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

[Lucas Nussbaum]

Source: sambamba
Version: 0.7.1-4
Severity: serious
Justification: FTBFS on amd64
Tags: bullseye sid ftbfs
Usertags: ftbfs-20200802 ftbfs-bullseye

Hi,

During a rebuild of all packages in sid, your package failed to build
on amd64.

Relevant part (hopefully):
> 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-s4fhbx_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
> lto1: fatal error: bytecode stream in file ‘/usr/lib/x86_64-linux-gnu/libhts.a’ generated with GCC compiler older than 10.0
> compilation terminated.
> lto-wrapper: fatal error: /usr/bin/cc returned 1 exit status
> compilation terminated.
> /usr/bin/ld.gold: fatal error: lto-wrapper failed
> collect2: error: ld returned 1 exit status

The full build log is available from:
   http://qa-logs.debian.net/2020/08/02/sambamba_0.7.1-4_unstable.log

A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!

About the archive rebuild: The rebuild was done on EC2 VM instances from
Amazon Web Services, using a clean, minimal and up-to-date chroot. Every
failed build was retried once to eliminate random failures.