[Debian-med-packaging] Bug#606004: Fix FTBFS with ld --as-needed

[Matthias Klose]

Package: samtools
Version: 0.1.12a-1
Tags: patch
User: debian-gcc at lists.debian.org
Usertags: ld-as-needed

patch at
http://launchpadlibrarian.net/60144486/samtools_0.1.12a-1_0.1.12a-1ubuntu1.diff.gz


gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -lm -lz -L.. -lbam
../libbam.a(bgzf.o): In function `deflate_block':
/build/buildd/samtools-0.1.12a/bgzf.c:272: undefined reference to `deflate'
/build/buildd/samtools-0.1.12a/bgzf.c:274: undefined reference to `deflateEnd'
/build/buildd/samtools-0.1.12a/bgzf.c:266: undefined reference to `deflateInit2_'
/build/buildd/samtools-0.1.12a/bgzf.c:290: undefined reference to `deflateEnd'
/build/buildd/samtools-0.1.12a/bgzf.c:306: undefined reference to `crc32'
/build/buildd/samtools-0.1.12a/bgzf.c:307: undefined reference to `crc32'
../libbam.a(bgzf.o): In function `inflate_block':
/build/buildd/samtools-0.1.12a/bgzf.c:340: undefined reference to `inflateInit2_'
/build/buildd/samtools-0.1.12a/bgzf.c:345: undefined reference to `inflate'
/build/buildd/samtools-0.1.12a/bgzf.c:347: undefined reference to `inflateEnd'
/build/buildd/samtools-0.1.12a/bgzf.c:351: undefined reference to `inflateEnd'
../libbam.a(bam_import.o): In function `ks_getuntil':
/build/buildd/samtools-0.1.12a/bam_import.c:17: undefined reference to `gzread'
../libbam.a(bam_import.o): In function `__bam_get_lines':
/build/buildd/samtools-0.1.12a/bam_import.c:76: undefined reference to `gzdopen'
/build/buildd/samtools-0.1.12a/bam_import.c:92: undefined reference to `gzclose'
/build/buildd/samtools-0.1.12a/bam_import.c:76: undefined reference to `gzopen64'
../libbam.a(bam_import.o): In function `sam_header_read2':
/build/buildd/samtools-0.1.12a/bam_import.c:126: undefined reference to `gzdopen'
/build/buildd/samtools-0.1.12a/bam_import.c:126: undefined reference to `gzopen64'
../libbam.a(bam_import.o): In function `ks_getc':
/build/buildd/samtools-0.1.12a/bam_import.c:17: undefined reference to `gzread'
../libbam.a(bam_import.o): In function `sam_header_read2':
/build/buildd/samtools-0.1.12a/bam_import.c:147: undefined reference to `gzclose'
../libbam.a(bam_import.o): In function `sam_open':
/build/buildd/samtools-0.1.12a/bam_import.c:442: undefined reference to `gzdopen'
/build/buildd/samtools-0.1.12a/bam_import.c:442: undefined reference to `gzopen64'
../libbam.a(bam_import.o): In function `sam_close':
/build/buildd/samtools-0.1.12a/bam_import.c:455: undefined reference to `gzclose'
../libbam.a(razf.o): In function `_razf_write':
/build/buildd/samtools-0.1.12a/razf.c:197: undefined reference to `deflate'
../libbam.a(razf.o): In function `razf_open_w':
/build/buildd/samtools-0.1.12a/razf.c:170: undefined reference to `deflateInit2_'
/build/buildd/samtools-0.1.12a/razf.c:186: undefined reference to `deflateSetHeader'
../libbam.a(razf.o): In function `razf_open_r':
/build/buildd/samtools-0.1.12a/razf.c:389: undefined reference to `inflateInit2_'
/build/buildd/samtools-0.1.12a/razf.c:390: undefined reference to `inflateEnd'
../libbam.a(razf.o): In function `_razf_read':
/build/buildd/samtools-0.1.12a/razf.c:602: undefined reference to `inflate'
../libbam.a(razf.o): In function `razf_flush':
/build/buildd/samtools-0.1.12a/razf.c:230: undefined reference to `deflate'
../libbam.a(razf.o): In function `_razf_reset_read':
/build/buildd/samtools-0.1.12a/razf.c:709: undefined reference to `inflateReset'
/build/buildd/samtools-0.1.12a/razf.c:709: undefined reference to `inflateReset'
../libbam.a(razf.o): In function `razf_end_flush':
/build/buildd/samtools-0.1.12a/razf.c:254: undefined reference to `deflate'
../libbam.a(razf.o): In function `razf_close':
/build/buildd/samtools-0.1.12a/razf.c:800: undefined reference to `deflateEnd'
/build/buildd/samtools-0.1.12a/razf.c:826: undefined reference to `inflateEnd'
collect2: ld returned 1 exit status
make[1]: *** [calDepth] Error 1
make[1]: Leaving directory `/build/buildd/samtools-0.1.12a/examples'
make: *** [debian/stamp-makefile-check] Error 2