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-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
> 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
> install -o 0 -g 0 -d debian/libhts-dev/DEBIAN
> install -o 0 -g 0 -d debian/htslib-test/DEBIAN
> dh_installdeb
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