Re: Outreachy applicant

rg/sbuild [2]: https://wiki.debian.org/sbuild#Using_sbuild-debian-developer-setup [3]: https://salsa.debian.org/med-team > > On Fri, Apr 2, 2021 at 12:06 AM mehaboob shariff > wrote: > >> Thank you Pranav >> Message received. I will have a look at the page and get back

Re: Outreachy applicant

Hi, Thanks for your interest in working with Debian Med. Our main communication channel is this mailing list, so I'm also forwarding our communication here. I hope that's okay with you. I have recently added some more information to the Outreachy project page, including some application tasks and

RFS: pbdagcon

Hi, I've added autopkgtests to pbdagcon. Please review and sponsor. https://salsa.debian.org/med-team/pbdagcon Regards, Pranav ᐧ

Re: Please list your contributions to COVID-19 sprint as intput for my DebConf20 talk

Hi Andreas, Here are my contributions during Debian Med Sprints: Sprint 1 (April 5 - 11) New packages: * trinculo * r-bioc-htsfilter Sprint 2 (June 15-21) Added autopkgtests: * ivar * drop-seq * flash * pilon * ngmlr * wham-align Sprint 3 (August 16-22) Added autopkgtests: * bio-rainbow *

RFS: rampler

Hi, I've added autopkgtests to rampler. Please review and sponsor. https://salsa.debian.org/med-team/rampler Regards, Pranav ᐧ

RFS: maffilter

Hi, I've added autopkgtests to maffilter. Please review and sponsor. https://salsa.debian.org/med-team/maffilter Regards, Pranav ᐧ

RFS: bio-rainbow

Hi, I've added autopkgtests to bio-rainbow. Please review and sponsor. https://salsa.debian.org/med-team/bio-rainbow Regards, Pranav ᐧ

Re: semi-RFS: xenium - good enough for me (at the moment)

Hi, I was writing autopkgtests for busco and noticed that sepp is indeed a dependency. I tried continuing the packaging work for sepp, and I found a TODO in the changelog with the following: [javac] Note: Some input files use or override a deprecated API. [javac] Note: Recompile with

Re: ampliconnoise openmpi issue in autopkgtest

Hi Andreas, On Fri, Jul 24, 2020 at 12:29 PM Andreas Tille wrote: > Hi Pranav, > > seems ampliconnoise will keep us busy longer than other packages. The > fact that now no extra data are shipped somehow made my motivation to > put them into an extra package somehow void. So I reverted this

RFS: rdp-readseq

Hi, I've added autopkgtests to rdp-readseq. Please review and sponsor. https://salsa.debian.org/med-team/rdp-readseq Regards, Pranav ᐧ

Re: RFS: probabel and jmodeltest

Hi Andreas, On Tue, Aug 4, 2020 at 12:25 PM Andreas Tille wrote: > On Mon, Aug 03, 2020 at 09:15:37PM +0530, Pranav Ballaney wrote: > > I've added autopkgtests to probabel. > > Just rebuilding after adding DEP3 headers (please remember to add at > least fields Au

RFS: probabel and jmodeltest

Hi, I've added autopkgtests to probabel. However, since jmodeltest runs in a GUI, I am unable to write tests but I found that just to run it, two dependencies had to be installed, so I have added both. Please review and sponsor. https://salsa.debian.org/med-team/probabel

Re: RFS: king-probe

. Please review and sponsor. https://salsa.debian.org/med-team/king-probe Regards, Pranav On Wed, Jul 15, 2020 at 8:53 PM Pranav Ballaney wrote: > Hi, > I've added autopkgtests to king-probe [1], along with some information > about their sources in debian/README.test. > I've also list

RFS: dazzdb

Hi, I've added autopkgtests to dazzdb. Please review and sponsor. https://salsa.debian.org/med-team/dazzdb Regards, Pranav ᐧ

RFS: king-probe

Hi, I've added autopkgtests to king-probe [1], along with some information about their sources in debian/README.test. I've also listed them in d/copyright but I don't know which license to use for PDB files that I've used as input data. According to the wwPDB Usage Policy [2], "Data files

Re: RFS: ampliconnoise

ymlink-points-to-foreign-package Am I doing something wrong here? Regards, Pranav On Fri, Jul 10, 2020 at 8:10 PM Andreas Tille wrote: > Hi Pranav, > > (and list) > > On Fri, Jul 10, 2020 at 07:35:44PM +0530, Pranav Ballaney wrote: > > Thanks for uploading it! Would

Re: RFS: snap-aligner

tream source that lintian now > notices. > > Uploaded. Thanks! > > > On Thu, Jul 9, 2020 at 8:52 AM Pranav Ballaney > wrote: > >> Hi, >> I've added autopkgtests to snap-aligner. Please review and sponsor. >> https://salsa.debian.org/med-team/snap-aligner >> >> Regards, >> Pranav >> ᐧ >> >

RFS: ampliconnoise

Hi, I've added autopkgtests to ampliconnoise. Please review and sponsor. https://salsa.debian.org/med-team/ampliconnoise Regards, Pranav ᐧ

RFS: snap-aligner

Hi, I've added autopkgtests to snap-aligner. Please review and sponsor. https://salsa.debian.org/med-team/snap-aligner Regards, Pranav ᐧ

RFS: edtsurf

Hi, While adding autopkgtests to EDTSurf, I noticed that it returns 1 on successful execution, which breaks autopkgtests. So along with the autopkgtests, I've added a patch to fix this. It seems safe to make this change purely by looking at the code and I can't find any documentation anywhere.

RFS: jaligner

Hi, I've added autopkgtests to jaligner. Please review and sponsor. https://salsa.debian.org/med-team/jaligner Regards, Pranav ᐧ

Re: marginphase ready for upload

Hi Shayan and Andreas, I found a paper on marginphase which I've added to upstream/metadata. https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1709-0 I've also written a short description using excerpts from this paper and added it to d/control. Hope this helps. Regards, Pranav

RFS: maqview

Hi, I've added autopkgtests to maqview. Please review and sponsor. https://salsa.debian.org/med-team/maqview Regards, Pranav ᐧ

Need some help with bbmap

Hi, I was trying to add autopkgtests to bbmap [1] but I'm having some trouble getting it to work. Here is the command I'm trying to run along with the output (and I've attached the input file with this email). > bbduk.sh in=SRR1753664_1.min.fastq out=clean1.fq /usr/bin/bbduk.sh: line 348:

RFS: nanook

Hi, I've added autopkgtests to nanook. Please review and sponsor. https://salsa.debian.org/med-team/nanook Regards, Pranav ᐧ

RFS: wham-align

Hi, I've added autopkgtests to wham-align. Please review and sponsor. https://salsa.debian.org/med-team/wham-align Regards, Pranav ᐧ

RFS: pilon

Hi, I've added autopkgtests to pilon. Please review and sponsor. https://salsa.debian.org/med-team/pilon Regards, Pranav ᐧ

RFS: flash

Hi, I've added autopkgtests to flash. Please review and sponsor. https://salsa.debian.org/med-team/flash Regards, Pranav ᐧ

RFS: ivar

Hi, I've added autopkgtests to ivar. Please review and sponsor. https://salsa.debian.org/med-team/ivar Regards, Pranav ᐧ

RFS: drop-seq

Hi, I've added autopkgtests to drop-seq. Please review and sponsor. https://salsa.debian.org/med-team/drop-seq Regards, Pranav ᐧ

Re: RFS: indelible

> Hi Pranav, > > > > Wow, you have quite the bash skills. I can't run things locally at the > > moment, but I think it looks fine. Fingers crossed, it works > > consistently across architectures. > > > > Can s.o. please sponsor an upload? > > > >

RFS: mapsembler2

Hi, I've added reference data and autopkgtests to mapsembler2. All tests pass in a clean chroot. Please review and sponsor. https://salsa.debian.org/med-team/mapsembler2 Regards, Pranav ᐧ

RFS: cluster3

Hi, I've added reference data and autopkgtests to cluster3. All tests pass in a clean chroot. Please review and sponsor. https://salsa.debian.org/med-team/cluster3 Regards, Pranav ᐧ

RFS: bppsuite

Hi, I've added reference data and autopkgtests to bppsuite. All tests pass in a clean chroot. Please review and sponsor. https://salsa.debian.org/med-team/bppsuite Regards, Pranav ᐧ

Re: RFS: indelible

, but would be could if we had that. > > Best, > Fabian > > > On 11.06.20 21:28, Pranav Ballaney wrote: > > Hi, > > I've added autopkgtests to indelible. Please review and sponsor. > > https://salsa.debian.org/med-team/indelible > > > > Regards, > > Pranav > > ᐧ > >

RFS: indelible

Hi, I've added autopkgtests to indelible. Please review and sponsor. https://salsa.debian.org/med-team/indelible Regards, Pranav ᐧ

Fixed Bug#960760: tree-puzzle FTBFS on !amd64: test failures

Hi, I've pushed a patch for tree-puzzle to fix #960760. Please review. https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=960760 https://salsa.debian.org/med-team/tree-puzzle Regards, Pranav ᐧ

Re: pll-modules tests failing

Hi, I've committed a few changes to 2to3.patch along with a test.patch file that I used to try and debug this. It reports the following errors while running test/runtest.py: obj/binary/binary-random: error while loading shared libraries: libpll_binary.so.0: cannot open shared object file: No such

RFS: norsp

Hi, I've added autopkgtests to norsp. pp-popularity-contest was listed earlier as a suggestion, but norsp wasn't working without it, so I've listed it as a dependency. Please review and sponsor. https://salsa.debian.org/med-team/norsp Regards, Pranav ᐧ

RFS: seer

Hi, I've added autopkgtests to seer. Please review and sponsor. https://salsa.debian.org/med-team/seer Regards, Pranav ᐧ

RFS: freebayes

Hi, I've added autopkgtests to freebayes. Please review and sponsor. https://salsa.debian.org/med-team/freebayes Regards, Pranav PS. There was an issue with debian/rules and test/t/00*.t due to which the build was failing on my system (and I managed to fix it), but since the build logs are

RFS: bandage

Hi, I've added autopkgtests to bandage. Please review and sponsor. https://salsa.debian.org/med-team/bandage Regards, Pranav ᐧ

RFS: paml

Hi, I've added autopkgtests to paml. Please review and sponsor. https://salsa.debian.org/med-team/paml Regards, Pranav ᐧ

Re: loki2.4.x for binary traits

Hi Wouter, I think some support has been introduced for qualitative traits as well from version 2.4 onwards, but the description has not been updated. The original website of the package is not accessible anymore, but please take a look at this archived version,

Re: RFS: transrate-tools

Hi Andreas, Sure, I'll keep that in mind for next time. Thanks a lot! Regards, Pranav On Mon, 25 May, 2020, 2:07 PM Andreas Tille, wrote: > Hi Pranav, > > On Mon, May 25, 2020 at 01:38:34AM +0530, Pranav Ballaney wrote: > > I've added autopkgtests to transrate-tools. Please rev

RFS: transrate-tools

Hi, I've added autopkgtests to transrate-tools. Please review and sponsor. https://salsa.debian.org/med-team/transrate-tools Regards, Pranav ᐧ

RFS: libsmithwaterman

Hi, I've added autopkgtests to libsmithwaterman. Please review and sponsor. https://salsa.debian.org/med-team/libsmithwaterman Regards, Pranav ᐧ

Patch to avoid segfault in kallisto

Hi, I investigated the segfault issue in kallisto, and found a fix for it. Details can be found at https://github.com/pachterlab/kallisto/issues/254#issuecomment-629546051 I've written a patch to avoid the segfault, for the time being, until upstream fixes it. Please take a look.

RFS: Tree-puzzle tests updated

Hi, I've confirmed from upstream for tree-puzzle that the failing tests were only due to formatting and rounding changes in the tests/check* files. I've pushed a patch to update these files and also added autopkgtests. Please review and sponsor. https://salsa.debian.org/med-team/tree-puzzle

Re: RFS: gasic

, bowtie will no longer be required to test gasic, so these tests should pass for you as well, now. Regards, Pranav On Wed, 13 May, 2020, 12:59 PM Andreas Tille, wrote: > Hi Pranav, > > On Wed, May 13, 2020 at 02:47:11AM +0530, Pranav Ballaney wrote: > > Hi Andreas, > > I've c

Re: RFS: gasic

On Sun, May 10, 2020 at 10:53 AM Andreas Tille wrote: > Hi Pranav, > > On Sun, May 10, 2020 at 02:58:32AM +0530, Pranav Ballaney wrote: > > I've added autopkgtests to gasic. Please review and sponsor. > > https://salsa.debian.org/med-team/gasic/ > > thank you for addi

RFS: fitgcp

Hi, While adding autopkgtests for fitgcp, I ran into several bugs - some of which are changes that 2to3 probably missed. I've pushed a patch along with the tests. Please review and sponsor. https://salsa.debian.org/med-team/fitgcp Regards, Pranav ᐧ

Re: RFS: cgview

Hi Andreas, On Sun, May 10, 2020 at 1:21 AM Andreas Tille wrote: > Hi Pranav, > > On Sat, May 09, 2020 at 09:54:56PM +0530, Pranav Ballaney wrote: > > I've added autopkgtests to cgview. Since the output is an image, I > haven't > > compared it to a reference -

RFS: gasic

Hi, I've added autopkgtests to gasic. Please review and sponsor. https://salsa.debian.org/med-team/gasic/ Regards, Pranav ᐧ

RFS: cgview

Hi, I've added autopkgtests to cgview. Since the output is an image, I haven't compared it to a reference - is that alright? If not, how do we usually test packages like this? I tried running a diff but that reported the files to be different, even though they were visually the same. Please take

Re: RFS: parsnp

Hi Andreas, On Thu, May 7, 2020 at 10:04 AM Andreas Tille wrote: > Hi Pranav, > > On Thu, May 07, 2020 at 06:12:03AM +0530, Pranav Ballaney wrote: > > I've added autopkgtests to parsnp, and also a missing dependency: > > harvest-tools. > > This also fixes an i

RFS: parsnp

Hi, I've added autopkgtests to parsnp, and also a missing dependency: harvest-tools. This also fixes an issue raised here: https://github.com/marbl/parsnp/issues/58 Please review and sponsor. https://salsa.debian.org/med-team/parsnp/ Regards, Pranav ᐧ

RFS: ncbi-entrez-direct

Hi, I've added autopkgtests to ncbi-entrez-direct. Since autopkgtests don't always run in an environment with an internet connection, most of the programs in this package can't be tested. I've added tests for all the programs that run locally. Please review and sponsor.

Re: Welcoming GSoC students

Thank you so much, and congratulations to you too, Nilesh! It's always been wonderful working with the Med team and I'm glad to finally be a part of GSoC as well! Regards, Pranav On Tue, 5 May, 2020, 10:34 AM Andreas Tille, wrote: > Hi, > > I'm hereby welcoming > >

RFS: hunspell-en-med

Hi, I've added autopkgtests to hunspell-en-med. Please review and sponsor. https://salsa.debian.org/med-team/hunspell-en-med Regards, Pranav ᐧ

Re: Can someone habe a look at bioperl-run in connection with kalign (was: bioperl-run is marked for autoremoval from testing]

Hi, Yes, Kalign is on v3 now. I've pushed some patches to fix this bug. All build-time tests pass now. Autopkgtests don't, however, but that issue seems to be unrelated. Please take a look at https://salsa.debian.org/med-team/bioperl-run and verify the patches. This is my first time working with

Re: Autopkgtest fails (Was: Kalign3)

On Fri, Mar 20, 2020 at 1:38 AM Nilesh Patra wrote: > Just checked. My best guess here is that -i invokes interaction, which > won't work in a chroot. > The best way to pass input inside a chroot is via either STDIN, or > redirecting input with pipes. > > Also > Just a suggestion: Autopkgtests

Request for sponsorship: Added autopkgtests for sortmerna

Hi, I have added autopkgtests for sortmerna. Please review and sponsor. https://salsa.debian.org/med-team/sortmerna Regards, Pranav ᐧ

Re: Autopkgtest fails (Was: Kalign3)

Hi Andreas, I've added some more tests to kalign, but there's a slight problem. As specified in the README file, kalign supports two ways of taking input: one is through stdin and the other through the -i flag (or even without it). For some reason, all tests using the -i flag fail inside my

Re: Bug#909716: Request for sponsoring changes in idba

Hi Andreas, On Tue, 10 Mar, 2020, 9:21 PM Andreas Tille, wrote: > > Fine. That works. Sorry when I have given a bit short-cutted advise. > I've completed the long description. > Oh sorry I missed. Actually I changed it at first but it didn't work so I went back and forth a few times and

Re: [GSoC] Re: Help with the package medicalterms

Hi Andreas, On Tue, Mar 10, 2020 at 4:03 PM Andreas Tille wrote: > Hi Pranav, > So, one of the binaries in this package is a dictionary for hunspell, but > > debian/control doesn't list hunspell as a dependency. > > Ahhh, nice catch! Things like this are the reason why we add those tests! > >

Re: [GSoC] Re: Help with the package medicalterms

Hi Andreas and Samyak, Coincidentally, I had also been working on medicalterms. So, one of the binaries in this package is a dictionary for hunspell, but debian/control doesn't list hunspell as a dependency. The dependencies listed are other dictionaries, so the actual program isn't installed, and

Re: Bug#909716: Request for sponsoring changes in idba

Hi Andreas, On Sun, Mar 8, 2020 at 12:54 PM Andreas Tille wrote: > Hi Pranav, > I hope you are happy with your result. > Thank you, they went quite well. May be adding some binary package idba-extra (or some better name you > might find) to ship these additional tools that might be not needed

Re: Request for sponsoring changes in idba

Hi Andreas, My mid-sem exams are over now, and I can resume work on idba. On Mon, Feb 24, 2020 at 2:21 PM Andreas Tille wrote: I'm now realising that idba build system builds a lot of other tools > inside $(CURDIR)/bin which might (or might not?) be sensible to install. > Yes, there are over

Re: Failure in autopkgtest for loki (Was: Working tests seem to exist for epcr)

ere the test failed (for whatever reason). >> >> So thanks for your work on this >> >> Andreas. >> >> On Mon, Feb 24, 2020 at 09:02:23AM +0100, Andreas Tille wrote: >> > Hi Pranav, >> > >> > On Sun, Feb 23, 2020 at 03:14:49PM +053

Re: Failure in autopkgtest for loki (Was: Working tests seem to exist for epcr)

Hi Andreas, On Sat, Feb 22, 2020 at 12:39 PM Andreas Tille wrote: > Hi Pranav, > > I need to admit that your contributions had a high level and its hard to > believe for me that its your first time contributing to open source. > I'm always happy to see competent students in GSoC. > Thank you

Request for sponsoring changes in idba

Hi, I have added autopkgtests for idba . (Closes #909716 ) I need a few suggestions on how these tests can be improved. 1. The test data can be generated using the sim_reads command that comes with the package, but for

Re: Working tests seem to exist for epcr

Hi Andreas, On Thu, Feb 20, 2020 at 8:40 PM Andreas Tille wrote: > Hi Pranav, > > On Thu, Feb 20, 2020 at 10:30:58PM +0530, Pranav Ballaney wrote: > > Hi Andreas, > > Thanks for looking into this and sending the guide about packages. > > I saw the CI page for epcr, a

Re: Failure in autopkgtest for loki (Was: Working tests seem to exist for epcr)

y only to the list. > On Fri, Feb 21, 2020 at 12:42:10PM +0530, Pranav Ballaney wrote: > > Hi Andreas, > > Thanks for taking the time out to look into my work. > > You are perfectly welcome. On one hand I see this as my duty as a > (pontential) GSoC mentor. On the other

Re: Failure in autopkgtest for loki (Was: Working tests seem to exist for epcr)

Hi Andreas, Thanks for taking the time out to look into my work. On Fri, Feb 21, 2020 at 1:54 AM Andreas Tille wrote: > Hi Pranav, > > On Thu, Feb 20, 2020 at 10:30:58PM +0530, Pranav Ballaney wrote: > > other day, and I've now added to loki > > <https://salsa.debian.or

Re: Working tests seem to exist for epcr

bin/bugreport.cgi?bug=909710>) be marked closed? Or is it enough if the tests are working on my local machine, and can I close them right away? Thanks a lot for your help. Pranav On Tue, Feb 18, 2020 at 8:35 PM Andreas Tille wrote: > Hi Pranav, > > On Tue, Feb 18, 2020 at 05:07:44PM +0

Working tests seem to exist for epcr

Hello, I am Pranav Ballaney, a Biology and Computer Science student from India, and I have recently joined the Debian Med team, primarily writing autopkgtests for various packages. I tried running the tests present in this package, and they seem to work well on my local machine. Can this bug