in the second case. The only git-dependant code that I found is to create a package version, but I override it in debian/rules by the Debian package's version. In Makefile: ifneq $(wildcard .git) original_version := $(PACKAGE_VERSION) PACKAGE_VERSION := $(shell git describe --always --dirty) In debian/rules: override_dh_auto_build: dh_auto_build -- \ CFLAGS=$$(dpkg-buildflags --get CFLAGS) \ CPPFLAGS=-I. -DSAMTOOLS=1 $$(dpkg-buildflags --get CPPFLAGS) \ LDFLAGS=$$(dpkg-buildflags --get LDFLAGS) \ PACKAGE_VERSION=$(DEB_VERSION) override_dh_auto_install: dh_auto_install -- prefix=/usr PACKAGE_VERSION=$(DEB_VERSION) (Digression: I do this because after tagging a debian revision, for instance 'debian/0.2.0_rc3-1', the package will fail to build from the Git repository since the tag becomes used for the soversion of the library, and the slash is mistaken as a directory separator. Is there a smart solution to this problem ?) You can get the source with 'gbp clone https://github.com/Debian/htslib'. Does anybody see why the hardening-no-relro is triggered when building in presence of the .git directory ? Cheers, -- Charles Plessy Debian Med packaging team, http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20131120054439.gb16...@falafel.plessy.net
