Bug#985071: smalt: native FTBFS with DEB_BUILD_OPTIONS=nocheck

2021-03-12 Thread Nilesh Patra
Package: smalt Version: 0.7.6-9 Severity: important X-Debbugs-Cc: nil...@debian.org Dear Maintainer, On running with NOCHECK build opts and profile nocheck enabled, smalt Fails to build from source with: dh binary dh_testroot dh_prep debian/rules override_dh_auto_install make[1]:

Bug#985069: seqprep FTCBFS -- multiple reasons

2021-03-12 Thread Nilesh Patra
Package: seqprep Version: 1.3.2-5 Severity: normal X-Debbugs-Cc: nil...@debian.org Dear Maintainer, seqprep has a B-D on markdown, which needs to be marked 'M-A: foreign', check #982406. But in any case, a maintainer html can be easily maintained, thus mitigating the problem anyway. It also has

Bug#985061: fsm-lite -- Passes -msse4.2: Baseline violation on amd64

2021-03-12 Thread Nilesh Patra
Package: fsm-lite Version: 1.0-4 Severity: serious X-Debbugs-Cc: nil...@debian.org Dear Maintainer, fsm-lite forcibly passes -msse4.2 on amd54, which is a baseline violation. Please compile for either all SIMD levels from sse4.2 down to base, and use a selector like simd-dispatch [1] [1]:

Bug#984978: subread FTCBFS -- multiple reasons

2021-03-11 Thread Nilesh Patra
Package: subread Version: 2.0.1+dfsg-1 Severity: normal Tags: patch User: debian-cr...@lists.debian.org Usertags: ftcbfs X-Debbugs-Cc: nil...@debian.org Dear Maintainer, Subread has a unsatisfiable dep on python3. Since python3 and bc are used only for tests, they can easily be annotated with .

Bug#984973: mash FTBFS -- multiple reasons

2021-03-11 Thread Nilesh Patra
Package: mash Version: 2.2.2+dfsg-2 Severity: normal Tags: patch User: debian-cr...@lists.debian.org Usertags: ftcbfs X-Debbugs-Cc: nil...@debian.org Dear Maintainer, Mash currently has cross-satisfiablity issues, due to python3-sphinx in B-D. Since python3-sphinx is used for documentation, and

Bug#984890: assembly-stats FTCBFS: uses DEB_BUILD_GNU_TYPE

2021-03-09 Thread Nilesh Patra
Package: assembly-stats Version: 1.0.1+ds-2 Severity: normal Tags: patch User: debian-cr...@lists.debian.org Usertags: ftcbfs X-Debbugs-Cc: nil...@debian.org Dear Maintainer, assembly-stats FTCBFS due to two reasons: * It forces compilation of test files, report with patch has

Bug#984889: assembly-stats natively FTBFS: error: gtest/gtest.h: No such file or directory

2021-03-09 Thread Nilesh Patra
Package: assembly-stats Version: 1.0.1+ds-2 Severity: important X-Debbugs-Cc: nil...@debian.org Control: tags -1 patch Dear Maintainer, assembly-stats natively FTBFS reason being it forcefully compiles test files, while the test dependency libgtest-dev is annotated with It should respect the

Bug#984854: seqsero: Seqsero invokes python2.7 during execution

2021-03-09 Thread Nilesh Patra
Package: seqsero Version: 1.0.1+dfsg-2 Severity: serious X-Debbugs-Cc: nil...@debian.org Dear Maintainer, Seqsero seems to invoke python2.7 during execution, for example here[1] Similar invocation statements have _not_ been patched out yet in the d/patches/2to3.patch, probably affecting the

Bug#984422: xwelltris: ftbfs with GCC-11

2021-03-05 Thread Nilesh Patra
control: tags -1 patch The  patch fixes this if seems ok, please consider to apply Nilesh --- a/src/sdl/sdlwelldrawing.cxx +++ b/src/sdl/sdlwelldrawing.cxx @@ -72,7 +72,7 @@   fields[i]=SDL_DisplayFormat(surface); SDL_FreeSurface(surface); -    if(fields[i]>0) +    if(fields[i]!=0)    

Bug#983994: bloboats: ftbfs with GCC-11

2021-03-05 Thread Nilesh Patra
The following patch seems to fix it. If seems appropriate, please consider applying Thanks, Nilesh --- a/src/menu.cpp +++ b/src/menu.cpp @@ -1567,7 +1567,7 @@ // Get resolutions vector resolutions; SDL_Rect** modes = SDL_ListModes(NULL, SDL_FULLSCREEN|SDL_HWSURFACE|SDL_OPENGL);

Bug#983723: Additional issues on arm64 and mips64el (Was: Bug#983723: rna-star FTBFS on ppc64el due to -march=native)

2021-03-01 Thread Nilesh Patra
Hi, On Mon, 1 Mar, 2021, 6:13 pm Andreas Tille, wrote: > Hi, > > besides this on arm64[1] and mips64el: > > ... > cd opal && \ > g++ -c -O3 -std=c++11 -march=native opal.cpp > opal.cpp:9:10: fatal error: immintrin.h: No such file or directory > 9 | #include // AVX2 and lower > |

Bug#983378: serd FTCBFS: build dependency python3-sphinx not installable

2021-02-23 Thread Nilesh Patra
Source: serd Version: 0.30.10-1 Tags: patch User: debian-cr...@lists.debian.org Usertags: cross-satisfiability Hi, serd cannot be cross built from source, because its dependency on the host architecture python3-sphinx fails to install. Since serd builds it's -doc package and only the doc

Bug#983343: xrootd: demote sphinx dependency to B-D-I

2021-02-22 Thread Nilesh Patra
Source: xrootd Version: 5.0.3-4 Tags: patch User: debian-cr...@lists.debian.org Usertags: cross-satisfiability Hi, xrootd cannot cross built from source, because its sphinx dependency is not satisfiable. Since the documentation is already split to an arch:all package and the documentation is

Bug#983234: xbanish FTCBFS: Uses host arch's strip

2021-02-21 Thread Nilesh Patra
Source: xbanish Version: 1.7-1.1 Tags: patch User: debian-cr...@lists.debian.org Usertags: ftcbfs Hi, xbanish does not cross build because it uses host's strip via "install -s". Defaulting to install fixes the situation. The patch is attached with the bug. Please consider to apply this and

Bug#983188: ITP: unikmer -- Toolkit for nucleic acid k-mer analysis

2021-02-20 Thread Nilesh Patra
Package: wnpp Severity: wishlist Owner: Nilesh Patra X-Debbugs-CC: debian-de...@lists.debian.org * Package name: unikmer Version : 0.17.2-1 Upstream Author : Wei Shen * URL : https://github.com/shenwei356/unikmer * License : Expat Programming Lang: Golang

Bug#983187: ITP: golang-github-will-rowe-nthash -- Go implementation of ntHash

2021-02-20 Thread Nilesh Patra
Package: wnpp Severity: wishlist Owner: Nilesh Patra X-Debbugs-CC: debian-de...@lists.debian.org * Package name: golang-github-will-rowe-nthash Version : 0.3.0-1 Upstream Author : Will Rowe * URL : https://github.com/will-rowe/nthash * License : Expat

Bug#983185: ITP: golang-github-twotwotwo-sorts -- Parallel and radix sorting in Go

2021-02-20 Thread Nilesh Patra
Package: wnpp Severity: wishlist Owner: Nilesh Patra X-Debbugs-CC: debian-de...@lists.debian.org * Package name: golang-github-twotwotwo-sorts Version : 0.0~git20160814.bf5c1f2-1 Upstream Author : Randall Farmer * URL : https://github.com/twotwotwo/sorts * License

Bug#982989: codonw FTCBFS: Multiple reasons

2021-02-17 Thread Nilesh Patra
Source: codonw Version: 1.4.4-5 Tags: patch User: debian-cr...@lists.debian.org Usertags: ftcbfs X-Debbugs-CC: debian-cr...@lists.debian.org Hi, codonw fails to cross build due to two reasons:     * It hardcodes $(MAKE) in d/rules. This is virtually useless since after the hardening.patch

Bug#982903: gitlab: Internal error caused by missing gitaly-git2go binary

2021-02-17 Thread Nilesh Patra
Hi, On Wed, 17 Feb 2021 at 14:21, Pirate Praveen wrote: > > > On Wed, Feb 17, 2021 at 2:06 pm, Pirate Praveen > wrote: > > This is a bug in golang-gopkg-libgit2-git2go.v28-dev > > > > We will have to patch this to look for libgit2.pc from system > > apt-file find libgit2.pc > libgit2-dev:

Bug#982912: repeatmasker-recon FTCBFS: hardcodes "make" in d/rules

2021-02-16 Thread Nilesh Patra
Source: repeatmasker-recon Version: 1.08-5 Tags: patch User: debian-cr...@lists.debian.org Usertags: ftcbfs X-Debbugs-Cc: debian-cr...@lists.debian.org Hi, Currently repeatmasker-recon seems to cross build from source because it harcodes make in d/rules everywhere. The attached patch here fixes

Bug#981753: [Debian-med-packaging] Bug#981753: COPY cannot find "/usr/share/nodejs/axios/dist/axios.min.js"

2021-02-14 Thread Nilesh Patra
Hi Sébastien, On Wed, 3 Feb 2021 17:10:13 +0100 =?UTF-8?Q?S=c3=a9bastien_Jodogne?= wrote: > Hello Mathieu, > > This issue comes from the fact that many JavaScript packages have > recently changed their installation paths. > > I guess that your issue can be fixed by reverting the following

Bug#977067: Bug#977060: cwltool FTBFS with pytest 6

2021-02-11 Thread Nilesh Patra
On Sun, 7 Feb 2021 22:08:58 +0100 =?utf-8?Q?=C3=89tienne?= Mollier wrote: > I tried to reproduce the bug by building igdiscover 0.11-3 using > sbuild in a clean Sid chroot which did include pytest 6: > > $ schroot -c unstable-amd64-sbuild -d / \ > -- apt-cache show python3-pytest \ > | grep

Bug#880316: teem: FTBFS: Test failures

2021-02-07 Thread Nilesh Patra
Control: severity -1 minor It looks like this is fixed: https://buildd.debian.org/status/fetch.php?pkg=teem=amd64=1.12.0%7E20160122-4=1606151763=0 Hence lowering the severity On Mon, 30 Oct 2017 21:10:20 +0100 Lucas Nussbaum wrote: > Source: teem > Version: 1.12.0~20160122-2 > Severity:

Bug#981876: gdpc: flaky autopkgtest on i386

2021-02-07 Thread Nilesh Patra
Control: Severity -1 important Hi Etienne, Thanks for filing ROM --RM. I'm lowering the severity so it migrates to testing. Nilesh

Bug#976735: fixed in spyder 4.2.1+dfsg1-1

2021-02-05 Thread Nilesh Patra
Thank you, Julien! :-) On Fri, 05 Feb 2021 14:49:37 + Debian FTP Masters wrote: > Source: spyder > Source-Version: 4.2.1+dfsg1-1 > Done: Julian Gilbey > > We believe that the bug you reported is fixed in the latest version of > spyder, which is due to be installed in the Debian FTP

Bug#957828: Please consider uploading sparskit (was: Re: sparskit: ftbfs with GCC-10)

2021-02-02 Thread Nilesh Patra
Hi Etienne, On Fri, 15 Jan 2021 13:16:30 +0100 =?utf-8?Q?=C3=89tienne?= Mollier wrote: > Control: tag -1 patch > > Hi, > > I prepared a targeted patch to fix Gcc-10 issues with sparskit, > and ran the embedded ./dotests to make sure it did not introduce > any errors. This fixes the argument

Bug#976735: spyder needs source upload for Python 3.9 transition

2021-02-01 Thread Nilesh Patra
Hi Julian I read through the rest of the thread. On Mon, 1 Feb, 2021, 6:31 pm Julian Gilbey, wrote: > I have a package of Spyder 4 waiting to upload, but it requires five > packages to be accepted into unstable from NEW first (pyls-server, > pyls-black, pyls-spyder, abydos, textdistance); once

Bug#976735: spyder needs source upload for Python 3.9 transition

2021-02-01 Thread Nilesh Patra
Hi Julian, On Sun, 13 Dec 2020 06:58:29 + Julian Gilbey wrote: > On Mon, Dec 07, 2020 at 05:38:26PM +0200, Adrian Bunk wrote: > > Package: spyder > > Version: 3.3.6+dfsg1-5 > > Severity: serious > > > > Since binNMUs are not possible for binary-all packages, > > a source upload is needed for

Bug#976735: spyder needs source upload for Python 3.9 transition

2021-02-01 Thread Nilesh Patra
Hi Julian, On Sun, 13 Dec 2020 06:58:29 + Julian Gilbey wrote: > On Mon, Dec 07, 2020 at 05:38:26PM +0200, Adrian Bunk wrote: > > Package: spyder > > Version: 3.3.6+dfsg1-5 > > Severity: serious > > > > Since binNMUs are not possible for binary-all packages, > > a source upload is needed for

Bug#978364: apertium-ukr: FTBFS: Error: Invalid dictionary (hint: the left side of an entry is empty)

2021-01-31 Thread Nilesh Patra
Hi Tino, On Tue, 5 Jan 2021 01:13:56 +0100 Tino Didriksen wrote: > apertium-ukr should be removed from Debian. The pair that needed it has > been upgraded to bundle the required version instead: If you agree, can I retitle and reassign to file in a removal bug for apertium-ukr, then? Also, I

Bug#971681: r-cran-openmx regression on arm, will not migrate to testing due to failing autopkgtests

2021-01-30 Thread Nilesh Patra
Hi Joshua, Many thanks for fixes, The freeze has started and soft freeze time is near as well.(2 weeks from now) OpenMx has removals of a bunch of packages from testing. Hence, please consider doing a new upstream release if it looks okay to you. Thanks and regards, Nilesh signature.asc

Bug#978279: marked as pending in afew

2021-01-28 Thread Nilesh Patra
On Thu, 28 Jan 2021 at 20:48, Håvard Flaget Aasen wrote: > > > > > I see that you are a DM, If you agree to add yourself to the uploader's > > field, I'll happily grant permissions. > > Thanks! I updated, and included myself in the uploader's field. > Done, please upload :-)

Bug#978279: marked as pending in afew

2021-01-28 Thread Nilesh Patra
On Thu, 28 Jan 2021 at 19:31, Håvard Flaget Aasen wrote: > Hi Nilesh > > The reason I haven't uploaded is because I'm not a DD, so I don't have > the necessary permissions. > I see that you are a DM, If you agree to add yourself to the uploader's field, I'll happily grant permissions. > I

Bug#978279: marked as pending in afew

2021-01-28 Thread Nilesh Patra
Hi Håvard Looks like you've fixed this, but not uploaded yet. Is there anything missing, or should I upload this one? Regards, Nilesh On Thu, 14 Jan 2021 11:09:50 + =?UTF-8?B?SMOldmFyZCBGbGFnZXQgQWFzZW4=?= wrote: > Control: tag -1 pending > > Hello, > > Bug #978279 in afew reported by

Bug#812504: swarp: breaks when coadding many overlapping files

2021-01-26 Thread Nilesh Patra
Hi Julian, On Sun, 24 Jan 2016 14:57:52 +0100 Julian Taylor wrote: > Package: swarp > Version: 2.38.0+dfsg-2 > Severity: important > > when coadding more than the openfile limit (normally 1024) overlapping > files swarp aborts due to too many open files. > To reproduce create some files with

Bug#962717: q2-quality-control seems so uncover segfaults in bowtie2

2021-01-14 Thread Nilesh Patra
On Fri, 15 Jan, 2021, 11:30 am Andreas Tille, wrote: > Hi, > > On Fri, Jan 15, 2021 at 10:16:45AM +0530, Nilesh Patra wrote: > > > > I don't know about the segfaults, but I don't see q2-taxa in NEW? You > > probably uploaded it more than 8 hours ago from the ti

Bug#962717: q2-quality-control seems so uncover segfaults in bowtie2

2021-01-14 Thread Nilesh Patra
On Fri, 15 Jan, 2021, 2:12 am Andreas Tille, wrote: > Hi, > > since q2-taxa is in new I intended to upload q2-quality-control as well. > I don't know about the segfaults, but I don't see q2-taxa in NEW? You probably uploaded it more than 8 hours ago from the time I'm typing this mail, it

Bug#978662: apertium-cy-en: autopkgtest failure

2021-01-03 Thread Nilesh Patra
Hi Tino, On Tue, 29 Dec 2020 23:21:15 +0100 Tino Didriksen wrote: > This is a chicken-and-egg problem that should solve itself. New apertium > 3.7.1 can't migrate until apertium-cy-en is fixed, but fixed apertium-cy-en > won't build correctly with existing apertium 3.6.1. On declaring hard

Bug#978760: man page for lua-busted (binary: busted)

2020-12-31 Thread Nilesh Patra
fault: off) .TP \fB\-\-[no\-]sort\-tests\fR sort test order within a file (default: off) .TP \fB\-\-[no\-]suppress\-pending\fR suppress `pending` test output (default: off) .TP \fB\-\-[no\-]defer\-print\fR defer print to when test suite is complete (default: off) .PP ; re\-run with \fB\-

Bug#977308: shasta: hardcoded dependencies on boost 1.71

2020-12-18 Thread Nilesh Patra
Hi Andreas, On Fri, 18 Dec 2020 at 15:53, Andreas Tille wrote: > Control: tags -1 help > > Hi, > > I tried to fix the issue by making dh_shlibdeps work. In > > > https://salsa.debian.org/med-team/shasta/-/commit/366edd672be428cc553b34b99bc614aa698175d6 > > I documented what I tried but all

Bug#976907: golang-github-boltdb-bolt: FTBFS on ppc64el (arch:all-only src pkg): dh_auto_test: error: cd obj-powerpc64le-linux-gnu && go test -vet=off -v -p 160 -short github.com/boltdb/bolt github.co

2020-12-13 Thread Nilesh Patra
Hi Andreas, On Sat, 12 Dec 2020 18:48:52 +0100 Andreas Henriksson wrote: > Hello again, > > So after wasting my time here I finally realized that apparently > boltdb is archived upstream. It will not receive any fixes. > > Apparently golang-github-coreos-bbolt is a maintained feature-extended >

Bug#977155: ITP: node-thenby: library that helps sorting arrays on multiple keys

2020-12-11 Thread Nilesh Patra
Package: wnpp Severity: wishlist Owner: Nilesh Patra X-Debbugs-CC: debian-de...@lists.debian.org * Package name: node-thenby Version : 1.3.4+git20200720.0fd165a+ds-1 Upstream Author : Teun Duynstee * URL : https://github.com/Teun/thenBy.js * License : Apache

Bug#976479: [Request for help] Bug: #976479 scrappie: FTBFS: scrappie_matrix.h:5:14: fatal error: immintrin.h: No such file or directory

2020-12-07 Thread Nilesh Patra
[update] On Mon, 7 Dec 2020 at 22:27, Nilesh Patra wrote: > > >> >>> >>> Also, another question: This package has a MPL-2.0 license and AFAIK, >>> MPL is a restrictive Free software license, so does this qualify for adding >>> in a

Bug#976479: [Request for help] Bug: #976479 scrappie: FTBFS: scrappie_matrix.h:5:14: fatal error: immintrin.h: No such file or directory

2020-12-07 Thread Nilesh Patra
Hi o/ First of all, thank you for the fixes and letting me know about cowbuilder-dist :-) On Mon, 7 Dec 2020 at 17:51, Michael Crusoe wrote: > > I'd be really grateful if you could take a look at my changes and let me >> know if they look fine. >> > > I'll leave comments on Salsa > Thanks a

Bug#976479: [Request for help] Bug: #976479 scrappie: FTBFS: scrappie_matrix.h:5:14: fatal error: immintrin.h: No such file or directory

2020-12-07 Thread Nilesh Patra
, another question: This package has a MPL-2.0 license and AFAIK, MPL is a restrictive Free software license, so does this qualify for adding in a "Built-Using" field? Thanks and regards Nilesh On Mon, 7 Dec 2020 at 16:19, Nilesh Patra wrote: > Hi Michael > > Thanks

Bug#976479: [Request for help] Bug: #976479 scrappie: FTBFS: scrappie_matrix.h:5:14: fatal error: immintrin.h: No such file or directory

2020-12-07 Thread Nilesh Patra
lsa.debian.org/med-team/scrappie/-/commit/a00691d910110a460ef5e61a6c74cc2cb0e1a626#5dc91bdd30262777c0556235b73413cd5865a144_0_31 > is the issue > You should add the regular simde includes here, so that v4sf typedef works > > define SIMDE_ENABLE_NATIVE_ALIASES#include > > > >

Bug#976479: [Request for help] Bug: #976479 scrappie: FTBFS: scrappie_matrix.h:5:14: fatal error: immintrin.h: No such file or directory

2020-12-07 Thread Nilesh Patra
Hi Michael and others, Scrappie looks like a candidate where we can use the simde trick. I tried doing a patch, and it works on amd64 machine, but not on an arm64 porter box :/ (with issues with __v4sf) And I'm not sure how to fix this, and hence this is a humble request to please take a look

Bug#976497: python-parasail: FTBFS: dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p 3.9 returned exit code 13 Inbox [Imap]/Sent

2020-12-06 Thread Nilesh Patra
Control: forwarded -1 https://github.com/jeffdaily/parasail-python/issues/56 Forwarded the issue upstream, hopefully we will have a fix soonish with arm64 becoming more popular.

Bug#976497: python-parasail: FTBFS: dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p 3.9 returned exit code 13

2020-12-06 Thread Nilesh Patra
part (hopefully): >> dpkg-buildpackage >> - >> >> Command: dpkg-buildpackage -us -uc -sa -rfakeroot >> dpkg-buildpackage: info: source package python-parasail >> dpkg-buildpackage: info: source version 1.2.1-1 >> dpkg-buildpackage: info: source

Bug#976497: python-parasail: FTBFS: dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p 3.9 returned exit code 13

2020-12-06 Thread Nilesh Patra
part (hopefully): > > dpkg-buildpackage > > - > > > > Command: dpkg-buildpackage -us -uc -sa -rfakeroot > > dpkg-buildpackage: info: source package python-parasail > > dpkg-buildpackage: info: source version 1.2.1-1 > > dpkg-buildpackage: info: source

Bug#962184: [Help] Re: jellyfish FTBFS on 32bit

2020-12-02 Thread Nilesh Patra
Hi Andreas, On Thu, 3 Dec 2020 at 03:04, Andreas Tille wrote: > Control: tags -1 help > > Hi, > > I guess this bug is relatively easy to fix by some explicit typing - but > I'm lacking the C++ knowledge to find out where. > Attaching a patch for this, it goes past this. However, the build-time

Bug#968045: golang-gonum-v1-plot: please make the build reproducible

2020-11-30 Thread Nilesh Patra
Hi again, On Fri, 06 Nov 2020 09:18:34 + "Chris Lamb" wrote: > Chris Lamb wrote: > > > Source: golang-gonum-v1-plot > > Version: 0.7.0-2 > > Tags: patch > > Gentle ping on the above? > Thanks again, but unfortunately this patch breaks the autopkgtests :/ The only way to make it reproducible

Bug#974178: python3-biom-format: debci tests fail: Object of type bytes is not JSON serializable

2020-11-21 Thread Nilesh Patra
Hi, debci seems happy now. https://ci.debian.net/packages/p/python-biom-format/unstable/amd64/ https://ci.debian.net/data/autopkgtest/unstable/amd64/p/python-biom-format/8336917/log.gz Should this bug be closed now? Please let me know/do so if you feel this is done. (I can close it myself in a

Bug#974178: python3-biom-format: debci tests fail: Object of type bytes is not JSON serializable

2020-11-21 Thread Nilesh Patra
Hi, On Wed, 11 Nov 2020 11:56:10 +0800 Drew Parsons wrote: > Package: python3-biom-format > Version: 2.1.9-2 > Severity: normal > > debci tests for python3-biom-format are show test error triggered by > python3-h5py 3.1.0-1exp1 from experimental. > > The odd thing is that the error trace does

Bug#974834: ITP: gsort -- Sort genomic data

2020-11-15 Thread Nilesh Patra
Package: wnpp Severity: wishlist Owner: Nilesh Patra X-Debbugs-CC: debian-de...@lists.debian.org * Package name: gsort Version : 0.1.4-1 Upstream Author : Brent Pedersen * URL : https://github.com/brentp/gsort * License : Expat Programming Lang: Golang

Bug#974798: ITP: ggd-utils -- programs for use in ggd

2020-11-14 Thread Nilesh Patra
Package: wnpp Severity: wishlist Owner: Nilesh Patra X-Debbugs-CC: debian-de...@lists.debian.org * Package name: ggd-utils Version : 0.0.7+ds Upstream Author : gogetdata * URL : github.com/gogetdata/ggd-utils * License : Expat Programming Lang: Golang

Bug#974774: ITP: golang-github-alexflint-go-arg -- Struct-based argument parsing in Go

2020-11-14 Thread Nilesh Patra
Package: wnpp Severity: wishlist Owner: Nilesh Patra X-Debbugs-CC: debian-de...@lists.debian.org * Package name: golang-github-alexflint-go-arg Version : 1.3.0+ds Upstream Author : Alex Flint * URL : https://github.com/alexflint/go-arg * License : BSD-2-Clause

Bug#926079: ITP: golang-github-alexflint-go-scalar -- Go-lang Scalar parsing library

2020-11-14 Thread Nilesh Patra
Hi, Any update on this package? It seems that it hasn't landed in the archive yet. We need this to package https://github.com/alexflint which is another chain of deps to get bcbio working. If there's no issue at your end, this shall be uploaded to NEW. Please let me know if there's any update

Bug#965114: golang-github-shenwei356-bwt: FTBFS: unsatisfiable build dependency

2020-11-10 Thread Nilesh Patra
Control: severity -1 minor On Tue, 10 Nov 2020 21:39:40 +0530 Nilesh Patra wrote: > sbuild (Debian sbuild) 0.79.1 (22 April 2020) on debian > > ++ > | golang-github-shenwei356-bwt 0.0

Bug#972759: ITP: golang-github-iafan-cwalk -- Concurrent filepath.Walk replacement

2020-10-23 Thread Nilesh Patra
Package: wnpp Severity: wishlist Owner: Nilesh Patra X-Debbugs-CC: debian-de...@lists.debian.org * Package name: golang-github-iafan-cwalk Version : 0.0~git20191125.dd7f505-1 Upstream Author : Igor Afanasyev * URL : https://github.com/iafan/cwalk * License

Bug#972757: ITP: golang-github-smallfish-simpleyaml -- Go package to interact with arbitrary YAML

2020-10-23 Thread Nilesh Patra
Package: wnpp Severity: wishlist Owner: Nilesh Patra X-Debbugs-CC: debian-de...@lists.debian.org * Package name: golang-github-smallfish-simpleyaml Version : 0.0~git20170911.a320310-1 Upstream Author : 陈小玉 * URL : https://github.com/smallfish/simpleyaml * License

Bug#920545: [RFS] python-intervaltree-bio

2020-10-05 Thread Nilesh Patra
Hi, I've attempted to fix: #920545 which is about failing autopkgtests for python-intervaltree-bio. It seems to pass on my chroot and I've pushed the corresponding changes to the team repo here[1]. It'd be great if someone could try testing my changes once - and either sponsor or grant me access

Bug#971148: umap-learn: FTBFS: unsatisfiable build-dependency: python3-llvmlite (< 0.34) but 0.34.0-1 is to be installed

2020-09-29 Thread Nilesh Patra
I suppose this FTBFS is due to numba[1] instead of umap-learn. Hence, this would as well FTBFS. It might be a better idea to close this bug and open a bug report against numba instead, so that umap-learn migrates to testing after the bug is fixed in numba, w/o having to close this bug manually.

Bug#970462: [RFS] Bug#970462: sweed: autopkgtest arm64 failure

2020-09-20 Thread Nilesh Patra
Hi, On Sun, 20 Sep 2020 at 20:34, Étienne Mollier wrote: > Control: tags -1 pending > > Greetings, > > I tried to investigate the issue of running SweeD autopkgtests > on arm64. It turned out to be caused by the assumption that the > "char" type was "signed" by default, while it is "unsigned"

Bug#970550: [Pkg-javascript-devel] Bug#970550: replacing browserify with webpack or rollup - need help

2020-09-20 Thread Nilesh Patra
Hi, On Sun, 20 Sep 2020 at 15:18, Pirate Praveen wrote: > Control: tags -1 help > > On Sun, Sep 20, 2020 at 14:44, Pirate Praveen > wrote: > > The warning now changes to, > > > > (!) Missing shims for Node.js built-ins > > Creating a browser bundle that depends on 'path', 'url' and 'os'. You >

Bug#970447: ITP: pinfish -- Collection of tools to annotate genomes using long read transcriptomics data

2020-09-16 Thread Nilesh Patra
Package: wnpp Severity: wishlist Owner: Nilesh Patra X-Debbugs-CC: debian-de...@lists.debian.org * Package name: pinfish Version : 0.1.0+ds-1 Upstream Author : Oxford Nanopore Technologies Ltd. * URL : https://github.com/nanoporetech/pinfish * License : MPL

Bug#970404: shovill: Please provide autopkgtest

2020-09-15 Thread Nilesh Patra
Package: shovill Severity: wishlist X-Debbugs-Cc: npatra...@gmail.com Dear Maintainer, Please provide autopkgtest for this package. This also doesn't work properly at the moment and needs minor patching for the same. -- System Information: Debian Release: bullseye/sid   APT prefers testing  

Bug#970385: src:swissknife: Please provide autopkgtest

2020-09-15 Thread Nilesh Patra
Source: swissknife Version: 1.75-2 Severity: wishlist Tags: newcomer Dear Maintainer, Please provide autopkgtest for this package. -- System Information: Debian Release: bullseye/sid   APT prefers testing   APT policy: (500, 'testing') Architecture: amd64 (x86_64) Kernel: Linux 5.7.0-2-amd64

Bug#970312: src:intake: Please provide autopkgtest

2020-09-14 Thread Nilesh Patra
Source: intake Version: 0.6.0-3 Severity: wishlist Tags: newcomer Dear Maintainer, Please provide autopkgtest for this package. -- System Information: Debian Release: bullseye/sid   APT prefers testing   APT policy: (500, 'testing') Architecture: amd64 (x86_64) Kernel: Linux 5.7.0-2-amd64

Bug#970309: src:python-loompy: Please provide autopkgtest

2020-09-14 Thread Nilesh Patra
Source: python-loompy Version: 3.0.6+dfsg-2 Severity: wishlist Tags: newcomer Dear Maintainer, Please provide autopkgtest for this package. -- System Information: Debian Release: bullseye/sid   APT prefers testing   APT policy: (500, 'testing') Architecture: amd64 (x86_64) Kernel: Linux

Bug#970301: phybin: Please provide autopkgtest

2020-09-14 Thread Nilesh Patra
Package: phybin Severity: wishlist X-Debbugs-Cc: npatra...@gmail.com Tags: newcomer Dear Maintainer, Please provide autopkgtest for this package. -- System Information: Debian Release: bullseye/sid   APT prefers testing   APT policy: (500, 'testing') Architecture: amd64 (x86_64) Kernel: Linux

Bug#970238: ITP: survivor -- Tool set for simulating/evaluating SVs

2020-09-13 Thread Nilesh Patra
Package: wnpp Severity: wishlist Owner: Nilesh Patra X-Debbugs-CC: debian-de...@lists.debian.org * Package name: survivor Version : 1.0.6-1 Upstream Author : Fritz Sedlazeck * URL : https://github.com/fritzsedlazeck/SURVIVOR * License : Expat Programming

Bug#970157: ITP: seriation --- Finds a suitable linear order for a set of objects

2020-09-12 Thread Nilesh Patra
Package: wnpp Severity: wishlist Owner: Nilesh Patra X-Debbugs-CC: debian-de...@lists.debian.org * Package name: seriation Version : 0.1+git20200810 Upstream Author : Alexandre Amory * URL : https://github.com/amamory/seriation * License : Expat Programming

Bug#969743: ITP: svim: Structural variant caller for long sequencing reads

2020-09-07 Thread Nilesh Patra
Package: wnpp Severity: wishlist Owner: Nilesh Patra X-Debbugs-CC: debian-de...@lists.debian.org * Package name: svim Version : 1.4.1+ds-1 Upstream Author : David Heller * URL : https://github.com/eldariont/svim/ <https://github.com/knsv/mermaid> * L

Bug#969423: ITP: h5sparse: Scipy sparse matrix in HDF5

2020-09-02 Thread Nilesh Patra
Package: wnpp Severity: wishlist Owner: Nilesh Patra X-Debbugs-CC: debian-de...@lists.debian.org * Package name: h5sparse Version : 0.1.0-1 Upstream Author : Appier Inc * URL : https://github.com/appier/h5sparse <https://github.com/knsv/mermaid> * L

Bug#967051: ITP: seqkit: Cross-platform and ultrafast toolkit for FASTA/Q file manipulation

2020-08-03 Thread Nilesh Patra
Package: wnpp Severity: wishlist Owner: Nilesh Patra X-Debbugs-CC: debian-de...@lists.debian.org * Package name: seqkit Version : 0.12.1+ds-1 Upstream Author : 2016-2020 Wei Shen, 2019 Oxford Nanopore Technologies <https://github.com/knsv/mermaid> * License

Bug#967009: ITP: golang-github-bsipos-thist :Generates online histograms and plots them with golang

2020-08-03 Thread Nilesh Patra
Package: wnpp Severity: wishlist Owner: Nilesh Patra X-Debbugs-CC: debian-de...@lists.debian.org * Package name: golang-github-bsipos-thist Version : 1.0.0-1 Upstream Author : 2019 Botond Sipos * URL : https://github.com/bsipos/thist <https://github.com/knsv/merm

Bug#966681: ITP: golang-gonum-v1-plot :Provides an API for building and drawing plots in Go

2020-08-01 Thread Nilesh Patra
Package: wnpp Severity: wishlist Owner: Nilesh Patra X-Debbugs-CC: debian-de...@lists.debian.org * Package name: golang-gonum-v1-plot Version : 0.7.0-1 Upstream Author : 2013-2019 Ethan Burns Steve McCoy Dan Kortschak

Bug#964610: nibabel: FTBFS: dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p 3.8 returned exit code 13

2020-07-27 Thread Nilesh Patra
On Tue, 21 Jul 2020 15:52:22 +0200 Andreas Tille wrote: > Control: tags -1 - upstream > Control: tags -1 pending > > The build time test issue was solved thanks to upstream (switched from > nose to pytest). Unfortunately there are now issues with sphinx to > build the docs. My dirty workaroung

Bug#965383: ITP: golang-github-tatsushid-go-prettytable: Builds a simple text table with a multibyte, doublewidth character support

2020-07-20 Thread Nilesh Patra
Package: wnpp Severity: wishlist Owner: Nilesh Patra X-Debbugs-CC: debian-de...@lists.debian.org * Package name: golang-github-tatsushid-go-prettytable Version : 0.0~git20141013.ed2d14c-1 Upstream Author : Tatsushi Demachi * URL : https://github.com/tatsushid/go

Bug#962863: r-cran-rdflib: autopkgtest regression

2020-07-20 Thread Nilesh Patra
On Mon, 15 Jun 2020 11:17:24 +0200 Graham Inggs wrote: > Source: r-cran-rdflib > Version: 0.2.3+dfsg-1 > Severity: serious > X-Debbugs-CC: debian...@lists.debian.org > User: debian...@lists.debian.org > Usertags: regression > > Hi Maintainer > > Sometime in the last month, r-cran-rdflib started

Bug#964933: ITP: golang-github-brentp-goluaez: Easy embedding Lua in go

2020-07-12 Thread Nilesh Patra
Package: wnpp Severity: wishlist Owner: Nilesh Patra X-Debbugs-CC: debian-de...@lists.debian.org * Package name: golang-github-brentp-goluaez Version : 0.0~git20160116.dd35d08-1 Upstream Author : Brent Pedersen * URL : https://github.com/brentp/goluaez <ht

Bug#964932: ITP: golang-github-yuin-gluare: Regular expression library for the GopherLua

2020-07-12 Thread Nilesh Patra
Package: wnpp Severity: wishlist Owner: Nilesh Patra X-Debbugs-CC: debian-de...@lists.debian.org * Package name: golang-github-yuin-gluare Version : 0.0~git20170607.d7c94f1-1 Upstream Author : Yusuke Inuzuka * URL : https://github.com/yuin/gluare <https://github.

Bug#963764: [Pkg-javascript-devel] Bug#963764: Bug#963764: node-node-sass: uses embedded old security-buggy libsass

2020-07-08 Thread Nilesh Patra
On Wed, 8 Jul 2020, 20:38 Jonas Smedegaard, wrote: > Quoting Nilesh Patra (2020-07-08 17:00:01) > > On Wed, 8 Jul 2020, 20:22 Jonas Smedegaard, wrote: > > > > > Quoting Nilesh Patra (2020-07-08 16:26:34) > > > > On Wed, 8 Jul 2020, 19:30 Jonas Smedegaar

Bug#963764: [Pkg-javascript-devel] Bug#963764: Bug#963764: node-node-sass: uses embedded old security-buggy libsass

2020-07-08 Thread Nilesh Patra
On Wed, 8 Jul 2020, 20:22 Jonas Smedegaard, wrote: > Quoting Nilesh Patra (2020-07-08 16:26:34) > > On Wed, 8 Jul 2020, 19:30 Jonas Smedegaard, wrote: > > > Please strongly consider to not only make the package link with > > > system-shared libsass, but also

Bug#963764: [Pkg-javascript-devel] Bug#963764: Bug#963764: node-node-sass: uses embedded old security-buggy libsass

2020-07-08 Thread Nilesh Patra
Hi, On Wed, 8 Jul 2020, 19:30 Jonas Smedegaard, wrote: > Quoting mer...@debian.org (2020-07-08 15:13:06) > > The upstream has updated the libsass support to 3.6.3 [1], it's just > > not released yet. I have successfully used head of their git > > repository to build node-node-sass without the

Bug#964307: ITP: golang-github-brentp-bix: Tabix file access with golang using biogo machinery (library)

2020-07-05 Thread Nilesh Patra
Package: wnpp Severity: wishlist Owner: Nilesh Patra X-Debbugs-CC: debian-de...@lists.debian.org * Package name: golang-github-brentp-bix Version : 0.0~git20190718.00aa7a7+ds-1 Upstream Author : Brent Pedersen * URL : https://github.com/brentp/bix <https://github.

Bug#964273: ITP: golang-github-brentp-vcfgo: Golang library to read, write, manipulate VCF format files

2020-07-04 Thread Nilesh Patra
Package: wnpp Severity: wishlist Owner: Nilesh Patra X-Debbugs-CC: debian-de...@lists.debian.org * Package name: golang-github-brentp-vcfgo Version : 0.0~git20190824.654ed2e-1 Upstream Author : Brent Pedersen * URL : https://github.com/brentp/vcfgo <ht

Bug#964266: ITP: golang-github-brentp-irelate: Streaming relation testing of sorted files of intervals

2020-07-04 Thread Nilesh Patra
Package: wnpp Severity: wishlist Owner: Nilesh Patra X-Debbugs-CC: debian-de...@lists.debian.org * Package name: golang-github-brentp-irelate Version : 0.0~git20180801.1bf7c8f+ds-1 Upstream Author : Brent Pedersen * URL : https://github.com/brentp/irelate <ht

Bug#963927: Bug-report severity fix

2020-06-28 Thread Nilesh Patra
Control: severity -1 serious thanks

Bug#963927: predictprotein:Unusable, fails with: Assigning non-zero to $[ is no longer possible

2020-06-28 Thread Nilesh Patra
Package: predictprotein Version: 1.1.09-2 Severity: severe Dear Maintainer, predictprotein uses `$[ = 1` which is no longer supported with newer perl versions. Way to reproduce: Get the predictprotein source package, and cd there. Try running examples with predictprotein: $ cd examples $

Bug#963628: [Pkg-javascript-devel] Bug#963628: Bug#963628: Node-jest fails with: Error: Cannot find module 'import-local'

2020-06-27 Thread Nilesh Patra
Also, as I dug in a bit, the "import-local" module has this description: """ Let a globally installed package use a locally installed version of itself if available For our use-case we would need modules only from /usr/share/* right? So _maybe_ this has no real use here? Let me know if this

Bug#963628: [Pkg-javascript-devel] Bug#963628: Bug#963628: Node-jest fails with: Error: Cannot find module 'import-local'

2020-06-27 Thread Nilesh Patra
On Sun, 28 Jun 2020, 02:45 Xavier, wrote: > Control: severity -i grave > Thanks. > Le 24/06/2020 à 21:18, Nilesh Patra a écrit : > > Package: node-jest > > Severity: serious > > > > Dear Maintainer, > > > > Node-jest fails with the follo

Bug#963628: Node-jest fails with: Error: Cannot find module 'import-local'

2020-06-24 Thread Nilesh Patra
Package: node-jest Severity: serious Dear Maintainer, Node-jest fails with the following on all the node-modules I've tried yet. Sample examples on node-compression-webpack-plugin version 2.0.0-3 and node-proper-lockfile version 4.1.1-2 internal/modules/cjs/loader.js:800 throw err; ^

Bug#963465: ITP: node-natural-sort: Sorting with support for numbers, dates, unicode and more

2020-06-21 Thread Nilesh Patra
Package: wnpp Severity: wishlist Owner: Nilesh Patra X-Debbugs-CC: debian-de...@lists.debian.org * Package name: node-natural-sort Version : 1.0.0-1 Upstream Author : Studio B12 GmbH * URL : https://github.com/studio-b12/natural-sort <https://github.com/knsv/merm

Bug#963189: ITP: sorted-nearest: Cython helper library for pyranges

2020-06-20 Thread Nilesh Patra
Package: wnpp Severity: wishlist Owner: Nilesh Patra X-Debbugs-CC: debian-de...@lists.debian.org * Package name: sorted-nearest Version : 0.0+git20200319.8204815+ds Upstream Author : Endre Bakken Stovner * URL : https://github.com/pyranges/sorted_nearest <ht

Bug#963164: ITP: pyrle: Run length arithmetic in Python using Cython

2020-06-19 Thread Nilesh Patra
Package: wnpp Severity: wishlist Owner: Nilesh Patra X-Debbugs-CC: debian-de...@lists.debian.org * Package name: pyrle Version : 0.0.31 Upstream Author : Endre Bakken Stovner * URL : https://github.com/pyranges/pyrle <https://github.com/knsv/mermaid> * L

Bug#963137: ITP: ncls: Datastructure for interval overlap queries

2020-06-19 Thread Nilesh Patra
Package: wnpp Severity: wishlist Owner: Nilesh Patra X-Debbugs-CC: debian-de...@lists.debian.org * Package name: ncls Version : 0.0.53 Upstream Author : Endre Bakken Stovner * URL : https://github.com/biocore-ntnu/ncls <https://github.com/knsv/mermaid> * L

Bug#963078: ITP: paryfor: Parallel_for implementation based on atomic queues

2020-06-18 Thread Nilesh Patra
Package: wnpp Severity: wishlist Owner: Nilesh Patra X-Debbugs-CC: debian-de...@lists.debian.org * Package name: paryfor Version : 0.1 Upstream Author : Erik Garrison * URL : https://github.com/ekg/paryfor <https://github.com/knsv/mermaid> * License :

Bug#963047: ITP: ngmlr: CoNvex Gap-cost alignMents for Long Reads

2020-06-18 Thread Nilesh Patra
Package: wnpp Severity: wishlist Owner: Nilesh Patra X-Debbugs-CC: debian-de...@lists.debian.org * Package name: ngmlr Version : 0.2.7 Upstream Author : Philipp Rescheneder * URL : https://github.com/philres/ngmlr <https://github.com/knsv/mermaid> * L

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