Bug#986170: ITP: r-bioc-ioniser -- Quality Assessment Tools for Oxford Nanopore MinION data

2021-03-30 Thread Nilesh Patra
Package: wnpp Severity: wishlist Owner: Nilesh Patra X-Debbugs-Cc: debian-de...@lists.debian.org, nil...@debian.org * Package name: r-bioc-ioniser Version : 2.14.0+dfsg Upstream Author : Mike Smith * URL : https://bioconductor.org/packages/IONiseR * License

Bug#986137: ITP: pullseq -- Extract sequence from a fasta or fastq

2021-03-30 Thread Nilesh Patra
Package: wnpp Severity: wishlist Owner: Nilesh Patra X-Debbugs-Cc: debian-de...@lists.debian.org, nil...@debian.org * Package name: pullseq Version : 1.0.2 Upstream Author : Brian C. Thomas * URL : https://github.com/bcthomas/pullseq/releases * License

Bug#986102: ITP: r-cran-uniqtag -- Abbreviate Strings to Short, Unique Identifiers

2021-03-29 Thread Nilesh Patra
Package: wnpp Severity: wishlist Owner: Nilesh Patra X-Debbugs-Cc: debian-de...@lists.debian.org, nil...@debian.org * Package name: r-cran-uniqtag Version : 1.0 Upstream Author : Shaun Jackman * URL : https://cran.r-project.org/package=uniqtag * License

Bug#986078: ITP: ssshtest -- stupid simple (ba)sh testing

2021-03-29 Thread Nilesh Patra
Package: wnpp Severity: wishlist Owner: Nilesh Patra X-Debbugs-Cc: debian-de...@lists.debian.org, nil...@debian.org * Package name: ssshtest Version : 0.0+git20190416.6f5438a Upstream Author : Ryan Layer * URL : https://github.com/ryanlayer/ssshtest.git * License

Bug#986067: ITP: r-cran-sampling -- Draw random samples using different sampling schemes

2021-03-29 Thread Nilesh Patra
Package: wnpp Severity: wishlist Owner: Nilesh Patra X-Debbugs-Cc: debian-de...@lists.debian.org, nil...@debian.org * Package name: r-cran-sampling Version : 2.9 Upstream Author : Yves Tille , Alina Matei * URL : https://cran.r-project.org/package=sampling * License

Bug#986052: ITP: r-bioc-qtlizer -- Comprehensive QTL annotation of GWAS results

2021-03-28 Thread Nilesh Patra
Package: wnpp Severity: wishlist Owner: Nilesh Patra X-Debbugs-Cc: debian-de...@lists.debian.org, nil...@debian.org * Package name: r-bioc-qtlizer Version : 1.4.0+dfsg Upstream Author : Matthias Munz * URL : https://bioconductor.org/packages/Qtlizer/ * License

Bug#986039: ITP: r-cran-svmisc -- SciViews - Miscellaneous Functions

2021-03-28 Thread Nilesh Patra
Package: wnpp Severity: wishlist Owner: Nilesh Patra X-Debbugs-Cc: debian-de...@lists.debian.org, nil...@debian.org * Package name: r-cran-svmisc Version : 1.1.0 Upstream Author : Philippe Grosjean * URL : https://cran.r-project.org/package=svMisc * License

Bug#986032: ITP: r-bioc-netsam -- Network Seriation And Modularization

2021-03-28 Thread Nilesh Patra
Package: wnpp Severity: wishlist Owner: Nilesh Patra X-Debbugs-Cc: debian-de...@lists.debian.org, nil...@debian.org * Package name: r-bioc-netsam Version : 1.30.0 Upstream Author : Jing Wang * URL : https://bioconductor.org/packages/NetSAM * License : LGPL-2

Bug#985992: ITP: fastani -- Fast alignment-free computation of whole-genome Average Nucleotide Identity

2021-03-27 Thread Nilesh Patra
Package: wnpp Severity: wishlist Owner: Nilesh Patra X-Debbugs-Cc: debian-de...@lists.debian.org, nil...@debian.org * Package name: fastani Version : 1.32-1 Upstream Author : Georgia Institute of Technology * URL : https://github.com/ParBLiSS/FastANI * License

Bug#985988: ITP: r-cran-genoplotr -- Plot Publication-Grade Gene and Genome Maps

2021-03-27 Thread Nilesh Patra
Package: wnpp Severity: wishlist Owner: Nilesh Patra X-Debbugs-Cc: debian-de...@lists.debian.org, nil...@debian.org * Package name: r-cran-genoplotr Version : 0.8.11 Upstream Author : Lionel Guy * URL : https://cran.r-project.org/package=genoPlotR * License

Bug#985931: golang-github-aryann-difflib-dev --

2021-03-26 Thread Nilesh Patra
fix your debian/ dir accordingly. I fixed it above for the ITP subject. Also please note that the subject of ITP includes also a brief description. [1]: https://lists.debian.org/debian-go/2021/03/msg00022.html Cheers, Nilesh

Bug#985945: ITP: nthash -- recursive hash function for hashing all possible k-mers in a DNA/RNA sequence

2021-03-26 Thread Nilesh Patra
Package: wnpp Severity: wishlist Owner: Nilesh Patra X-Debbugs-Cc: debian-de...@lists.debian.org, nil...@debian.org * Package name: nthash Version : 2.2.0-1 Upstream Author : Hamid Mohamadi * URL : https://github.com/bcgsc/ntHash * License : Expat

Bug#985895: Any volunter to write a test for bamclipper?

2021-03-26 Thread Nilesh Patra
On Fri, 26 Mar 2021 at 02:48, Andreas Tille wrote: > I'll do so for every package I'm touching and would have probably done > soon for this package. However, what I would love even more if someone > would fix inject-into-salsa-git to approach this automatically. > I wonder if there is a central

Bug#985895: Any volunter to write a test for bamclipper?

2021-03-25 Thread Nilesh Patra
st a preliminary functioning test :-) I added a autopkgtest to the salsa repo, please take in a look. PS: Please consider enabling salsa CI for any new packages that you might push. I did so for this one for now. [1]: https://github.com/tommyau/bamclipper Nilesh

Bug#984136: fplll: ftbfs with GCC-11

2021-03-21 Thread Nilesh Patra
control: tags -1 patch Fixed in the commit: https://salsa.debian.org/science-team/fplll/-/commit/af75e051c4ffd116b0d7ed0eb1e38dacee913123 and can be uploaded post bullseye release. Nilesh

Bug#985231: [Pkg-javascript-devel] Bug#985231: Bug#985231: TypeError: Cannot use 'in' operator to search for 'dependencies' in ../package.json

2021-03-18 Thread Nilesh Patra
On 18 March 2021 8:22:54 pm IST, Andrius Merkys wrote: >Hello, > >On 2021-03-15 13:45, Pirate Praveen wrote: >> On 2021, മാർച്ച് 15 4:21:37 PM IST, Nilesh Patra >wrote: >>>> $ node-sass >>>> /usr/share/nodejs/normalize-package-data/lib/fix

Bug#984854: fixed in seqsero 1.0.1+dfsg-3

2021-03-17 Thread Nilesh Patra
Pinging the bug in case the autoremoval warning causes a problem

Bug#985410: bioawk FTCBFS -- execute maketab during build

2021-03-17 Thread Nilesh Patra
.f74bbe9 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,3 +1,10 @@ +bioawk (1.0-4) UNRELEASED; urgency=medium + + * d/p/cross.patch: Fix non-cross buildability + * Use dpkg buildtools to set CC and CC_FOR_BUILD + + -- Nilesh Patra Wed, 17 Mar 2021 22:23:42 +0530 + bioawk (1.0-3) un

Bug#985403: bam FTCBFS -- multiple reasons

2021-03-17 Thread Nilesh Patra
On Wed, 17 Mar 2021 at 19:42, Helmut Grohne wrote: > Hi Nilesh, > > On Wed, Mar 17, 2021 at 07:09:28PM +0530, Nilesh Patra wrote: > > --- /dev/null > > +++ b/debian/patches/cross.patch > > @@ -0,0 +1,15 @@ > > +Description: Do not hardcode pkg-config, build

Bug#985403: bam FTCBFS -- multiple reasons

2021-03-17 Thread Nilesh Patra
* It's main script: make_unix.sh hardcodes pkg-config as well as CC as cc by default. The patch attached with the mail fixes it, please consider applying. Nilesh -- System Information: Debian Release: bullseye/sid APT prefers testing APT policy: (500, 'testing') Arch

Bug#985231: [Pkg-javascript-devel] Bug#985231: TypeError: Cannot use 'in' operator to search for 'dependencies' in ../package.json

2021-03-15 Thread Nilesh Patra
node-node-sass is supposed to be used as a library, probably we do not need to vendor this binary: /usr/bin/node-sass -> ../lib/x86_64-linux-gnu/nodejs/node-sass/bin/node-sass Also maybe this bug should be reassigned to node-normalize-package-data? @Team, thoughts? Nilesh

Bug#985300: frogdata -- Mark M-A:foreign

2021-03-15 Thread Nilesh Patra
uploaded. Filing this bug report so this changes does not get lost and can be uploaded after bullseye release. [1]: https://salsa.debian.org/science-team/frogdata/-/commit/4d384dd476d08bf686fcd2fc3b133374b4723928 Nilesh -- System Information: Debian Release: bullseye/sid APT prefers unstable

Bug#985276: unblock: fsm-lite/1.0-5

2021-03-15 Thread Nilesh Patra
Package: release.debian.org Severity: normal User: release.debian@packages.debian.org Usertags: unblock X-Debbugs-Cc: nil...@debian.org, debian-med-packag...@lists.alioth.debian.org Please unblock package fsm-lite (Please provide enough (but not too much) information to help the release team

Bug#985219: xbs -- Fails to build reproducibly due to varying umask

2021-03-14 Thread Nilesh Patra
values result in different permissions for the "runex" example binary. Please either defer this to dh_fixperms, or manually set permissions for this file. The attached patch does that job. Nilesh diff --git a/debian/rules b/debian/rules index 86ab906..5501154 100755 --- a/debian/r

Bug#985210: wordnet -- Fails to build reproducibly

2021-03-14 Thread Nilesh Patra
ense. The patch for the same is commited into salsa here[1] This should be ready for upload after bullseye release. I am reporting bug so that this change is not lost somehow. [1]: https://salsa.debian.org/science-team/wordnet/-/blob/master/debian/patches/make-reproducible.patch Nilesh

Bug#985160: simrisc -- Fails to build reproducibly

2021-03-13 Thread Nilesh Patra
]: https://salsa.debian.org/med-team/simrisc/-/blob/master/debian/patches/make-reproducible.patch Nilesh -- System Information: Debian Release: bullseye/sid APT prefers unstable APT policy: (500, 'unstable'), (1, 'experimental') Architecture: amd64 (x86_64) Kernel: Linux

Bug#852051: libvigraimpex: captures build path (doesn't build reproducible)

2021-03-13 Thread Nilesh Patra
Hi, On Sat, 13 Mar 2021 at 21:23, Andreas Metzler wrote: > On 2021-03-13 Nilesh Patra wrote: > > On Sat, 21 Jan 2017 07:34:35 +0100 Daniel Stender < > deb...@danielstender.com> wrote: > [...] > > > libvigraimpex doesn't build reproducible [1] because the

Bug#985144: pigx-rnaseq -- Fails to build reproducibly: different binaries on usrmerge system

2021-03-13 Thread Nilesh Patra
this change is not lost somehow. [1]: https://salsa.debian.org/med-team/pigx-rnaseq/-/commit/70b31a920f5985c70214f77e47a5e3b26ee42f07 Nilesh -- System Information: Debian Release: bullseye/sid APT prefers unstable APT policy: (500, 'unstable'), (1, 'experimental') Archite

Bug#985143: bmtk -- Fails to build reproducibly

2021-03-13 Thread Nilesh Patra
release. I am reporting bug so that this change is not lost somehow. [1]: https://salsa.debian.org/med-team/bmtk/-/commit/b180351ac09ad816018467a64bfd4b6d9e0c7e05 Nilesh -- System Information: Debian Release: bullseye/sid APT prefers unstable APT policy: (500, 'unstable'), (1, &#x

Bug#852051: libvigraimpex: captures build path (doesn't build reproducible)

2021-03-13 Thread Nilesh Patra
; captured during build [2]. I'll get into this shortly. I know it's been quite a while, but any progress on this one? Please let me know. Nilesh

Bug#985103: src:purify: Uses DEB_BUILD_MULTIARCH for install paths

2021-03-12 Thread Nilesh Patra
i-bin/bugreport.cgi?bug=983219 [2]: https://salsa.debian.org/debian-astro-team/purify/-/commit/dadfde95e14768c66573aa23d4c473fac7558a56 PS: I'll try my best to upload it myself after the release :-) Nilesh -- System Information: Debian Release: bullseye/sid APT prefers unstable APT po

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

2021-03-12 Thread Nilesh Patra
consider adding a check for nocheck profile, and install this file *only* when there is no nocheck. Cheers, Nilesh -- System Information: Debian Release: bullseye/sid APT prefers unstable APT policy: (500, 'unstable'), (1, 'experimental') Architecture: amd64 (x86_64) Kernel:

Bug#985069: seqprep FTCBFS -- multiple reasons

2021-03-12 Thread Nilesh Patra
1]: https://salsa.debian.org/med-team/seqprep/-/commit/8db0a1de9c9abde0d4fd4541e162768d7cac56ad [2]: https://salsa.debian.org/med-team/seqprep/-/commit/314202b3e8c26e937d944172382f46c4dc18a419 Cheers, Nilesh -- System Information: Debian Release: bullseye/sid APT prefers unstable APT policy: (500, '

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

2021-03-12 Thread Nilesh Patra
]: https://salsa.debian.org/med-team/mmseqs2/-/blob/6aa90afc8db6414362d4e2df15e7deedbcc6e1a5/debian/bin/simd-dispatch Nilesh -- System Information: Debian Release: bullseye/sid APT prefers unstable APT policy: (500, 'unstable'), (1, 'experimental') Architecture: amd64 (x86_64) K

Bug#984978: subread FTCBFS -- multiple reasons

2021-03-11 Thread Nilesh Patra
-team/subread/-/commit/589cf53eb9fc82952f41e247548dd7c2b8e11812 [3]: https://salsa.debian.org/med-team/subread/-/commit/f9d90bfa07bdc5c0227df9e17af8a56cb80b082a [4]: https://salsa.debian.org/med-team/subread/-/commit/5c9b138901d065a45134ccf5e458b49084107f8e Nilesh -- System Information: Debian

Bug#984973: mash FTBFS -- multiple reasons

2021-03-11 Thread Nilesh Patra
rg/med-team/mash/-/commit/55c5ce27e6a1f8692ab6d7ec22485e4759c0a7a9 Nilesh -- System Information: Debian Release: bullseye/sid APT prefers unstable APT policy: (500, 'unstable'), (1, 'experimental') Architecture: amd64 (x86_64) Kernel: Linux 5.7.0-2-amd64 (SMP w/8 CPU

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 no

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 funct

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]

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
'm running out of time to finalize this. Discussion for the same has also been done on the mailing list PS: this bug is on new version currently in unstable but *not* in testing, and the bug report will probably not cause any removal warnings. It is however best to fix this bug Best Regards, Nilesh >

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

2021-02-23 Thread Nilesh Patra
e doc package seems to use sphinx for building, python3-sphinx can simply be demoted to Build-Depends-Indep. On doing so, serd cross builds from source. Please consider applying the attached patch. Nilesh diff --git a/debian/control b/debian/control index 351927c..cf8ad1c 100644 --- a/debian/control

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

2021-02-22 Thread Nilesh Patra
only built during an arch-only build, all that needs doing is restricting the usage of the shpinxdoc addon to the indep part. Please consider applying the attached patch. Nilesh diff --git a/debian/control b/debian/control index 02c4c08..3df1f2c 100644 --- a/debian/control +++ b/debian/control

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

2021-02-21 Thread Nilesh Patra
apply this and upload. Nilesh --- a/Makefile +++ b/Makefile @@ -8,7 +8,7 @@ BINDIR ?= $(PREFIX)/bin MANDIR ?= $(PREFIX)/share/man/man1 -INSTALL_PROGRAM ?= install -s +INSTALL_PROGRAM ?= install INSTALL_DATA ?= install X11BASE ?= /usr/X11R6

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 appli

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

2021-02-17 Thread Nilesh Patra
l enough, it's difficult to ascertain if this is intentional or not, (or if it needs another file just for static linking?) Probably first patching gitaly to use libgit2.pc from right location can help us move forward with this. Nilesh

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

2021-02-16 Thread Nilesh Patra
it, please consider applying. Nilesh diff --git a/debian/rules b/debian/rules index 5e67508..9983fbf 100755 --- a/debian/rules +++ b/debian/rules @@ -17,19 +17,18 @@ export DEB_BUILD_MAINT_OPTIONS = hardening=+all # main packaging script based on dh7 syntax %: - dh $@ + dh

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

2021-02-14 Thread Nilesh Patra
ting: simply building on a buster schroot and uploading to buster-backports would work. (Provided that the uploaders is listed on backports.d.o ACL) Nilesh

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

2021-02-11 Thread Nilesh Patra
failure? [1]: https://tests.reproducible-builds.org/debian/history/amd64/igdiscover.html Nilesh

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&arch=amd64&ver=1.12.0%7E20160122-4&stamp=1606151763&raw=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

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 archive

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

2021-02-02 Thread Nilesh Patra
is fixes the argument type mismatch in the csrcsc > call by introducing the one dimension vector iziama of type > real(8), instead of an integer(4) scalar, while trying to > maintain compatibility with Fortran 77. I just granted you DM access for sparskit, please consider to upload it with your patch applied. Nilesh

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

2021-02-01 Thread Nilesh Patra
ce); once that happens, the > rest of the packages are almost ready to go. I requested on IRC (probably again after you) to process these ASAP, however I don't see pyls-server in NEW or at the archive yet. Has this been rejected, or am I missing something? Nilesh > >

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

2021-02-01 Thread Nilesh Patra
om the definition of PYBUILD_AFTER_INSTALL in debian/rules. Please consider to apply the fix if it works, also for #976966 Since freeze is near, it would be unfortunate to loose spyder and spyder-* packages in bullseye. Nilesh

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

2021-02-01 Thread Nilesh Patra
om the definition of PYBUILD_AFTER_INSTALL in debian/rules. Please consider to apply the fix if it works, also for #976966 Since freeze is near, it would be unfortunate to loose spyder and spyder-* packages in bullseye. Nilesh

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

2021-01-31 Thread Nilesh Patra
lso, I do not see apertium-rus-ukr at either the archive or the tracker - did this not get uploaded, yet? Nilesh

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&

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

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 ov

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

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 usually

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

2021-01-03 Thread Nilesh Patra
nd give a green signal, I'll happily upload this package. [1]: https://salsa.debian.org/science-team/apertium-cy-en/-/merge_requests/1/ Thanks and Regards, Nilesh signature.asc Description: OpenPGP digital signature

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

2020-12-31 Thread Nilesh Patra
Package: lua-busted Tags: patch Hi, Please consider adding the attached manpage for the binary: busted Thanks and regards, Nilesh .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16. .TH BUSTED "1" "December 2020" "busted 2.0.0" "Us

Bug#973154: apertium-kaz-tat: FTBFS: hfst-concatenate: .deps/any-symbol.hfst is not a valid transducer file

2020-12-24 Thread Nilesh
------+ Local sources ----- /home/nilesh/packages/kaz/apertium-kaz-tat_0.2.1~r57554-2.dsc exists in /home/nilesh/packages/kaz; copying to chroot I: NOTICE: Log filtering will replace 'build/apertium-kaz-tat-9

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 fail

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
them with bbolt work? This may also need upstream patching in the future. Please let me know Kind Regards, Nilesh signature.asc Description: OpenPGP digital signature

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
fted stuff? Because fundamentally we seem to be making similar changes everywhere. And ofcourse, apologies if this doesn't sound good. > Please also update https://wiki.debian.org/SIMDEverywhere#Packages_Status > & https://wiki.debian.org/SIMDEverywhere#Candidate_packages as you add > SIMDe support to packages. > I'll definitely update this in the next couple of days. Kind Regards, Nilesh

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
ook fine. 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 "Built-Using" field? Thanks and regards Nilesh On Mon, 7 Dec 2020 at 16:19, Nilesh Patra wrote: > Hi Michael > > Th

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
checked the code for xmmintrin.h and indeed the typedef should be included on the above diff simde patch - I've no idea why this doesn't.) On Mon, 7 Dec 2020 at 16:04, Michael Crusoe wrote: > Hey Nilesh, > > No problem for me when you ask for help! > > I suspect that >

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
ory '/home/nilesh/scrappie/scrappie' mkdir build cd build && \ cmake .. -DCMAKE_BUILD_TYPE=Release && \ make -- The C compiler identification is GNU 10.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - ski

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
Control: tags -1 help Hi Debian Arm team, I've no clue of where to even start debugging this. Any help/hints are welcome and highly appreciated. Thanks and regards Nilesh On Sat, 5 Dec 2020 13:51:16 +0100 Lucas Nussbaum wrote: > Source: python-parasail > Version: 1.2.1-1

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
Control: tags -1 help Hi Debian Arm team, I've no clue of where to even start debugging this. Any help/hints are welcome and highly appreciated. Thanks and regards Nilesh On Sat, 5 Dec 2020 13:51:16 +0100 Lucas Nussbaum wrote: > Source: python-parasail > Version: 1.2.1-1 > Sev

Bug#976551: ngmlr: FTBFS on arm64: ConvexAlignFast.cpp:11:10: fatal error: x86intrin.h: No such file or directory

2020-12-06 Thread Nilesh
Control: reopen -1 Control: severity -1 important Re-opeinging since it's not "fundamentally" fixed since it still FTBFS on arm64 I'll hopefully be uploading a proper fix in a while. signature.asc Description: OpenPGP digital signature

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

2020-12-02 Thread Nilesh Patra
d autopkgtest) for that 32-bit arch, but I leave that up to you to check and decide :-) Kind regards Nilesh --- a/include/jellyfish/rectangular_binary_matrix.hpp +++ b/include/jellyfish/rectangular_binary_matrix.hpp @@ -118,7 +118,7 @@ uint64_t *p = _columns; while(*p == 0 &&am

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

2020-11-30 Thread Nilesh Patra
sts :/ The only way to make it reproducible and allow testing migration would be to disable the tests. What do you think would be better? Please let me know. The tests currently are the default autodep8 ones - autopkgtest-pkg-go Best Regards, Nilesh

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

2020-11-21 Thread Nilesh Patra
few days when there are more logs) Nilesh

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

2020-11-21 Thread Nilesh Patra
lure autopkgtest [13:08:27]: test run-unit-test: ---] autopkgtest [13:08:27]: test run-unit-test:  - - - - - - - - - - results - - - - - - - - - - run-unit-test    PASS autopkgtest [13:08:27]: test autodep8-python3: preparing testbed But lets wait for debci results Regards, Nilesh

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
27;s any update regarding this. Nilesh

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

2020-11-09 Thread Nilesh
few days. Thank you for your effort on reproducible builds! Nilesh

Bug#959059: sibelia: autopkgtest arm64 failure: times out after multial.c:459: readSubstMatrix: Assertion `file` failed.

2020-10-26 Thread Nilesh
ipt_pid; set -C; echo > $$ > /tmp/autopkgtest_script_pid; set +C; trap "rm -f > /tmp/autopkgtest_script_pid" EXIT INT QUIT PIPE; cd "$buildtree"; chmod > +x It passes for me in an arm64 schroot. Futher more, it passes even armhf as per CI logs[1]. This creates further suspicion for not passing on arm64 Is this an occasional failure, or am I missing something here? - Please let me know. [1]: https://ci.debian.net/data/autopkgtest/testing/armhf/s/sibelia/7169740/log.gz Kind Regards, Nilesh

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
grant me access to do so. [1]: https://salsa.debian.org/med-team/python-intervaltree-bio Kind regards Nilesh

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
. This will also prevent other packages depending on numba from migrating. [1]: https://salsa.debian.org/science-team/numba/-/blob/debian/master/debian/control#L11 Kind Regards, Nilesh

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

2020-09-20 Thread Nilesh Patra
e unchanged compared to > other CPU architectures, and as far as I could see, they the > same on arm64 (with the patch) and on amd64 (without the patch). > > Changes are available on Salsa for review: > > https://salsa.debian.org/med-team/sweed > > Thanks Paul for having

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

2020-09-20 Thread Nilesh Patra
re - with webpack specifically - and manually creating a symlink helped. I did the same in this case and the build passes with "Buffer: true" I've pushed the commit to the same webpack branch Could you take a look and let me know if it made the situation better/worse? Thanks and Regards, Nilesh

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