search

biod / sambamba

Tools for working with SAM/BAM data
http://thebird.nl/blog/D_Dragon.html
GNU General Public License v2.0
563 stars 105 forks source link

Sambamba has remaining references to libbiod #484

Closed tillea closed 2 years ago

tillea commented 2 years ago

Hi, when I try to build Sambamba, I get

[4/34] ldc2 -I=sambamba.p -I=. -I=.. -enable-color -wi -O -g -release -wi -O3 -release -enable-inlining -boundscheck=off -J../ -J. -makedeps=sambamba.p/sambamba_fixbins.d.o.deps -of=sambamba.p/sambamba_fixbins.d.o -c ../sambamba/fixbins.d
FAILED: sambamba.p/sambamba_fixbins.d.o 
ldc2 -I=sambamba.p -I=. -I=.. -enable-color -wi -O -g -release -wi -O3 -release -enable-inlining -boundscheck=off -J../ -J. -makedeps=sambamba.p/sambamba_fixbins.d.o.deps -of=sambamba.p/sambamba_fixbins.d.o -c ../sambamba/fixbins.d
../sambamba/fixbins.d(25): Error: module `reader` is in file 'bio/std/hts/bam/reader.d' which cannot be read

So there seem to be some remaining references to BioD which are not yet taken over in the source base of Sambamba.

BTW, @pjotrp I tried to send this via e-mail to you but your mail address is bouncing.

Kind regards, Andreas.

pjotrp commented 2 years ago

meson should be fixed, but I did not do a release yet. Do you mind trying the latest commit?

On Wed, Jan 12, 2022 at 08:06:37AM -0800, Andreas Tille wrote:

Hi, when I try to build Sambamba, I get [4/34] ldc2 -I=sambamba.p -I=. -I=.. -enable-color -wi -O -g -release -wi -O3 -r elease -enable-inlining -boundscheck=off -J../ -J. -makedeps=sambamba.p/sambamba _fixbins.d.o.deps -of=sambamba.p/sambamba_fixbins.d.o -c ../sambamba/fixbins.d FAILED: sambamba.p/sambamba_fixbins.d.o ldc2 -I=sambamba.p -I=. -I=.. -enable-color -wi -O -g -release -wi -O3 -release -enable-inlining -boundscheck=off -J../ -J. -makedeps=sambamba.p/sambamba_fixbin s.d.o.deps -of=sambamba.p/sambamba_fixbins.d.o -c ../sambamba/fixbins.d ../sambamba/fixbins.d(25): Error: module reader is in file 'bio/std/hts/bam/re ader.d' which cannot be read

So there seem to be some remaining references to BioD which are not yet taken over in the source base of Sambamba.

BTW, @.*** I tried to send this via e-mail to you but your mail address is bouncing.

Kind regards, Andreas.

— Reply to this email directly, [2]view it on GitHub, or [3]unsubscribe. Triage notifications on the go with GitHub Mobile for [4]iOS or [5]Android. You are receiving this because you were mentioned. Message ID: @.***>

References

  1. https://github.com/pjotrp
  2. https://github.com/biod/sambamba/issues/484
  3. https://github.com/notifications/unsubscribe-auth/AAADJ355MLVEIU5QWAAOFXTUVWRI3ANCNFSM5LZLVBLQ
  4. https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675
  5. https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign=notification-email&utm_medium=email&utm_source=github
tillea commented 2 years ago

Am Wed, Jan 12, 2022 at 09:01:28PM -0800 schrieb Pjotr Prins:

meson should be fixed, but I did not do a release yet. Do you mind trying the latest commit? Do you mean just releasing current HEAD or just using a specific commit as a patch (link to that actual patch would be welcome). A single patch would be OK but switching from release tags to HEAD is a bit more invasive and I'm not really in a hurry to force this. Kind regards, Andreas.

pjotrp commented 2 years ago

I am working on a release. It would be good if someone could test the meson build before we release.

Other than that I am trying to remove deprecation warnings and update the docs a bit.

On Wed, Jan 12, 2022 at 10:33:43PM -0800, Andreas Tille wrote:

Am Wed, Jan 12, 2022 at 09:01:28PM -0800 schrieb Pjotr Prins:

meson should be fixed, but I did not do a release yet. Do you mind trying the latest commit? Do you mean just releasing current HEAD or just using a specific commit as a patch (link to that actual patch would be welcome). A single patch would be OK but switching from release tags to HEAD is a bit more invasive and I'm not really in a hurry to force this. Kind regards, Andreas.

— Reply to this email directly, [1]view it on GitHub, or [2]unsubscribe. Triage notifications on the go with GitHub Mobile for [3]iOS or [4]Android. You are receiving this because you were mentioned. Message ID: @.***>

References

  1. https://github.com/biod/sambamba/issues/484#issuecomment-1011837685
  2. https://github.com/notifications/unsubscribe-auth/AAADJ34N2ZNCXMIY33ABOVTUVZW4PANCNFSM5LZLVBLQ
  3. https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675
  4. https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign=notification-email&utm_medium=email&utm_source=github
tillea commented 2 years ago

OK, when trying to build current HEAD locally I get:

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/ssambamba_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/BioD_bio_co_re_base.d.o sambamba.p/BioD_bio_core_bgzf_block.d.o sambamba.p/BioD_bio_core_bgzf_chunk.d.o sambamba.p/BioD_bio_core_bgzf_compress. d.o sambamba.p/BioD_bio_core_bgzf_constants.d.o sambamIba.p/BioD_bio_core_bgzf_inputstream.d.o sambamba.p/BioD_bio_core_bgzf_outputstream.d.o sambamba.p/BioD_bio_core_bgzf_virtualoffset.d.o sambamba.p/BioD_bio_core_call.d.o sambamba.p/BioD_bbio_core_decompress.d.o sambamba.p/BioD_bio_core_genotype.d.o sambamba.p/BioD_bio_core_kmer.d.o sambamba.p/BioD_bio_core_region.d. o sambamba.p/BioD_bio_core_sequence.d.o sambamba.p/BioD/_bio_core_tinymap.d.o sambamba.p/BioD_bio_core_utils_algo.d.o sambamba.p/BioD_bio_core_utils_bylinefast.d.o sambamba.p/           BioD_bio_core_utils_exception.d.o sambamba.p/BioD_bio_core_utils_fnormat.d.o sambamba.p/BioD_bio_core_utils_memoize.d.o sambamba.p/BioD_bio_core_utils_outbuffer.d.o sambamba.p/          BioD_bio_core_utils_range.d.o sambamba.p/BioD_bio_core_utils_roundbuf.d.o sa1mbamba.p/BioD_bio_core_utils_stream.d.o sambamba.p/BioD_bio_core_utils_switchendianness.d.o sambamba.p/      BioD_bio_core_utils_tmpfile.d.o sambamba.p/BioD_bio_core_utils_zlib.d.o sambamba.pl/BioD_bio_std_experimental_hts_bam_header.d.o sambamba.p/BioD_bio_std_experimental_hts_bam_reader.d.o  sambamba.p/BioD_bio_std_experimental_hts_bam_writer.d.o sambamba.p/BioD_bio_std_expperimental_hts_bgzf.d.o sambamba.p/BioD_bio_std_experimental_hts_bgzf_writer.d.o sambamba.p/           BioD_bio_std_experimental_hts_constants.d.o sambamba.p/BioD_bio_std_experimental_hts_hashing.dy.o sambamba.p/BioD_bio_std_experimental_hts_logger.d.o sambamba.p/                         BioD_bio_std_experimental_hts_pileup.d.o sambamba.p/BioD_bio_std_experimental_hts_reads.d.o sambamba.p/BioD_bio_std_expeerimental_hts_unpack.d.o sambamba.p/BioD_bio_std_file_fai.d.o     sambamba.p/BioD_bio_std_file_fasta.d.o sambamba.p/BioD_bio_std_file_fastq.d.o sambamba.p/BioD_bio_std_genotype_maf.d.o sambtamba.p/BioD_bio_std_genotype_snp.d.o sambamba.p/              BioD_bio_std_hts_bam_abstractreader.d.o sambamba.p/BioD_bio_std_hts_bam_bai_bin.d.o sambamba.p/BioD_bio_std_hts_bam_baifile.d.o sambamba..p/BioD_bio_std_hts_bam_bai_indexing.d.o         sambamba.p/BioD_bio_std_hts_bam_baseinfo.d.o sambamba.p/BioD_bio_std_hts_bam_cigar.d.o sambamba.p/BioD_bio_std_hts_bam_constants.d.o sambamba.p/BioD_bio_std_hts_bam_md_core.d.o sambamba.p/BioD_bio_std_hts_bam_md_operation.d.o sambamba.p/BioD_bio_std_hts_bam_md_parse.d.o sambamba.p/BioD_bio_std_hts_bam_md_reconstruct.d.o sambamba.p/BioD_bio_std_hts_bam_multireader.d.o   sambamba.p/BioD_bio_std_hts_bam_pileup.d.o sambamba.p/BioD_bio_std_hts_bam_randomaccessmanager.d.o sambamba.p/BioD_bio_std_hts_bam_read.d.o sambamba.p/BioD_bio_std_hts_bam_reader.d.o    sambamba.p/BioD_bio_std_hts_bam_readrange.d.o sambamba.p/BioD_bio_std_hts_bam_reference.d.o sambamba.p/BioD_bio_std_hts_bam_referenceinfo.d.o sambamba.p/BioD_bio_std_hts_bam_region.d.o  sambamba.p/BioD_bio_std_hts_bam_splitter.d.o sambamba.p/BioD_bio_std_hts_bam_tagvalue.d.o sambamba.p/BioD_bio_std_hts_bam_validation_alignment.d.o sambamba.p/                            BioD_bio_std_hts_bam_validation_samheader.d.o sambamba.p/BioD_bio_std_hts_bam_writer.d.o sambamba.p/BioD_bio_std_hts_iontorrent_flowcall.d.o sambamba.p/                                  BioD_bio_std_hts_iontorrent_flowindex.d.o sambamba.p/BioD_bio_std_hts_sam_header.d.o sambamba.p/BioD_bio_std_hts_sam_reader.d.o sambamba.p/BioD_bio_std_hts_sam_utils_fastrecordparser.d. o sambamba.p/BioD_bio_std_hts_sam_utils_recordparser.d.o sambamba.p/BioD_bio_std_hts_snpcallers_maq.d.o sambamba.p/BioD_bio_std_hts_snpcallers_simple.d.o sambamba.p/                     BioD_bio_std_hts_thirdparty_msgpack.d.o sambamba.p/BioD_bio_std_hts_utils_array.d.o sambamba.p/BioD_bio_std_hts_utils_graph.d.o sambamba.p/BioD_bio_std_hts_utils_samheadermerger.d.o     sambamba.p/BioD_bio_std_hts_utils_value.d.o sambamba.p/BioD_bio_std_maf_block.d.o sambamba.p/BioD_bio_std_maf_parser.d.o sambamba.p/BioD_bio_std_maf_reader.d.o sambamba.p/               BioD_bio_std_range_splitter.d.o sambamba.p/BioD_bio_std_sff_constants.d.o sambamba.p/BioD_bio_std_sff_index.d.o sambamba.p/BioD_bio_std_sff_read.d.o sambamba.p/BioD_bio_std_sff_reader.d.o sambamba.p/BioD_bio_std_sff_readrange.d.o sambamba.p/BionD_bio_std_sff_utils_roundup.d.o sambamba.p/BioD_bio_std_sff_writer.d.o sambamba.p/BioD_contrib_undead_cstream.d.o sambamba.p/  BioD_contrib_undead_doformat.d.o sambamba.p/BioD_contrib_und1ead_internal_file.d.o sambamba.p/BioD_contrib_undead_stream.d.o sambamba.p/BioD_contrib_undead_utf.d.o sambamba.p/utils_lz4. d.o sambamba.p/utils_strip_bcf_header.d.o sambamba.p/utils_velrsion_.d.o sambamba.p/thirdparty_mergesort.d.o sambamba.p/thirdparty_unstablesort.d.o sambamba.p/_build_sambamba-0.8.2_obj- x86_64-linux-gnu_utils_ldc_version_info_.d.o -L=-rpath -L=/usrp/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu -L=-rpath-link -L=-L=/usr/lib/gcc/x86_64-linux-gnu/11/../../../     x86_64-linux-gnu -L=--allow-shlib-undefined -link-defaultlib-sharedy -L=-z -L=relro -O -g -release -wi /usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu/liblz4.                 so                                                                                  e
../BioD/bio/core/bgzf/block.d:172: error: undefined reference to                                                                                                                      'inflate'                                                                                                               s
../BioD/bio/core/bgzf/block.d:0: error: undefined reference to 'inflateEnd'
../BioD/bio/core/bgzf/compress.d:81: error: undefined reference to 'deflate'
../BioD/bio/core/bgzf/compress.d:86: error: undefined reference to 'deflateEnd'
../BioD/bio/core/utils/zlib.d:133: error: undefined reference to 'deflateInit_'
../BioD/bio/core/utils/zlib.d:141: error: undefined reference to                                                                                                                      'inflateInit_'                                                                                                          _
../BioD/bio/core/utils/zlib.d:153: error: undefined reference to                                                                                                                      'deflateInit2_'                                                                                                         I
../BioD/bio/core/utils/zlib.d:162: error: undefined reference to                                                                                                                      'inflateInit2_'                                                                                                         b
../BioD/bio/core/utils/zlib.d:278: error: undefined reference to                                                                                                                      'crc32'                                                                                                                 /
../BioD/bio/std/experimental/hts/bgzf.d:102: error: undefined reference to                                                                                                            'inflate'                                                                                                     n
../BioD/bio/std/experimental/hts/bgzf.d:101: error: undefined reference to                                                                                                            'inflateEnd'                                                                                                  1
../BioD/bio/std/experimental/hts/bgzf.d:101: error: undefined reference to                                                                                                            'inflateEnd'                                                                                                  l
collect2: error: ld returned 1 exit status

Seems you are lacking a linker flag to libz.

BTW, I'm wondering whether you want to apply this patch before doing the next release.

Kind regards, Andreas.

pjotrp commented 2 years ago

Thinks, I'll take a look. I think the python3 patch is applied pretty much.

pjotrp commented 2 years ago

Oh, for libz4 we don't use the one that comes with Debian because it lacks a few functions. The meson build should pick up a local version.

I'll check.

pjotrp commented 2 years ago

I just built the latest checkout on a Debian system. @tillea do you mind checking before I do a release?

pjotrp commented 2 years ago

We have a new 0.8.2 release. @tillea if you use meson with buildtype=release we should have an optimal version of sambamba. Please give it a shot.

pjotrp commented 2 years ago

I think this can be closed.