[Debian-med-packaging] Bug#966914: sambamba: FTBFS: collect2: error: ld returned 1 exit status

[Matthias Klumpp]

Am Di., 4. Aug. 2020 um 11:23 Uhr schrieb Andreas Tille <tille at debian.org>:
>
> Control: tags -1 help
>
> Hi,
>
> On Mon, Aug 03, 2020 at 10:06:32AM +0200, Lucas Nussbaum wrote:
> > > lto1: fatal error: bytecode stream in file ‘/usr/lib/x86_64-linux-gnu/libhts.a’ generated with GCC compiler older than 10.0
>
> I've uploaded a new htslib that is now build with GCC 10 and used a
> versioned Build-Depends inside sambamba.  Now the build issue changed
> to:
>
> [38/41] ldc2 -enable-color -O -g -release -wi -I/usr/include/x86_64-linux-gnu -I/usr/include/d/bio -O3 -release -enable-inlining -boundscheck=off -J../ -I=.. -I=. -I=sambamba.p -I=sambamba.p -of=sambamba.p/_build_sambamba-0.7.1_obj-x86_64-linux-gnu_utils_ldc_version_info_.d.o -c /build/sambamba-0.7.1/obj-x86_64-linux-gnu/utils/ldc_version_info_.d
> [39/41] ldc2 -enable-color -O -g -release -wi -I/usr/include/x86_64-linux-gnu -I/usr/include/d/bio -O3 -release -enable-inlining -boundscheck=off -J../ -I=.. -I=. -I=sambamba.p -I=sambamba.p -of=sambamba.p/thirdparty_unstablesort.d.o -c ../thirdparty/unstablesort.d
> [40/41] ldc2 -enable-color -O -g -release -wi -I/usr/include/x86_64-linux-gnu -I/usr/include/d/bio -O3 -release -enable-inlining -boundscheck=off -J../ -I=.. -I=. -I=sambamba.p -I=sambamba.p -of=sambamba.p/sambamba_view.d.o -c ../sambamba/view.d
> [41/41] ldc2  -of=sambamba sambamba.p/sambamba_main.d.o sambamba.p/sambamba_depth.d.o sambamba.p/sambamba_fixbins.d.o sambamba.p/sambamba_flagstat.d.o sambamba.p/sambamba_index.d.o sambamba.p/sambamba_markdup2.d.o sambamba.p/sambamba_markdup.d.o sambamba.p/sambamba_merge.d.o sambamba.p/sambamba_pileup.d.o sambamba.p/sambamba_slice.d.o sambamba.p/sambamba_sort.d.o sambamba.p/sambamba_subsample.d.o sambamba.p/sambamba_utils_common_bed.d.o sambamba.p/sambamba_utils_common_file.d.o sambamba.p/sambamba_utils_common_filtering.d.o sambamba.p/sambamba_utils_common_intervaltree.d.o sambamba.p/sambamba_utils_common_ldc_gc_workaround.d.o sambamba.p/sambamba_utils_common_overwrite.d.o sambamba.p/sambamba_utils_common_pratt_parser.d.o sambamba.p/sambamba_utils_common_progressbar.d.o sambamba.p/sambamba_utils_common_queryparser.d.o sambamba.p/sambamba_utils_common_readstorage.d.o sambamba.p/sambamba_utils_common_tmpdir.d.o sambamba.p/sambamba_utils_view_alignmentrangeprocessor.d.o sambamba.p/sambamba_utils_view_headerserializer.d.o sambamba.p/sambamba_validate.d.o sambamba.p/sambamba_view.d.o sambamba.p/utils_lz4.d.o sambamba.p/utils_strip_bcf_header.d.o sambamba.p/utils_version_.d.o sambamba.p/cram_exception.d.o sambamba.p/cram_htslib.d.o sambamba.p/cram_reader.d.o sambamba.p/cram_reference.d.o sambamba.p/cram_slicereader.d.o sambamba.p/cram_wrappers.d.o sambamba.p/cram_writer.d.o sambamba.p/thirdparty_mergesort.d.o sambamba.p/thirdparty_unstablesort.d.o sambamba.p/_build_sambamba-0.7.1_obj-x86_64-linux-gnu_utils_ldc_version_info_.d.o -L=--allow-shlib-undefined -link-defaultlib-shared -O -g -release -wi -L=-z -L=relro -L=/usr/lib/x86_64-linux-gnu/libbiod.a -L=/usr/lib/x86_64-linux-gnu/libz.a -L=/usr/lib/x86_64-linux-gnu/libhts.a -L=-z -L=relro -L=-z -L=now -L=-flto -fvisibility=hidden -L=/usr/lib/x86_64-linux-gnu/libbz2.a -L=/usr/lib/x86_64-linux-gnu/libdeflate.a -L=-lm -L=-lpthread -L=/usr/lib/x86_64-linux-gnu/liblzma.a /usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu/liblz4.so /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/liblzma.so -L=-rpath -L=/usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu -L=-rpath-link -L=/usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu -L=-rpath-link -L=/usr/lib/x86_64-linux-gnu
> FAILED: sambamba
> ldc2  -of=sambamba sambamba.p/sambamba_main.d.o sambamba.p/sambamba_depth.d.o sambamba.p/sambamba_fixbins.d.o sambamba.p/sambamba_flagstat.d.o sambamba.p/sambamba_index.d.o sambamba.p/sambamba_markdup2.d.o sambamba.p/sambamba_markdup.d.o sambamba.p/sambamba_merge.d.o sambamba.p/sambamba_pileup.d.o sambamba.p/sambamba_slice.d.o sambamba.p/sambamba_sort.d.o sambamba.p/sambamba_subsample.d.o sambamba.p/sambamba_utils_common_bed.d.o sambamba.p/sambamba_utils_common_file.d.o sambamba.p/sambamba_utils_common_filtering.d.o sambamba.p/sambamba_utils_common_intervaltree.d.o sambamba.p/sambamba_utils_common_ldc_gc_workaround.d.o sambamba.p/sambamba_utils_common_overwrite.d.o sambamba.p/sambamba_utils_common_pratt_parser.d.o sambamba.p/sambamba_utils_common_progressbar.d.o sambamba.p/sambamba_utils_common_queryparser.d.o sambamba.p/sambamba_utils_common_readstorage.d.o sambamba.p/sambamba_utils_common_tmpdir.d.o sambamba.p/sambamba_utils_view_alignmentrangeprocessor.d.o sambamba.p/sambamba_utils_view_headerserializer.d.o sambamba.p/sambamba_validate.d.o sambamba.p/sambamba_view.d.o sambamba.p/utils_lz4.d.o sambamba.p/utils_strip_bcf_header.d.o sambamba.p/utils_version_.d.o sambamba.p/cram_exception.d.o sambamba.p/cram_htslib.d.o sambamba.p/cram_reader.d.o sambamba.p/cram_reference.d.o sambamba.p/cram_slicereader.d.o sambamba.p/cram_wrappers.d.o sambamba.p/cram_writer.d.o sambamba.p/thirdparty_mergesort.d.o sambamba.p/thirdparty_unstablesort.d.o sambamba.p/_build_sambamba-0.7.1_obj-x86_64-linux-gnu_utils_ldc_version_info_.d.o -L=--allow-shlib-undefined -link-defaultlib-shared -O -g -release -wi -L=-z -L=relro -L=/usr/lib/x86_64-linux-gnu/libbiod.a -L=/usr/lib/x86_64-linux-gnu/libz.a -L=/usr/lib/x86_64-linux-gnu/libhts.a -L=-z -L=relro -L=-z -L=now -L=-flto -fvisibility=hidden -L=/usr/lib/x86_64-linux-gnu/libbz2.a -L=/usr/lib/x86_64-linux-gnu/libdeflate.a -L=-lm -L=-lpthread -L=/usr/lib/x86_64-linux-gnu/liblzma.a /usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu/liblz4.so /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/liblzma.so -L=-rpath -L=/usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu -L=-rpath-link -L=/usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu -L=-rpath-link -L=/usr/lib/x86_64-linux-gnu
> bgzf.c:415: error: undefined reference to 'compressBound'
> collect2: error: ld returned 1 exit status
> Error: /usr/bin/cc failed with status: 1
> ninja: build stopped: subcommand failed.
> dh_auto_build: error: cd obj-x86_64-linux-gnu && LC_ALL=C.UTF-8 ninja -j4 -v returned exit code 1

The undefined reference issue makes it looks like the binary isn't
linked against zlib, but the linker command line clearly shows that it
is included - multiple times even, for some reason. Where does the
`bgzf.c` file reference come from?
I think I'll have to try to build this myself again to see what may be
wrong here...

Cheers,
    Matthias

-- 
I welcome VSRE emails. See http://vsre.info/