Bug#961011: g++-9: internal compiler error: in asan_expand_mark_ifn, at asan.c:3194

On Tue, 19 May 2020 12:38:57 +0200 "Michael R. Crusoe" wrote: > Attached is the reduced example. Pardon me, that first attachment only fails on gcc-snapshot's g++ Attached is an example that does fail on g++-9, g++-10, and gcc-snapshot's g++ class a { public: long b(); }; cla

Bug#961011: g++-9: internal compiler error: in asan_expand_mark_ifn, at asan.c:3194

Package: g++-9 Version: 9.3.0-12 Severity: normal Tested with g++10 and g++ from gcc-snapshot 1:20200507-3 $ g++ -Og -g -fsanitize=address -fno-omit-frame-pointer -fno-optimize-sibling-calls -fopenmp -o clusthash.cpp.o -c clusthash_prep.cpp during GIMPLE pass: sanopt clusthash_prep.cpp: In

Bug#961004: creduce: Man page references nonexistant Texinfo manual

5-19 09:49:31.0 +0200 @@ -1,3 +1,10 @@ +creduce (2.10.0+20200116-1.1) UNRELEASED; urgency=medium + + * Non-maintainer upload. + * debian/rules: Remove reference to non-existant Texinfo manual + + -- Michael R. Crusoe Tue, 19 May 2020 09:49:31 +0200 + creduce (2.10.0+20200116-1) unstable; urge

Bug#960112: ITP: rust-elfx86exts -- Print instruction sets used by x86 binaries (ELF or MachO)

Package: wnpp Severity: wishlist Subject: ITP: rust-elfx86exts -- Print instruction sets used by x86 binaries (ELF or MachO) Package: wnpp Owner: Michael R. Crusoe Severity: wishlist * Package name: rust-elfx86exts Version : 0.3.0 Upstream Author : Peter Williams * URL

Bug#959722: isa-support: Please build "sse4.1-support"

Package: isa-support Version: 5 Severity: normal Please build a "sse4.1-support" binary package. A merge request to accomplish this is at https://salsa.debian.org/debian/isa-support/-/merge_requests/1 Thanks! -- System Information: Debian Release: bullseye/sid APT prefers testing APT

Bug#959721: datatables.js: Mark libjs-jquery-datatables as Multi-Arch: foreign

Package: datatables.js Version: 1.10.20+dfsg-1 Severity: normal Please mark the libjs-jquery-datatables binary package as "Multi-Arch: foreign" which allows for cross-building packages that depend on this package A merge request that accomplishes this is at

Bug#959719: obs-studio: use the libsimde-dev package

Package: obs-studio Version: 25.0.3+dfsg1-2 Severity: normal I've made a merge request at https://salsa.debian.org/multimedia-team/obs-studio/-/merge_requests/2 to use the packaged "simde" library instead of the code copy in upstream's source. >From the changelog * debian/patches: - Use the

Bug#959720: datatables-extensions: mark package as Multi-Arch: foreign

Package: datatables-extensions Version: 0.0+git20150910.28fd64e+dfsg-3 Severity: normal Please mark the binary package as "Multi-Arch: foreign" which allows cross-building packages that build-depend on libjs-jquery-datatables-extensions A merge request to accomplish this is at

Bug#959718: tklib: mark the tklib binary package as Multi-Arch: foreign

Package: tklib Version: 0.7-1 Severity: normal This allow packages that build-dep on tklib to be cross-compiled See also https://salsa.debian.org/tcltk-team/tklib/-/merge_requests/1 Thanks! -- System Information: Debian Release: bullseye/sid APT prefers testing APT policy: (500, 'testing')

Bug#959237: ITP: odgi -- optimized dynamic genome/graph implementation

Package: wnpp Severity: wishlist Subject: ITP: odgi -- optimized dynamic genome/graph implementation Package: wnpp Owner: Michael R. Crusoe Severity: wishlist * Package name: odgi Version : 0.4.1 Upstream Author : , Erik Garrison * URL : https://github.com/vgteam

Bug#958967: ITP: r-bioc-dexseq -- Inference of differential exon usage in RNA-Seq

Package: wnpp Severity: wishlist Subject: ITP: r-bioc-dexseq -- Inference of differential exon usage in RNA-Seq Package: wnpp Owner: Michael R. Crusoe Severity: wishlist * Package name: r-bioc-dexseq Version : 1.32.0 Upstream Author : Simon Anders and Alejandro Reyes * URL

Bug#958962: ITP: r-cran-goplot -- Visualization of Functional Analysis Data

Package: wnpp Severity: wishlist Subject: ITP: r-cran-goplot -- Visualization of Functional Analysis Data Package: wnpp Owner: Michael R. Crusoe Severity: wishlist * Package name: r-cran-goplot Version : 1.0.2 Upstream Author : Wencke Walter, * URL : https://cran.r

Bug#958952: ITP: r-cran-findpython -- Functions to Find an Acceptable Python Binary

Package: wnpp Severity: wishlist Subject: ITP: r-cran-findpython -- Functions to Find an Acceptable Python Binary Package: wnpp Owner: Michael R. Crusoe Severity: wishlist * Package name: r-cran-findpython Version : 1.0.5 Upstream Author : Trevor L Davis, * URL

Bug#958936: ITP: r-cran-argparse -- Command Line Optional and Positional Argument Parser

Package: wnpp Severity: wishlist Subject: ITP: r-cran-argparse -- Command Line Optional and Positional Argument Parser Package: wnpp Owner: Michael R. Crusoe Severity: wishlist * Package name: r-cran-argparse Version : 2.0.1 Upstream Author : Trevor L Davis * URL

Bug#956961: RM: macs [mipsel mips64el] -- ROM; Nonviable for biomedical research

Package: ftp.debian.org Severity: normal MIPS hardware is not viable for doing biomedical research, so remove these archs for the macs package so it can migrate to testing Thanks!

Bug#956228: ITP: libbio-tradis-perl -- set of tools to analyse the output from TraDIS analyses.

Package: wnpp Severity: wishlist Subject: ITP: libbio-tradis-perl -- set of tools to analyse the output from TraDIS analyses. Package: wnpp Owner: Michael R. Crusoe Severity: wishlist * Package name: libbio-tradis-perl Version : 1.4.5 Upstream Author : , Carla Cummins * URL

Bug#955717: RM: lambda-align2/stable [arm64 armel armhf i386 mips64el ppc64el s390x] -- ROM; Does not yet build correctly on non-amd64

Package: ftp.debian.org Severity: normal See also: https://bugs.debian.org/953081 and https://bugs.debian.org/955363 Thanks,

Bug#955363: RM: lambda-align2 [arm64 armel armhf i386 mips64el ppc64el s390x alpha hppa m68k powerpcspe ppc64 riscv64 sparc64] -- ROM; Does not yet build on non-amd64

Package: ftp.debian.org Severity: normal See also: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=953081 Thanks!

Bug#955282: ITP: ruamel.yaml.clib -- C version of reader, parser and emitter for ruamel.yaml

Package: wnpp Severity: wishlist Subject: ITP: ruamel.yaml.clib -- C version of reader, parser and emitter for ruamel.yaml Package: wnpp Owner: Michael R. Crusoe Severity: wishlist * Package name: ruamel.yaml.clib Version : 0.2.0 Upstream Author : , Anthon van der Neut, Ruamel

Bug#952695: Request for sponsorship or upload rights Re: r-cran-xml2: autopkgtest failure against libxml2 2.9.10

On Thu, 27 Feb 2020 19:20:06 +0100 Mattia Rizzolo wrote: > Source: r-cran-xml2 > Version: 1.2.2-2 > Severity: serious > User: debian...@lists.debian.org > Usertags: breaks needs-update > > Dear maintainer, > > With a recent upload of libxml2 the autopkgtest of r-cran-xml2 fails > in testing when

Bug#920282: Your mail

ers, [0] https://salsa.debian.org/med-team/abyss -- Michael R. Crusoe

Bug#950856: fmtlib: Please upload source package to salsa.debian.org and set Vcs-*

On Tue, 18 Feb 2020 14:25:33 +0100 "Eugene V. Lyubimkin" wrote: > Hello, > > Michael R. Crusoe kirjoitti 7.2.2020 klo 14.33: > > Hello, please upload source package to salsa.debian.org and set Vcs-*; thanks > > I currently don't have plans to upload packagi

Bug#953023: fmtlib: Please add Multi-Arch hints

+0100 @@ -1,3 +1,11 @@ +fmtlib (6.1.2+ds-2.1) UNRELEASED; urgency=medium + + * Non-maintainer upload. + * Enable cross-building using fmtlib: mark libfmt-dev as Multi-Arch: same +and libfmt-doc as Multi-Arch: foreign + + -- Michael R. Crusoe Tue, 03 Mar 2020 12:31:08 +0100 + fmtlib (6.1.2+ds

Bug#952681: rocksdb: Please build rocksdb for riscv64

2020-02-18 19:34:59.0 +0100 +++ rocksdb-6.6.4/debian/changelog 2020-02-26 14:59:30.0 +0100 @@ -1,3 +1,11 @@ +rocksdb (6.6.4-1.1) UNRELEASED; urgency=medium + + * Non-maintainer upload. + * Build on riscv64 + * Build in parallel + + -- Michael R. Crusoe Wed, 26 Feb 202

Bug#949493: RFS Re: ruby-libxml: FTBFS with libxml2 2.9.10

On Tue, 21 Jan 2020 15:48:48 +0100 Mattia Rizzolo wrote: > Source: ruby-libxml > Version: 3.1.0-1 > Severity: important > Tags: ftbfs > User: libx...@packages.debian.org > Usertags: ftbfs-2.9.10 > > > Dear maintainer, > > your package fails tests when build against libxml2 2.9.10 as > available

Bug#952543: Using old libfmt breaks sopt and purify

On Tue, 25 Feb 2020 19:01:02 +0100 "Michael R. Crusoe" wrote: > On Tue, 25 Feb 2020 15:22:10 +0100 Ole Streicher wrote: > > > Since spdlog uses the old (included) libfmt, the builds of purify and > > sopt fail with linker errors like: > > > > u

Bug#952543: Using old libfmt breaks sopt and purify

On Tue, 25 Feb 2020 15:22:10 +0100 Ole Streicher wrote: > Since spdlog uses the old (included) libfmt, the builds of purify and > sopt fail with linker errors like: > > undefined reference to `fmt::v6::internal::assert_fail(char const*, int, > char const*) > > See the merged bugs for the

Bug#951763: openjdk-14-jre-headless:s390x: crashes during configuration of ca-certificates-java under qemu-s390x-static

Package: openjdk-14-jre-headless Version: 14~36-1 Severity: normal Dear Maintainer, Like with openjdk-11-jre-headless:290x, openjdk-14-jre-headless also crashes during the configuration stage of ca-certificates-java under qemu-s390x-static. Though it is able add the first 5 certificates, the 6

Bug#951512: ITP: r-cran-sna -- Tools for Social Network Analysis

Package: wnpp Severity: wishlist Subject: ITP: r-cran-sna -- Tools for Social Network Analysis Package: wnpp Owner: Michael R. Crusoe Severity: wishlist * Package name: r-cran-sna Version : 2.5 Upstream Author : Carter T. Butts * URL : https://cran.r-project.org

Bug#951511: ITP: r-cran-statnet.common -- Common R Scripts and Utilities Used by the Statnet Project

Package: wnpp Severity: wishlist Subject: ITP: r-cran-statnet.common -- Common R Scripts and Utilities Used by the Statnet Project Package: wnpp Owner: Michael R. Crusoe Severity: wishlist * Package name: r-cran-statnet.common Version : 4.3.0 Upstream Author : Pavel N

Bug#951510: ITP: r-cran-network -- Classes for Relational Data

Package: wnpp Severity: wishlist Subject: ITP: r-cran-network -- Classes for Relational Data Package: wnpp Owner: Michael R. Crusoe Severity: wishlist * Package name: r-cran-network Version : 1.16.0 Upstream Author : Carter T. Butts, * URL : https://cran.r

Bug#951483: ITP: ataqv -- ATAC-seq QC and visualization

Package: wnpp Severity: wishlist Subject: ITP: ataqv -- ATAC-seq QC and visualization Package: wnpp Owner: Michael R. Crusoe Severity: wishlist * Package name: ataqv Version : 1.1.1+ds Upstream Author : Stephen Parker * URL : https://github.com/ParkerLab/ataqv

Bug#951425: ITP: gerp++ -- identifies constrained elements in multiple alignments

Package: wnpp Severity: wishlist Subject: ITP: gerp++ -- identifies constrained elements in multiple alignments Package: wnpp Owner: Michael R. Crusoe Severity: wishlist * Package name: gerp++ Version : 2.1 Upstream Author : , George Asimenos * URL : http

Bug#951361: ITP: libfile-sort-perl -- module to sort a file or merge sort multiple files

Package: wnpp Severity: wishlist Subject: ITP: libfile-sort-perl -- module to sort a file or merge sort multiple files Package: wnpp Owner: Michael R. Crusoe Severity: wishlist * Package name: libfile-sort-perl Version : 1.01 Upstream Author : , Chris Nandor , http://pudge.net

Bug#951072: ITP: htscodecs -- Custom compression for CRAM and others

Package: wnpp Severity: wishlist Subject: ITP: htscodecs -- Custom compression for CRAM and others Package: wnpp Owner: Michael R. Crusoe Severity: wishlist * Package name: htscodecs Version : 0.5 Upstream Author : , Genome Research Ltd. * URL : https://github.com

Bug#950992: ITP: routine-update -- routine updater for a Debian source package

Package: wnpp Severity: wishlist Subject: ITP: routine-update -- routine updater for a Debian source package Package: wnpp Owner: Michael R. Crusoe Severity: wishlist * Package name: routine-update Version : 0.0.1 Upstream Author : Andreas Tille * URL : https

Bug#950857: fmtlib: Please upload a package for version 6.1.2

Source: fmtlib Severity: normal spdlog is currently using an embedded copy of version 6+, so if fmtlib is updated we can use the packaged version instead Thanks!

Bug#950856: fmtlib: Please upload source package to salsa.debian.org and set Vcs-*

Source: fmtlib Severity: normal Hello, please upload source package to salsa.debian.org and set Vcs-*; thanks -- System Information: Debian Release: buster/sid APT prefers eoan-updates APT policy: (500, 'eoan-updates'), (500, 'eoan-security'), (500, 'eoan') Architecture: amd64 (x86_64)

Bug#950607: ITP: bwa-mem2 -- the next version of the bwa-mem algorithm in bwa

Package: wnpp Severity: wishlist Subject: ITP: bwa-mem2 -- the next version of the bwa-mem algorithm in bwa Package: wnpp Owner: Michael R. Crusoe Severity: wishlist * Package name: bwa-mem2 Version : 2.0~pre2 Upstream Author : , Vasimuddin Md, Sanchit Misra, Intel Corporation

Bug#949378: RM: tophat [s390x] -- ROM; Blocking migration of samtools to testing

Package: ftp.debian.org Severity: normal Hello, The tophat binary package depends on samtools, but samtools is no longer built for s390x due to "htslib FTBFS on big-endian systems" https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=947462 Please remove the s390x binary package for tophat so

Bug#948518: RM: grabix [s390x] -- ROM; upstream htslib broke s390x and is holding up several transitions

Package: ftp.debian.org Severity: important A follow on to https://bugs.debian.org/948092 as I forgot to include grabix in the list; this appears to be holding up the transition to testing if I'm reading https://release.debian.org/britney/update_output.txt correctly. Thanks!

Bug#948330: ITP: libsys-info-perl -- Fetch information from the host system

Package: wnpp Severity: wishlist Subject: ITP: libsys-info-perl -- Fetch information from the host system Package: wnpp Owner: Michael R. Crusoe Severity: wishlist * Package name: libsys-info-perl Version : 0.7811 Upstream Author : , Burak Gursoy * URL : https

Bug#948329: ITP: libsys-info-driver-linux-perl -- Linux driver for Sys::Info

Package: wnpp Severity: wishlist Subject: ITP: libsys-info-driver-linux-perl -- Linux driver for Sys::Info Package: wnpp Owner: Michael R. Crusoe Severity: wishlist * Package name: libsys-info-driver-linux-perl Version : 0.7905 Upstream Author : , Burak Gursoy * URL

Bug#948325: ITP: libbio-featureio-perl -- Modules for reading, writing, and manipulating sequence features

Package: wnpp Severity: wishlist Subject: ITP: libbio-featureio-perl -- Modules for reading, writing, and manipulating sequence features Package: wnpp Owner: Michael R. Crusoe Severity: wishlist * Package name: libbio-featureio-perl Version : 1.6.905 Upstream Author : BioPerl

Bug#948092: RM: htslib, delly, fastqtl, kallisto, libtabixpp, qtltools, rsem, samtools, segemehl, shapeit4, stringtie, stacks [s390x] -- ROM; upstream htslib broke s390x and is holding up several tran

Package: ftp.debian.org Severity: normal Dear ftp.debian.org people, htslib FTBFS on big-endian systems https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=947462 and this is blocking the following transitions: auto-htslib, python2-rm, python3.8, and auto-pbbam I propose we delete the affected

Bug#946638: ITP: hopscotch-map -- C++ fast hash map and hash set using hopscotch hashing

Package: wnpp Severity: wishlist Subject: ITP: hopscotch-map -- C++ fast hash map and hash set using hopscotch hashing Package: wnpp Owner: Michael R. Crusoe Severity: wishlist * Package name: hopscotch-map Version : 2.2.1 Upstream Author : Tessil * URL : https

Bug#946611: ITP: golang-github-abeconnelly-autoio -- Golang io functions that provide standard scanner interfaces for compressed files.

Package: wnpp Severity: wishlist Package: wnpp Severity: wishlist Owner: Michael R. Crusoe * Package name: golang-github-abeconnelly-autoio Version : 0.0~git20150803.989b7b0-1 Upstream Author : Abram Connelly * URL : https://github.com/abeconnelly/autoio * License

Bug#946468: ITP: libbio-variation-perl -- BioPerl variation-related functionality

Package: wnpp Severity: wishlist Subject: ITP: libbio-variation-perl -- BioPerl variation-related functionality Package: wnpp Owner: Michael R. Crusoe Severity: wishlist * Package name: libbio-variation-perl Version : 1.7.4 Upstream Author : Copyright: Allen Day , Heikki

Bug#946299: ITP: simde -- Implementations of SIMD instructions for all systems

Package: wnpp Severity: wishlist Subject: ITP: simde -- Implementations of SIMD instructions for all systems Package: wnpp Owner: Michael R. Crusoe Severity: wishlist * Package name: simde Version : 0.0.0.git.20191205.c2e740c Upstream Author : , Evan Nemerson * URL

Bug#946272: ITP: libbio-procedural-perl -- Simple low-dependency procedural interfaces to BioPerl

Package: wnpp Severity: wishlist Subject: ITP: libbio-procedural-perl -- Simple low-dependency procedural interfaces to BioPerl Package: wnpp Owner: Michael R. Crusoe Severity: wishlist * Package name: libbio-procedural-perl Version : 1.7.4 Upstream Author : Copyright: Ewan

Bug#946269: ITP: libbio-db-refseq-perl -- Database object interface for RefSeq retrieval

Package: wnpp Severity: wishlist Subject: ITP: libbio-db-refseq-perl -- Database object interface for RefSeq retrieval Package: wnpp Owner: Michael R. Crusoe Severity: wishlist * Package name: libbio-db-refseq-perl Version : 1.7.3 Upstream Author : Copyright: Heikki Lehvaslaiho

Bug#946266: ITP: libbio-db-swissprot-perl -- Database object interface to SwissProt retrieval

Package: wnpp Severity: wishlist Subject: ITP: libbio-db-swissprot-perl -- Database object interface to SwissProt retrieval Package: wnpp Owner: Michael R. Crusoe Severity: wishlist * Package name: libbio-db-swissprot-perl Version : 1.7.3 Upstream Author : Copyright: Jason

Bug#944905: RM: jellyfish [arm64 mips64el ppc64el riscv64] -- ANAIS; Non-AMD64 not supported by upstream

Package: ftp.debian.org Severity: normal Thanks!

Bug#944785: ITP: pufferfish -- An efficient index for the colored, compacted, de Bruijn graph

Package: wnpp Severity: wishlist Subject: ITP: pufferfish -- An efficient index for the colored, compacted, de Bruijn graph Package: wnpp Owner: Michael R. Crusoe Severity: wishlist * Package name: pufferfish Version : 1.0.0 Upstream Author : , 2016 Rob Patro, Avi Srivastava

Bug#944735: RM: rapmap [arm64 mips64el ppc64el] -- ANAIS; non-amd64 not supported by upstream

Package: ftp.debian.org Severity: normal Thanks!

Bug#940258: ITP: libbio-db-ncbihelper-perl -- collection of routines useful for queries to NCBI databases.

Package: wnpp Severity: wishlist Subject: ITP: libbio-db-ncbihelper-perl -- collection of routines useful for queries to NCBI databases. Package: wnpp Owner: Michael R. Crusoe Severity: wishlist * Package name: libbio-db-ncbihelper-perl Version : 1.7.4 Upstream Author

Bug#940257: ITP: libbio-tools-run-remoteblast-perl -- Object for remote execution of the NCBI Blast via HTTP

Package: wnpp Severity: wishlist Subject: ITP: libbio-tools-run-remoteblast-perl -- Object for remote execution of the NCBI Blast via HTTP Package: wnpp Owner: Michael R. Crusoe Severity: wishlist * Package name: libbio-tools-run-remoteblast-perl Version : 1.7.3 Upstream Author

Bug#940256: ITP: libbio-cluster-perl -- BioPerl cluster modules

Package: wnpp Severity: wishlist Subject: ITP: libbio-cluster-perl -- BioPerl cluster modules Package: wnpp Owner: Michael R. Crusoe Severity: wishlist * Package name: libbio-cluster-perl Version : 1.7.3 Upstream Author : Copyright: Allen Day , Andrew Macgregor , David Green

Bug#940255: ITP: libbio-db-seqfeature-perl -- Normalized feature for use with Bio::DB::SeqFeature::Store

Package: wnpp Severity: wishlist Subject: ITP: libbio-db-seqfeature-perl -- Normalized feature for use with Bio::DB::SeqFeature::Store Package: wnpp Owner: Michael R. Crusoe Severity: wishlist * Package name: libbio-db-seqfeature-perl Version : 1.7.3 Upstream Author : Copyright

Bug#940254: ITP: libbio-db-embl-perl -- Database object interface for EMBL entry retrieval

Package: wnpp Severity: wishlist Subject: ITP: libbio-db-embl-perl -- Database object interface for EMBL entry retrieval Package: wnpp Owner: Michael R. Crusoe Severity: wishlist * Package name: libbio-db-embl-perl Version : 1.7.4 Upstream Author : Copyright: Heikki Lehvaslaiho

Bug#940253: ITP: libbio-db-ace-perl -- Database object interface to ACeDB servers

Package: wnpp Severity: wishlist Subject: ITP: libbio-db-ace-perl -- Database object interface to ACeDB servers Package: wnpp Owner: Michael R. Crusoe Severity: wishlist * Package name: libbio-db-ace-perl Version : 1.7.3 Upstream Author : Copyright: Ewan Birney , Lincoln Stein

Bug#940252: ITP: libbio-db-gff-perl -- Storage and retrieval of sequence annotation data

Package: wnpp Severity: wishlist Subject: ITP: libbio-db-gff-perl -- Storage and retrieval of sequence annotation data Package: wnpp Owner: Michael R. Crusoe Severity: wishlist * Package name: libbio-db-gff-perl Version : 1.7.3 Upstream Author : Copyright: (c) 2001-2003, 2005

Bug#940248: ITP: libbio-db-biofetch-perl -- Database object interface to BioFetch retrieval

Package: wnpp Severity: wishlist Subject: ITP: libbio-db-biofetch-perl -- Database object interface to BioFetch retrieval Package: wnpp Owner: Michael R. Crusoe Severity: wishlist * Package name: libbio-db-biofetch-perl Version : 1.7.3 Upstream Author : Copyright: Lincoln Stein

Bug#940244: ITP: libbio-alignio-stockholm-perl -- stockholm sequence input/output stream

Package: wnpp Severity: wishlist Subject: ITP: libbio-alignio-stockholm-perl -- stockholm sequence input/output stream Package: wnpp Owner: Michael R. Crusoe Severity: wishlist * Package name: libbio-alignio-stockholm-perl Version : 1.7.3 Upstream Author : Copyright: Peter

Bug#940180: ITP: libbio-searchio-hmmer-perl -- perl parser for HMMER2 and HMMER3 output (hmmscan, hmmsearch, hmmpfam)

Package: wnpp Severity: wishlist Subject: ITP: libbio-searchio-hmmer-perl -- perl parser for HMMER2 and HMMER3 output (hmmscan, hmmsearch, hmmpfam) Package: wnpp Owner: Michael R. Crusoe Severity: wishlist * Package name: libbio-searchio-hmmer-perl Version : 1.7.3 Upstream

Bug#939933: ITP: megadock -- ultra-high-performance protein-protein docking for heterogeneous supercomputers

Package: wnpp Severity: wishlist Subject: ITP: megadock -- ultra-high-performance protein-protein docking for heterogeneous supercomputers Package: wnpp Owner: Michael R. Crusoe Severity: wishlist * Package name: megadock Version : 4.1.1 Upstream Author : Copyright: © 2014-2018

Bug#939537: ITP: vg -- tools for working with genome variation graphs

Package: wnpp Severity: wishlist Subject: ITP: vg -- tools for working with genome variation graphs Package: wnpp Owner: Michael R. Crusoe Severity: wishlist * Package name: vg Version : 1.18.0+ds Upstream Author : Copyright: © 2014 Erik Garrison * URL : https

Bug#934629: ITP: seqan3 -- C++ library for the analysis of biological sequences (development)

Package: wnpp Severity: wishlist Subject: ITP: seqan3 -- C++ library for the analysis of biological sequences (development) Package: wnpp Owner: Michael R. Crusoe Severity: wishlist * Package name: seqan3 Version : 3.0.0+ds Upstream Author : , Knut Reinert, FU Berlin * URL

Bug#932003: ITP: mypyc -- Mypy to Python C Extension Compile

Package: wnpp Severity: wishlist Subject: ITP: mypyc -- Mypy to Python C Extension Compile Package: wnpp Owner: Michael R. Crusoe Severity: wishlist * Package name: mypyc Version : 0.0.git.20190713T1002.833151a+ds1 Upstream Author : Copyright: © 2017-2018 Jukka Lehtosalo

Bug#924246: 12

Package: wnpp Severity: normal test

Bug#923386: RM: python-schema-salad & python-typing-extensions -- ROM; binary packages for Python 2 no longer needed

Package: ftp.debian.org Severity: normal Hello, Please remove the binary package python-schema-salad version 2.6.20171201034858-3 and the binary package python-typing-extensions version 3.7.2-1 from the archive. We now only need and build for Python 3 and these packages are holding up the

Bug#922285: libpython3.7-stdlib: Please add ann_module, ann_module2, ann_module3

Package: libpython3.7-stdlib Version: 3.7.2-2 Severity: normal Dear Maintainer, As per the description of libpython3.7-testsuite I'm requesting that the ann_module{,2,3} be added to libpython3.x-stdlib so that the testsuite of python-typing-extensions can run. -- System Information: Debian

Bug#919681: ITP: sourmash -- tools for comparing DNA sequences with MinHash sketches

Package: wnpp Severity: wishlist Owner: Debian Med team * Package name: sourmash Version : 2.0.0~a11 Upstream Author : C. Titus Brown , Luiz C. Irber, Jr * URL : http://sourmash.readthedocs.io/en/latest/ * License : BSD-3-Clause Programming Lang: Python,

Bug#919570: ITP: python-mypy-extensions -- Experimental type system extensions for mypy typechecker (Python 3)

Package: wnpp Severity: wishlist Owner: Debian Med team * Package name: python-mypy-extensions Version : 0.4.1 Upstream Author : Jukka Lehtosalo and contributors * URL : https://github.com/python/mypy_extensions/ * License : Expat Programming Lang: Python

Bug#918871: RM: python-bd2k -- ROM; No longer needed by Debian, abandoned upstream

Package: ftp.debian.org Severity: normal Control: block -1 by 918869 To be removed after python-cgloud, #918869 [1] for the same reasons: python-bd2k was originally packaged as a dependency of Toil[2], but by the time Toil arrived in the NEW queue it had dropped its dependency on python-bd2k.

Bug#918869: RM: python-cgcloud -- ROM; No longer need by Debian, abandoned upstream

Package: ftp.debian.org Severity: normal This was originally packaged as a dependency of Toil[1], but by the time that made it to the NEW queue Toil had dropped its dependency on cgcloud. [1] https://ftp-master.debian.org/new/toil_3.18.0-1.html

Bug#918343: RM: tnseq-transit [arm64 armel armhf i386 mips mips64el mipsel ppc64el s390x] -- ANAIS; has missing (build-)dependency on amd64 only package

Package: ftp.debian.org Severity: normal Hello, This package was missing a source and binary dependency on BWA which is only built for amd64. Please remove the non-amd64 binary packages of tnseq-transit so that the new Debian package can migrate from sid to testing. Thanks!

Bug#918251: d-shlibs: devlibs error: There is no package matching [libsvm3-dev] and noone provides it

Package: d-shlibs Version: 0.83 Severity: normal Dear Maintainer, While fixing the missing linkage to libsvm in libpsortb I received the following message: devlibs error: There is no package matching [libsvm3-dev] and noone provides it, please report bug to d-shlibs maintainer So here I am :-)

Bug#918117: RM: python-htseq-doc/0.6.1p1-4

Package: release.debian.org Severity: normal User: release.debian@packages.debian.org Usertags: rm Hello, Please remove python-htseq-doc from the testing distribution. It is no longer build by the source package and its presence is blocking a migration from unstable. Thanks! -- System

Bug#917936: sparsehash: Please package 2.0.3

Source: sparsehash Severity: normal Dear Maintainer, Please package version 2.0.3 found at https://github.com/sparsehash/sparsehash/releases/tag/sparsehash-2.0.3 This fixes https://bugs.debian.org/914337 and will be a good opportunity to apply the patch already provided for

Bug#917935: uvcdynctrl: 0.2.5 available, please package

Package: uvcdynctrl Version: 0.2.4-1.1+b2 Severity: normal Dear Maintainer, Please package 0.2.5, available at https://sourceforge.net/p/libwebcam/code/ci/v0.2.5/tree/ It contains fixes for https://bugs.debian.org/733094 and others. If you want, I can prepare a non-maintainers upload --

Bug#915852: ITP: bagit -- Create and validate BagIt packages

Package: wnpp Severity: wishlist Owner: Debian Med team * Package name: bagit Version : 1.7.0 Upstream Author : Ed Summers * URL : https://libraryofcongress.github.io/bagit-python/ * License : CC0 Programming Lang: Python Description : Create and

Bug#915829: ITP: arcp -- (Archive and Package) URI parser and generator

Package: wnpp Severity: wishlist Subject: ITP: arcp -- (Archive and Package) URI parser and generator Package: wnpp Owner: Debian Med team Severity: wishlist * Package name: arcp Version : 0.2.0 Upstream Author : Stian Soiland-Reyes * URL :

Bug#914991: RM: testing/htslib [i386 hurd-i386 kfreebsd-i386] -- ANAIS; ROM *i386 no longer supported upstream

Package: ftp.debian.org Severity: normal Owner: Debian Med team Upstream report: https://github.com/samtools/htslib/issues/565 The provided workaround does not fix the issue and it has now been a year with no progress Thanks!

Bug#914928: ITP: python-typing-extensions -- Backported and Experimental Type Hints for Python

Package: wnpp Severity: wishlist Owner: Debian Med team * Package name: python-typing-extensions Version : 3.6.6 Upstream Author : Guido van Rossum, Jukka Lehtosalo, Lukasz Langa, Michael Lee * URL :

Bug#911076: ITP: libdeflate -- fast, whole-buffer DEFLATE-based compression and decompression

Package: wnpp Severity: wishlist Owner: Debian Med team * Package name: libdeflate Version : 1.0 Upstream Author : Eric Biggers * URL : https://github.com/ebiggers/libdeflate * License : MIT Programming Lang: C Description : fast, whole-buffer

Bug#904097: bzr: ERROR: Not a branch: 'http://bazaar.launchpad.net/~doko/python/pkg3.7-debian/

://bazaar.launchpad.net/~doko/python/pkg3.7-debian Path: debian/changelog Browser: https://code.launchpad.net/~doko/python/pkg3.7-debian Last scan: 2018-07-19 06:33:02+00 Error: bzr: ERROR: Not a branch: "http://bazaar.launchpad.net/~doko/python/pkg3.7-debian/;. Thanks, -- Michael R. Crusoe

Bug#894299: RM: python-pybedtools -- ROM; No longer needed, only reverse build-dep has also been ROM'd

Package: ftp.debian.org Severity: normal Thanks!

Bug#894298: RM: python-gffutils -- ROM; No longer needed, no reverse-dependencies

Package: ftp.debian.org Severity: normal Thanks!

Bug#892896: RM: khmer [mips64el ppc64el] -- ROM; ANAIS

Package: ftp.debian.org Severity: normal These archs are supported by upstream

Bug#890755: ITP: ctdconverter -- Convert CTD files into Galaxy tool and CWL CommandLineTool files

Package: wnpp Severity: wishlist Owner: Debian Med team * Package name: ctdconverter Version : 2.0 Upstream Author : WorkflowConversion * URL : https://github.com/WorkflowConversion/CTDConverter/ * License : GPL-3 / Apache-2.0

Bug#890752: ITP: ctdopts -- Gives your Python tools a CTD-compatible interface

Package: wnpp Severity: wishlist Owner: Debian Med team * Package name: ctdopts Version : 1.2 Upstream Author : Andras Szolek et al. * URL : https://github.com/WorkflowConversion/CTDopts * License : GPL-3+ Programming Lang:

Bug#890667: lintian: Missing link between cwl-runner interpreter and package cwltool or virtual package cwl-runner

Package: lintian Version: 2.5.75 Severity: normal Dear Maintainer, Please update Lintian so that it knows about "cwl-runner" interpreters: they provide the "cwl-runner" virtual package. An example is the "cwltool" package and the upcoming "toil" package. Cheers, -- System Information: Debian

Bug#890061: ITP: galaxy-lib -- Subset of Galaxy core code base designed to be used

Package: wnpp Severity: wishlist Owner: Debian Med team * Package name: galaxy-lib Version : 17.9.10 Upstream Author : Galaxy Project and Community * URL : https://github.com/galaxyproject/galaxy-lib * License

Bug#860746: ITP: easel -- a library of C functions for biological sequence analysis

Package: wnpp Severity: wishlist Owner: Debian Med team * Package name: easel Version : 0.43 Upstream Author : Sean R. Eddy * URL : https://github.com/EddyRivasLab/easel * License : BSD-3-clause Programming

Bug#851488: ITP: python-gffutils -- Work with GFF and GTF files in a flexible database framework

Package: wnpp Severity: wishlist Owner: Debian Med team * Package name: python-gffutils Version : 0.8.7.1 Upstream Author : Ryan Dale * URL : http://daler.github.io/gffutils/ * License : MIT Programming

Bug#851358: ITP: python-pybedtools -- Python wrapper around BEDTools for bioinformatics work

Package: wnpp Severity: wishlist Owner: Debian Med team * Package name: python-pybedtools Version : 0.7.8 Upstream Author : Ryan Dale * URL : https://github.com/daler/pybedtools * License : GPL 2+

Bug#841047: ITP: r-hms-dbmi-spp -- GNU R package for processing ChIP-seq & other functional sequencing data

Package: wnpp Severity: wishlist Owner: Debian Med team * Package name: r-hms-dbmi-spp Version : 1.14 Upstream Author : peterK * URL : http://compbio.med.harvard.edu/Supplements/ChIP-seq/ * License

Bug#834592: ITP: hisat2 -- graph-based alignment of short nucleotide reads to many genomes

Package: wnpp Severity: wishlist Owner: Debian Med team * Package name: hisat2 Version : 2.0.4 Upstream Author : HISAT2 team * URL : https://ccb.jhu.edu/software/hisat2/index.shtml * License : GPL-3+

Bug#834590: ITP: python3-typed-ast -- AST with PEP 484 type comments support

Package: wnpp Severity: wishlist Owner: Debian Med team * Package name: python3-typed-ast Version : 0.5.5 Upstream Author : David Fisher * URL : https://pypi.python.org/pypi/typed-ast * License : Python,

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