Re: Your packaging of sumaclust today

e Debian Med mailing list and > would be really happy if you would answer there. No problem about that, thanks for letting me know. Please believe I did not intend to hide things, but only to reduce noise. Next time I shall use the mailing list. > > On Wed, Apr 01, 2020 at 10:30:42PM +02

Re: Your packaging of sumaclust today

Hi again, Le 02/04/2020 à 10:28, Andreas Tille a écrit : > >> If I may add something: having read the policy some days ago, I feel it >> lacks a kind of ``general habits'' section, like what you explained >> above: is it casual/rude to begin working on a package that already has >> uploaders who u

Re: Your packaging of sumaclust today

Hi Andreas, Le 03/04/2020 à 22:26, Andreas Tille a écrit : > > I tried with a new paragraph at the beginning of "How to Contribute". > Feel free to enhance that text! I think this paragraph clarifies things a lot. Having explained rules this way, there should be less hesitations. > > BTW, just

RFS: sumaclust with autopkgtest

Hi, I have worked on sumaclust and pushed it on salsa [0] with version ``unreleased''. Lines have been suppressed in the last patch because upstream has made the necessary changes so that sumaclust builds. I have also provided autopkgtests, which check the executable works fine in a few simple ca

Re: RFS: sumaclust with autopkgtest

Hi again, Le 04/04/2020 à 10:14, Andreas Tille a écrit : > > I try to put high priority on newcomer contributions so I just take > my time for a review. I can confirm that the tests are passing and > thus we could upload the package as is. Thanks a lot for the quick review! > There is some add

Re: sumatra uploaded using Debian packaged sumalibs

Hi Andreas, Le 09/04/2020 à 14:45, Andreas Tille a écrit : > Hi Pierre, > > as you might have noticed the Debian package for sumalibs was just > accepted. I've now built sumatra against this lib. I'd happily leave > the maintenance of all suma* packages to you. Yes, I noticed that sumalibs was

Re: sumatra uploaded using Debian packaged sumalibs

Hi Andreas, Le 09/04/2020 à 23:01, Andreas Tille a écrit : >> >> My question is: as I understand /4.13 Embedded code copies/ in the Debian >> policy, sumatra and sumaclust should use the libs in sumalibs to build, but >> the code of those libs that is duplicated inside sumaclust should remain >> t

[RFS] Bug fixed in uc-echo

Dear all, I have prepared an upload for the package uc-echo, of which autopkgtest was failing on arm64 due to a (by default unsigned) char type being used to store negative integer values. I will forward this fix to upstream. The package is in its Salsa repository [1]. Thanks in advance for the

Re: [RFS] Bug fixed in uc-echo

Hi Nilesh and Andreas, Le 17/04/2020 à 19:21, Nilesh Patra a écrit : > > > On Fri, 17 Apr 2020, 22:44 Pierre Gruet, <mailto:pgtdeb...@free.fr>> wrote: > > Dear all, > > I have prepared an upload for the package uc-echo, of which autopkgtest > was &g

Re: sumatra uploaded using Debian packaged sumalibs

Hi Andreas, Le 14/04/2020 à 18:53, Andreas Tille a écrit : >> >> If you have time, I would appreciate a review of the three packages, which >> are in their three Salsa repositories. >> >> https://salsa.debian.org/med-team/sumaclust/ >> https://salsa.debian.org/med-team/sumatra >> https://salsa.deb

Re: sumatra uploaded using Debian packaged sumalibs

Hi Andreas, Le 20/04/2020 à 13:00, Andreas Tille a écrit : > Hi Pierre, > > On Mon, Apr 20, 2020 at 11:29:04AM +0200, Pierre Gruet wrote: >> I have just seen that sumalibs has successfully entered unstable and that >> the automatic piuparts warnings have disappeared from i

RFS : new upstream version of jebl2

Hi, I have packaged the new upstream version of jebl2 and made various changes. Now the packaging is in Salsa [1], could someone please check and upload it when time permits? The changes are * New upstream version 0.1+git20190308 * Deleting now useless patch source_8.patch * Bumping Standar

Re: RFS : new upstream version of jebl2

Hi Andreas, Le 24/04/2020 à 22:34, Andreas Tille a écrit : > Hi Pierre, > > thanks a lot for your work. I usually would leave the commit ID inside > the version number (so 0.1+git20190308.a98448e) since this would silence > the new upstream available check - but I guess you thought about this >

Re: RFS : new upstream version of jebl2

Hi Andreas, Le 25/04/2020 à 11:20, Andreas Tille a écrit : > Hi again, > > perhaps also getting > >https://salsa.debian.org/med-team/libsis-jhdf5-java > > done would be helpful. I've pushed latest upstream but did not > found the time to update the old patches to the new version. > Getting

Packaging libsis-jhdf5-java -- help needed

Hi everyone, I have been trying to package libsis-jhdf5-java, after Andreas imported the last upstream version. This package builds a java package with a .jar file and a jni package with native code used by the .jar. I have been able to: - refresh patches; - get rid of the private header H5privat

Re: Packaging libsis-jhdf5-java -- help needed

Hi Gilles, Le 29/04/2020 à 17:53, Gilles Filippini a écrit : > Andreas Tille a écrit le 29/04/2020 à 17:36 : >> Hi Gilles, >> >> On Wed, Apr 29, 2020 at 05:10:38PM +0200, Gilles Filippini wrote: >>> >>> I've cloned the git repo and attempted a build. But the dh_auto_test >>> part doesn't execute a

Re: Packaging libsis-jhdf5-java -- help needed

Hello Gilles, Le 30/04/2020 à 23:17, Gilles Filippini a écrit : >>> >>> Thanks for checking; I had also seen that these tests did not run, this will >>> have to be fixed. More important is the fact that I have put and arranged >>> the piece of code of dh_auto_test override into a test in >>> debia

Re: Packaging libsis-jhdf5-java -- help needed

Hi Gilles, Le 01/05/2020 à 01:12, Gilles Filippini a écrit : > Pierre Gruet a écrit le 30/04/2020 à 23:45 : >> Thanks for looking at the issue and proposing a fix. It is very helpful! >> I will thus look at it and investigate further the failures that remain. > > This packa

Re: Packaging libsis-jhdf5-java -- help needed

Hi Andreas and Gilles, Andreas, I have just seen you uploaded my commits of libsis-jhdf5-java to unstable, thanks for that! I had not written to ask for it as I intended to do further changes before the upload (the script h5ar in /usr/bin should be removed or another jar should be compiled, as h

Re: Packaging libsis-jhdf5-java -- help needed

Hi Andreas, Le 07/05/2020 à 16:26, Andreas Tille a écrit : > On Thu, May 07, 2020 at 09:43:11AM +0200, Andreas Tille wrote: >> I also >> think that observing autobuilders and possibly fix issues there in a >> subsequent upload with your additional changes could be a good idea. > > As expected the

Re: Packaging libsis-jhdf5-java -- help needed

Hi again, Le 07/05/2020 à 16:26, Andreas Tille a écrit : > On Thu, May 07, 2020 at 09:43:11AM +0200, Andreas Tille wrote: >> I also >> think that observing autobuilders and possibly fix issues there in a >> subsequent upload with your additional changes could be a good idea. > > As expected there

Re: Packaging libsis-jhdf5-java -- help needed

Hi Andreas, Le 08/05/2020 à 22:05, Andreas Tille a écrit : > > Very nice. Thanks a lot for your work. I've built and installed the > package. When noticing that there is no manpage for h5ar I intended to > check whether it might be cheap to create one via help2man. However, > this ended up in

Re: Packaging libsis-jhdf5-java -- help needed

Hi Andreas, Le 08/05/2020 à 22:51, Andreas Tille a écrit : > Hi Pierre, > > On Fri, May 08, 2020 at 10:24:47PM +0200, Pierre Gruet wrote: >> >> Absolutely. This is part of the complementary tasks I was planning to do >> (my Salsa push of yesterday was only to fix t

Re: Packaging libsis-jhdf5-java -- help needed

Hi Andreas, Le 08/05/2020 à 22:51, Andreas Tille a écrit : > > If you think you might be able to care for the h5ar binary issue in the > next couple of days I would delay the upload to fix the RC bug. I guess > this will not have any practical drawback if the propagation of this > package to tes

Bug#961158: ITP: distlib -- Java library of statistical distribution functions

Package: wnpp Severity: wishlist Owner: Debian-med project * Package name: distlib Version : 0.9.1 Upstream Author : Peter N. Steinmetz * URL : https://sourceforge.net/projects/statdistlib * License : GPL-2 Programming Lang: Java Description : Java libr

Bug#961158: ITP: distlib -- Java library of statistical distribution functions

Control: retitle -1 ITP: libdistlib-java -- Java library of statistical distribution functions Hi Scott and Andreas, Le 21/05/2020 à 06:44, Scott Kitterman a écrit : > On Thursday, May 21, 2020 12:08:44 AM EDT Andreas Tille wrote: >> At least the name of the binary package should be >> >> l

RFS : libdistlib-java

Hi, I have packaged libdistlib-java, which is a Java implementation of several cdf, pdf, quantile and simulation functions from R, originally written in C. This was announced in ITP bug #961158. Would it be possible to have a review? It would be precious, as this is my first initial packaging! I

Re: RFS : libdistlib-java

Hi Andreas, Le 25/05/2020 à 23:12, Andreas Tille a écrit : > Hi Pierre, > > On Mon, May 25, 2020 at 10:47:58PM +0200, Pierre Gruet wrote: >> I have packaged libdistlib-java, which is a Java implementation of >> several cdf, pdf, quantile and simulation functions from R, ori

Maintaining non-med packages in the team only to satisfy dependencies

Dear all, Lastly I have begun packaging Java software needed as dependencies of snpeff, that we would need in Debian Med as it is related to genes and proteins. I have thus worked on a Java library related to cdf, pdf and random variates generation: libdistlib-java. It is currently in NEW. Now I

Re: Maintaining non-med packages in the team only to satisfy dependencies

Hi Andreas, Le 30/05/2020 à 07:51, Andreas Tille a écrit : > Hi Pierre, > > On Fri, May 29, 2020 at 11:48:39PM +0200, Pierre Gruet wrote: >> >> Lastly I have begun packaging Java software needed as dependencies of >> snpeff, that we would need in Debian Med as

Issue about mutual dependencies for aparapi

Hello everyone, I am currently beginning packaging aparapi, which is a Java API to execute Java code on a GPU. In Debian Med, we need it as dependency of the dependency apfloat of SnpEff. This package relies on a JNI (native code) package which the same upstream develops as aparapi-native. Yet ap

Re: Issue about mutual dependencies for aparapi

Hello, Le 04/06/2020 à 22:36, Thorsten Glaser a écrit : > On Thu, 4 Jun 2020, Mechtilde wrote: > >> This is an outdated information. You can collect all source tar.gz >> together in to one orig.tar.xz. In the d/gbp.conf you configure a > > DON’T DO THAT. > > MUTs (multi-origtgz) were invented f

Re: Any volunteer to spent some time on the new version of artemis (Was: Bug#963430: artemis: FTBFS: /bin/sh: 1: /usr/share/java/j2ssh-core.jar: Permission denied)

Hi Emmanuel, Le 22/06/2020 à 16:30, Andreas Tille a écrit : > Hi Emmanuel, > > On Mon, Jun 22, 2020 at 10:57:15AM -0300, Emmanuel Arias wrote: >> I would be happy to help on artemis. Obviously I will need >> a more experienced developer helping me. :) > > I'll try hard to answer any question you

Bug#963630: ITP: libaparapi-java -- framework for executing native Java code on the GPU

Package: wnpp Severity: wishlist Owner: Debian-med project * Package name: libaparapi-java Version : 2.0.0 Upstream Author : Gary Frost, Syncleus, Inc. * URL : http://aparapi.com/ * License : Apache-2.0 Programming Lang: Java Description : framework for

[RFS] libaparapi-java

Dear all, I have pushed the initial packaging of libaparapi-java to Salsa [0], I would need a review and an upload if time permits. This is a dependency of apfloat (to be packaged), which is a dependency of SpnEff that we would like to get packaged. libaparapi-java builds two binary packages.

Re: [RFS] libaparapi-java

Hi Andreas, Le 25/06/2020 à 22:49, Andreas Tille a écrit : > Hi Pierre, > > On Thu, Jun 25, 2020 at 10:20:46PM +0200, Pierre Gruet wrote: >> I have pushed the initial packaging of libaparapi-java to Salsa [0], I >> would need a review and an upload if time permits. > >

Re: [RFS] libaparapi-java

Hi Andreas, Le 26/06/2020 à 18:14, Andreas Tille a écrit : > On Fri, Jun 26, 2020 at 05:33:30PM +0200, Pierre Gruet wrote: >>> Did you noticed that I've just injected >>> >>> https://salsa.debian.org/java-team/libapfloat-java >>> >>> (and s

RFS : jebl2

Hello everyone, I have packaged the new upstream version of jebl2, available in the repository https://salsa.debian.org/med-team/jebl2 Could you please see and upload? Apart the new upstream version, there is just an update of the compat level. Regards, Pierre

Attributions concern for aparapi (currently in NEW)

Hi, I just realized there was a strange paragraph in the ATTRIBUTIONS.md file in libaparapi-java root folder : https://salsa.debian.org/med-team/libaparapi-java/-/blob/master/ATTRIBUTIONS.md It seems to be restrictive and perhaps annoying for us. Afterwards I saw that Andreas had already rais

About Snpeff packaging (Was : Re: Attributions concern for aparapi (currently in NEW))

Hi Andreas, Le 26/07/2020 à 17:22, Andreas Tille a écrit : > Hi Pierre, > >> >> https://github.com/aparapi/aparapi/issues/50 > > I've pinged that issue. > Thanks! > >> Yet I packaged libaparapi-java and we sent it in NEW, where it currently >> lies. Sorry for not seeing it before. > > Well,

Re: yanosim does not migrate to testing - does anybody understand the missing dependency thingy?

Hi Steffen, Le 27/07/2020 à 12:19, Steffen Möller a écrit : > Hello, > > I had felt much like informing upstream about yanosim in Debian but > somehow it does not migrate. I don't really get this since the build is > just fine. Is it a runtime dependency? And why isn't the site clearly > stating

Re: libgtextutils is marked for autoremoval from testing

Hello, C++11 introduced references on rvalues, which basically allows to use a non-constant reference on a temporary object (ie waiting for affectation). Before, temporary objects could only be references by a const reference. Thus, from there, it becomes a problem to have two implicit conversion

RFS : libgtextutils

Hi, I have prepared an upload of libgtextutils in https://salsa.debian.org/med-team/libgtextutils It solves RC bug #925745 and makes the package lintian-clean. I have also added a C++-filtered symbols file. Could you please review when time permits? All the best, Pierre

Re: RFS : libgtextutils

Hi Andreas, Le 29/07/2020 à 21:52, Andreas Tille a écrit : > Hi Pierre, > > On Wed, Jul 29, 2020 at 05:36:29PM +0200, Pierre Gruet wrote: >> I have prepared an upload of libgtextutils in >> >> https://salsa.debian.org/med-team/libgtextutils >> >> It solv

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

Hi Andreas, Congratulations for getting this opportunity to talk about our work! Personally, I have worked on * Sumaclust (and its close relatives Sumatra and Sumalibs); * Dependencies of Snpeff, which is part of the Covid-19 task. Bye, Pierre Le 28/07/2020 à 08:43, Andreas Tille a écrit : > Hi

Re: About Snpeff packaging (Was : Re: Attributions concern for aparapi (currently in NEW))

Hi Andreas, Le 26/07/2020 à 22:28, Andreas Tille a écrit : > Hi Pierre, > > >> While I am at it: >> - if aparapi cannot enter Debian, I should be able to deactivate the >> module of apfloat that uses it, as this module is not part of the main >> code. I have got a similar issue for the module u

RFS : snap

Hello, I have prepared an upload of snap, fixing the gcc-10 FTBFS: https://salsa.debian.org/med-team/snap I have let 2 Lintian warnings, one of them stating a policy violation due to traversing link usr/lib/debian-med/bin/snap -> usr/bin/snap-hmm . While I understand this link is useful for Debi

[RFS] libdistlib-java

Hi, I have packaged the new upstream version of libdistlib-java (taking into account many of our patches!), which lies in https://salsa.debian.org/med-team/libdistlib-java If time permits, could you please look at it and upload? Many thanks in advance, Pierre

Re: Sepp has build issued (Was: semi-RFS: xenium - good enough for me (at the moment))

this because sun.java2d.SunGraphicsEnvironment API has been deprecated, >> or is it just that it is missing a dependency so it can't import the API? I >> don't know much about Java packages, but if someone could point me in the >> right direction, I might be able to help. &

Re: Sepp has build issued (Was: semi-RFS: xenium - good enough for me (at the moment))

Hi Andreas, Le 14/08/2020 à 23:35, Andreas Tille a écrit : > Hi Pierre, > > On Fri, Aug 14, 2020 at 10:40:28PM +0200, Pierre Gruet wrote: >> I had not heard of this deprecation issue and I don't think it matters >> for us. It only causes warnings. >> >&

Re: [benjamin.redeli...@gmail.com: Bug#968739: igv will not run]

Hi, Le 21/08/2020 à 12:44, Andreas Tille a écrit : > Hi Pierre, > > On Fri, Aug 21, 2020 at 11:32:47AM +0200, Pierre Gruet wrote: >>> I injected the latest upstream version into Git. It does not include so >>> many binary jar's any more but I think its trying t

Re: [benjamin.redeli...@gmail.com: Bug#968739: igv will not run]

Hi Andreas, Le 24/08/2020 à 12:39, Andreas Tille a écrit : > Hi Pierre, > > On Mon, Aug 24, 2020 at 12:08:28PM +0200, Pierre Gruet wrote: >> Contrarily to what I wrote a few days ago, I do not think we are ready >> to remove all included jars in igv. >> For instan

Java packaging in Debian med [Was : Re: [benjamin.redeli...@gmail.com: Bug#968739: igv will not run] ]

Hi Steffen and Andreas, Le 25/08/2020 à 06:35, Andreas Tille a écrit : > On Tue, Aug 25, 2020 at 12:12:04AM +0200, Steffen Möller wrote: >> I created a "Java" tab on our spreadsheet. Would of course be great if >> that sees some momentum. Took the freedom to also add Cytoscape. And if >> I get thi

Re: Java packaging in Debian med [Was : Re: [benjamin.redeli...@gmail.com: Bug#968739: igv will not run] ]

Hi Andreas, Le 26/08/2020 à 07:13, Andreas Tille a écrit : >> >> BTW, snpeff depends on akka-actor, a (Scala+Java) library which still >> has to be packaged, and I am afraid it will be blocked by the version of >> Scala in Debian, itself being stuck to 2.11 as Scala build tool (SBT) >> requires wo

Re: Bug#845113: scala 2.12 released. Please upload version 2.12 ASAP into debian sid, so that it integrates into debian stable 9 stretch

Dear Maintainers, For our information, do you know if it might be possible to unblock the situation soon? Is there some ongoing work on sbt? In Debian-med, we would be interested in having Scala 2.12 or 2.13 to package the pre-dependency akka. Thanks a lot in any case, Best regards, Pierre

[RFS] igv 2.6.3

Hi, I have worked on the packaging of igv 2.6.3+dfsg, which is in https://salsa.debian.org/med-team/igv This igv packaging still relies on its embedded jars. I have solved build issues related to gradle, another one linked to the current version of htsjdk (solves Grave bug on igv), and had to sk

Re: [RFS] igv 2.6.3

Hi Andreas, Le 02/09/2020 à 09:09, Andreas Tille a écrit : > Hi Pierre, > > On Tue, Sep 01, 2020 at 10:54:52PM +0200, Pierre Gruet wrote: >> I have worked on the packaging of igv 2.6.3+dfsg, which is in >> >> https://salsa.debian.org/med-team/igv >> >>

[RFS] artemis

Hi, I have worked on artemis, which required some attention :-) We now have the most recent upstream version and the RC bug is fixed. Upstream now uses Maven for the build, which led to many changes. https://salsa.debian.org/med-team/artemis Could you please review and upload? My key is not in t

Re: libbarclay-java needs update, libpicard-java runtime tests by pigx-scrnaseq

Hi, Le 10/09/2020 à 17:11, Andreas Tille a écrit : > Hi Steffen, > > On Thu, Sep 10, 2020 at 03:32:49PM +0200, Steffen Möller wrote: >> libpicard-java needs an argparse class from the barclay library. This >> was found by the intense build-time testing of the PIGx-scRNAseq. >> ... >> How shall I

Re: libbarclay-java needs update, libpicard-java runtime tests by pigx-scrnaseq

Hi Steffen, Le 11/09/2020 à 02:23, Steffen Möller a écrit : > Hi again, > > On 11.09.20 00:01, Pierre Gruet wrote: >> Hi, >> >> Le 10/09/2020 à 17:11, Andreas Tille a écrit : >>> Hi Steffen, >>> >>> On Thu, Sep 10, 2020 at 03:32:49PM +02

Re: libbarclay-java needs update, libpicard-java runtime tests by pigx-scrnaseq

Hi Steffen, Le 11/09/2020 à 15:27, Steffen Möller a écrit : > Hello again, > > [...] > > and the error prevails when minimizing the invocation as to > > > ~/git/med-team/pigx/pigx-scrnaseq$ /usr/bin/java -XX:ParallelGCThreads=1 > -Xmx4G -Xss16M -Djava.io.tmpdir=/tmp -cp $PICARD_CLASSPATH -j >

Re: Problem when trying to upgrade htsjdk

Hi Andreas, hi everyone, Le 11/09/2020 à 09:08, Andreas Tille a écrit : > Hi, > > I tried to upgrade htsjdk[1] but unfortunately I got some build time > test errors. It would be great if somebody could have a look. > I have looked and tried to build, which succeeded. Then I looked at the log an

Re: Beast-mcmc2 upgrade is missing class net.jsign.JsignTask

Hello, Le 15/09/2020 à 09:02, Andrius Merkys a écrit : > Hello, > > On 2020-09-15 09:50, Andreas Tille wrote: >> Any idea what to do? Seems like a new dependency[2] but I want to make >> sure whether I'm right here and whether we really need this since it >> sounds pretty unrelated to that progr

Re: Git-lfs (Was: RFS: r-bioc-org.mm.eg.db)

Hi, Le 21/09/2020 à 08:43, Andreas Tille a écrit : > Hi again, > > [...] > > I once tried git-lfs for gatk but failed. Could anybody fix the > gatk repository (may be create a new one since as far as I understand > its necessary for git-lfs to declare this at creation time)? I gave > up last y

Re: Fails to build at my side but works somewhere else

tested is indeed one upon which the build results of (Andreas and ci.debian.net) and me are not the same. > >> >> On Mon, Sep 21, 2020 at 11:31:21PM +0200, Pierre Gruet wrote: >>> Thanks for providing me with this log file, it helps. I see 8 >>> failing >>>

Tests failing in many chroots but passing in some others

chroots and got 8 failing tests, which is also the case of ci.debian.net [0]. I would like to know if there have already been such problems with tests failing in some chroots and passing in others; if so, would you have examples or pointers to provide us with? Many thanks in advance, Pierre Gruet

Re: Tests failing in many chroots but passing in some others

Hi Paul, Thanks for the quick answer! Le 22/09/2020 à 22:11, Paul Gevers a écrit : > Hi Pierre, > > On 22-09-2020 21:45, Pierre Gruet wrote: >> Dear Debian CI project members, >> >> In Debian-med we have the package libsis-jhdf5-java. I can build it >> inside o

Re: Fails to build at my side but works somewhere else

Hi Olivier and Andreas, Le 23/09/2020 à 09:27, Andreas Tille a écrit : > On Wed, Sep 23, 2020 at 08:08:01AM +0200, olivier sallou wrote: >>> Given that you also have detailed knowledge in Java do you feel able >>> to >>> fix those 8 issues? That would really help several other packages. >> >> I h

Re: dependencies on new packages

Hi, Le 24/09/2020 à 11:27, Andrius Merkys a écrit : > Hi Maarten, > > On 2020-09-24 12:21, Maarten L. Hekkelman wrote: >> Suppose you want to submit two separate packages and one depends on the >> other, do you have to wait with the second until the first has been >> accepted and uploaded? Given

[RFS] libdistlib-java and charts4j

Hi, I have fixed some missing classpath entries for libdistlib-java and I need to do a source-only upload for charts4j, which has just exited NEW. Would you mine either reviewing them [0] [1] or giving me DM rights? dcut dm --uid "Pierre Gruet" --allow libdistlib-java charts4j (n

Re: [RFS] libdistlib-java and charts4j

Hi Andreas, Le 25/09/2020 à 11:22, Andreas Tille a écrit : > Hi Pierre, > > On Fri, Sep 25, 2020 at 07:50:13AM +0200, Pierre Gruet wrote: >> >> I have fixed some missing classpath entries for libdistlib-java and I >> need to do a source-only upload for charts4j

Re: Git-lfs (Was: RFS: r-bioc-org.mm.eg.db)

Hi Andreas, Le 21/09/2020 à 13:34, Andreas Tille a écrit : > Hi Pierre, > > On Mon, Sep 21, 2020 at 10:32:54AM +0200, Pierre Gruet wrote: >> Le 21/09/2020 à 08:43, Andreas Tille a écrit : >> >> Some days ago, I worked on gatk. The most recent upstream tarball is >

Re: Beast-mcmc2 upgrade is missing class net.jsign.JsignTask

Hi, Le 21/09/2020 à 09:01, Andreas Tille a écrit : > On Tue, Sep 15, 2020 at 04:04:49PM -0400, Aaron M. Ucko wrote: >> Andrius Merkys writes: >> >>> AFAIR, buildds are not guaranteed to have running X sessions, thus I >>> suggest skipping these tests (most likely by using patches). >> >> For test

Re: Beast-mcmc2 upgrade is missing class net.jsign.JsignTask

Hi Andreas, Le 28/09/2020 à 19:47, Andreas Tille a écrit : > Hi Pierre, > > On Mon, Sep 28, 2020 at 06:07:43PM +0200, Pierre Gruet wrote: >>> That's true but according to my experience the issue did not occured >>> on the build daemons. >>> >>> A

Re: Beast-mcmc2 upgrade is missing class net.jsign.JsignTask

Hi again Andreas, Le 28/09/2020 à 21:36, Andreas Tille a écrit : > On Mon, Sep 28, 2020 at 08:23:11PM +0200, Pierre Gruet wrote: > >> I have a question about "best practices": last uploaded version of >> beast2-mcmc is 2.6.3+dfsg-2, but I will need to repack t

Re: Beast-mcmc2 upgrade is missing class net.jsign.JsignTask

Hi Andrius, Le 29/09/2020 à 07:57, Andrius Merkys a écrit : > Hi Pierre, > > On 2020-09-28 22:47, Pierre Gruet wrote: >> Thanks for your advice! Nevertheless, this seems to rank before the >> current version number, as >> >> echo "2.6.3+dfsg-2,2.6.3+dfsg1-

[RFS] beast2-mcmc

Hi, I have worked on beast2-mcmc: autopkgtests have been added, which came along with some patches. Would you mind either reviewing [0] or giving me DM rights? dcut dm --uid "Pierre Gruet" --allow beast2-mcmc Thanks a lot in advance, Pierre [0] https://salsa.debian.org/med-team/beast2-mcmc

Sepp : including a dataset?

Hi, I have almost finished the initial packaging of sepp [0]. Beside the sepp program, upstream also provides the tipp program in the same tarball. Basically, tipp classifies sequences using sepp and a collection of alignments and placements data and statistical methods. People installing tipp are

Re: Sepp : including a dataset?

Hi Andreas, Le 07/10/2020 à 22:43, Andreas Tille a écrit : > Hi Pierre, > > On Wed, Oct 07, 2020 at 10:30:34PM +0200, Pierre Gruet wrote: >> I have almost finished the initial packaging of sepp [0]. Beside the >> sepp program, upstream also provides the tipp program i

Bug#971870: ITP: sepp -- methods using ensembles of Hidden Markov Models (HMM)

Package: wnpp Severity: wishlist Owner: Debian-med project X-Debbugs-Cc: debian-de...@lists.debian.org, debian-med@lists.debian.org * Package name: sepp Version : 4.3.10 Upstream Author : Siavash Mirarab * URL : https://github.com/smirarab/sepp/ * License : GP

[RFS] sepp

Hi, I have finished the initial packaging of sepp [0]. Could someone please review it and sponsor if everything is OK? As discussed recently on the list, the binary package sepp includes programs called sepp and tipp, the last one needing the user to download a given dataset to be run. This is do

Re: [RFS] sepp

Hi Andreas and Steffen, Le 09/10/2020 à 18:37, Steffen Möller a écrit : > ;) You win! > > Thanks! > > Steffen > > On 09.10.20 18:33, Andreas Tille wrote: >> On Fri, Oct 09, 2020 at 06:32:55PM +0200, Steffen Möller wrote: >>> @Andreas et al., I'll happily sponsor. >> Ups, just receiving this. I

[RFS] jebl2

Hi, I have worked on jebl2 which has a new upstream version. Would you mind either reviewing [0] or giving me DM rights? dcut dm --uid "Pierre Gruet" --allow jebl2 Thanks a lot in advance, Pierre [0] https://salsa.debian.org/med-team/jebl2

Re: [RFS] jebl2

Hi Andreas, Le 13/10/2020 à 09:40, Andreas Tille a écrit : > Hi Pierre, > > On Mon, Oct 12, 2020 at 09:34:04PM +0200, Pierre Gruet wrote: >> I have worked on jebl2 which has a new upstream version. > > Ahhh, I did so yesterday evening without actually reading your ma

Re: Tests failing in many chroots but passing in some others

Hi Paul, Le 22/09/2020 à 22:11, Paul Gevers a écrit : > Hi Pierre, > > On 22-09-2020 21:45, Pierre Gruet wrote: >> Dear Debian CI project members, >> >> In Debian-med we have the package libsis-jhdf5-java. I can build it >> inside or outside a chroot on my

Bug#972554: ITP: icb-utils -- Java library of utilities to manage files and compute statistics

Package: wnpp Severity: wishlist Owner: Debian-med project X-Debbugs-Cc: debian-de...@lists.debian.org, debian-med@lists.debian.org * Package name: icb-utils Version : 2.0.1+git20161002.afee1d9 Upstream Author : Fabien Campagne * URL : https://github.com/CampagneLabora

[RFS] icb-utils

Hello, I have prepared the package icb-utils [0], which is a dependency of goby, itself needed to move igv from non-free to main... It is a NEW source package and thus would need a review and upload when time permits. Thanks a lot in advance, Pierre [0] https://salsa.debian.org/med-team/icb-ut

[RFS] icb-utils

Hello, icb-utils has just exited NEW; I have prepared a source-only upload. Would you mind either reviewing [0] or giving me DM rights? dcut dm --uid "Pierre Gruet" --allow icb-utils Thanks a lot in advance, Pierre [0] https://salsa.debian.org:med-team/icb-utils

Bug#973568: ITP: libpj-java -- API and middleware for parallel programming in Java

Package: wnpp Severity: wishlist Owner: Debian-med project X-Debbugs-Cc: debian-de...@lists.debian.org, debian-med@lists.debian.org * Package name: libpj-java Version : 20150107 Upstream Author : Alan Kaminsky * URL : https://www.cs.rit.edu/~ark/pj.shtml * License

[RFS] libpj-java

Hi, I have prepared the initial packaging of libpj-java, a dependency of goby (needed for igv). If someone would have time to review it [0] and upload if convenient, it would be great :) Thanks a lot, Pierre [0] https://salsa.debian.org/med-team/libpj-java

Bug#963630: RFS-ing libaparapi-java due to licensing issues at the moment

considering packaging aparapi itself, but it would impose restrictions on other software that might be bundled with it. We will discuss it with upstream and consider packaging later. Pierre Gruet

Bug#963630: RFP-ing libaparapi-java due to licensing issues at the moment

not seem to be harming when considering packaging aparapi itself, but it would impose restrictions on other software that might be bundled with it. We will discuss it with upstream and consider packaging later. Pierre Gruet

[RFS] igv

Hi everyone, I have fixed the RC bug in igv. Would you mind either reviewing [0] or giving me DM rights? dcut dm --uid "Pierre Gruet" --allow igv Thanks a lot, Pierre [0] https://salsa.debian.org/med-team/igv

[RFS] artemis

Hi, artemis had only a superficial autopkgtest not marked as such. I have marked it and provided another autopkgtest running some build tests. Would you mind either reviewing [0] or giving me DM rights? dcut dm --uid "Pierre Gruet" --allow artemis Thanks a lot, Pierre

Re: Help to finalise libjloda-java needed

Hi Andreas, Le 18/11/2020 à 11:09, Andreas Tille a écrit : > Hi Pierre (and others) > > I tried to update libjloda-java but the build fails with > > ... > compile: > [javac] Compiling 360 source files to > /build/libjloda-java-2.0/antbuild/modules/jloda > [javac] error: the unnamed mod

Re: Help to finalise libjloda-java needed

Hi again, Le 18/11/2020 à 15:59, Pierre Gruet a écrit : > Hi Andreas, > > > Le 18/11/2020 à 11:09, Andreas Tille a écrit : >> Hi Pierre (and others) >> >> I tried to update libjloda-java but the build fails with >> >> ... >> compile: >>

Progress of Snpeff packaging (Was: Re: /usr/bin/picard Re: bcbio will need another while - needs gatk)

Hi, Le 15/11/2020 à 18:16, Andreas Tille a écrit : > >> >> This may be worth a sidenote - bcbio to me is something metaphorical. We >> have it in the distribution already. And now we work to get all the >> runtime-dependencies in to make it functional. And snpEff is pretty high >> up (it interpre

Re: libsis-jhdf5-java hasn't migrated to testing since last 18 days

Hi Nilesh and Andreas, Le 26/11/2020 à 17:14, Andreas Tille a écrit : Hi Nilesh, On Thu, Nov 26, 2020 at 06:00:38PM +0530, Nilesh Patra wrote: It seems that libsis-jhdf5-java hasn't migrated to testing due to build failure on s390x, log attached[1] This is preventing a chain of other packages

Packaging Jalview -- any general guidelines concerning privacy?

Hello, I'm currently on the packaging of Jalview. I would like to get some advice as Jalview upstream is collecting statistics on its use through the Internet. Basically this amounts to 4 things, I'm quoting/commenting their documentation: - HTTP logs on the Jalview website We record IP

Re: Packaging Jalview -- any general guidelines concerning privacy?

Hi Andreas, Le 27/11/2020 à 09:22, Andreas Tille a écrit : Hi Pierre, On Thu, Nov 26, 2020 at 10:11:14PM +0100, Pierre Gruet wrote: >> [...]>> - HTTP logs on the Jalview website We record IP addresses of machines which access the web site, either via the browser when dow

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