[Debian-med-packaging] Bug#948919: sambamba FTBFS: undefined reference to 'cram_to_bam'

[Andreas Tille]

Control: tags -1 help
Control: tags -1 upstream
Control: forwarded -1 Pjotr Prins <pjotr2018 at thebird.nl>

Hi Matthias and Pjotr,

I'd like to forward another bug in Sambabma.

Any idea how to finally get sambamba build smoothly?

Kind regards

      Andreas.


On Tue, Jan 14, 2020 at 08:32:08PM +0200, Juhani Numminen wrote:
> Source: libbiod
> Version: 0.7.1-1
> Severity: serious
> Tags: ftbfs
> 
> Hello,
> 
> This new FTBFS is also being discussed on #907489 but I think they
> are separate issues.
> 
> I have quoted the error message from the log below.
> https://buildd.debian.org/status/fetch.php?pkg=sambamba&arch=amd64&ver=0.7.1-1&stamp=1576381970&raw=0
> ----
> FAILED: sambamba 
> ldc2  -of=sambamba 'sambamba at exe/sambamba_main.d.o' 'sambamba at exe/sambamba_depth.d.o' 'sambamba at exe/sambamba_fixbins.d.o' 'sambamba at exe/sambamba_flagstat.d.o' 'sambamba at exe/sambamba_index.d.o' 'sambamba at exe/sambamba_markdup2.d.o' 'sambamba at exe/sambamba_markdup.d.o' 'sambamba at exe/sambamba_merge.d.o' 'sambamba at exe/sambamba_pileup.d.o' 'sambamba at exe/sambamba_slice.d.o' 'sambamba at exe/sambamba_sort.d.o' 'sambamba at exe/sambamba_subsample.d.o' 'sambamba at exe/sambamba_utils_common_bed.d.o' 'sambamba at exe/sambamba_utils_common_file.d.o' 'sambamba at exe/sambamba_utils_common_filtering.d.o' 'sambamba at exe/sambamba_utils_common_intervaltree.d.o' 'sambamba at exe/sambamba_utils_common_ldc_gc_workaround.d.o' 'sambamba at exe/sambamba_utils_common_overwrite.d.o' 'sambamba at exe/sambamba_utils_common_pratt_parser.d.o' 'sambamba at exe/sambamba_utils_common_progressbar.d.o' 'sambamba at exe/sambamba_utils_common_queryparser.d.o' 'sambamba at exe/sambamba_utils_common_readstorage.d.o' 'sambamba at exe/sambamba_utils_common_tmpdir.d.o' 'sambamba at exe/sambamba_utils_view_alignmentrangeprocessor.d.o' 'sambamba at exe/sambamba_utils_view_headerserializer.d.o' 'sambamba at exe/sambamba_validate.d.o' 'sambamba at exe/sambamba_view.d.o' 'sambamba at exe/utils_lz4.d.o' 'sambamba at exe/utils_strip_bcf_header.d.o' 'sambamba at exe/utils_version_.d.o' 'sambamba at exe/cram_exception.d.o' 'sambamba at exe/cram_htslib.d.o' 'sambamba at exe/cram_reader.d.o' 'sambamba at exe/cram_reference.d.o' 'sambamba at exe/cram_slicereader.d.o' 'sambamba at exe/cram_wrappers.d.o' 'sambamba at exe/cram_writer.d.o' 'sambamba at exe/thirdparty_mergesort.d.o' 'sambamba at exe/thirdparty_unstablesort.d.o' 'sambamba at exe/ldc_version_info_.d.o' -L=-L--allow-shlib-undefined -O -g -release -wi -L=-z -L=relro -L=--start-group -L=/usr/lib/x86_64-linux-gnu/libbiod.a -L=/usr/lib/x86_64-linux-gnu/libz.a /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/liblz4.so /usr/lib/x86_64-linux-gnu/libhts.so -L=--end-group -L=-rpath -L=/usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu
> slicereader.d:71: error: undefined reference to 'cram_to_bam'
> collect2: error: ld returned 1 exit status
> -----
> 
> Regards,
> Juhani
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