Re: Status of sbt package

2019-09-10 Thread merkys
Hi Frédéric and Thomas, Sorry for the delay. I must admit I wasn't aware the dogfooding problem is so difficult to avoid. On 2019-08-17 07:53, Thomas Finneid wrote: > The good news is that after talking with some of the maintainers of > Sbt and Scala, they would be very interrested in getting a

Status of sbt package

2019-08-07 Thread merkys
Hello, I am writing regarding the status of sbt Debian package. Version 0.13.13 is in sid, but it had never entered testing. Version 1.3.0-RC3 has already been released, are there any plans to update the package? If not, I would be willing to try my luck. Best wishes, Andrius

Re: Status of sbt package

2019-08-09 Thread merkys
On 2019-08-08 17:48, Emmanuel Bourg wrote: > I don't think there is a repository yet. I've just created an empty one > on Salsa if that helps. Thanks - I'll push once I have something. Best, Andrius

Re: Status of sbt package

2019-08-08 Thread merkys
Hi Emmanuel, On 2019-08-08 10:33, Emmanuel Bourg wrote: > sbt is in sid but hasn't been bootstrapped properly yet, it still uses > libraries not built from sources. Nobody is actively working on it, feel > free to give it a try. Thanks, I'll give it a look. By the way, the source package does

Re: Status of sbt package

2019-09-26 Thread merkys
Hi Thomas, On 2019-09-25 23:03, Thomas Finneid wrote: > Sorry for the delay in answering, I'm on daddy-leave so time is > scarce. (and sorry for the long mail... :) ) Thank you for finding some time to contribute to packaging Scala/sbt! :) > I have some more good news :) After battling with my

Re: Status of sbt package

2019-09-27 Thread merkys
Hi Thomas, I have managed to get around Scala FTBFS problem [1] for now, will continue looking into your script. [1] https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=941211 On 2019-09-27 02:07, Thomas Finneid wrote: > 1- The scala library depenencies are hardcoded, so it doesnt find the >

dependencies.dependency.version is missing in pom.xml

2019-10-04 Thread merkys
Hi all, Recently I have ran into maven-built package with POMs lacking '...' properties for its dependencies. This however seems to fail the build process: [ERROR] [ERROR] Some problems were encountered while processing the POMs: [ERROR] 'dependencies.dependency.version' for junit:junit:jar is

Re: Help needed to upgrade cdk

2019-11-21 Thread merkys
Hi Egon, On 2019-11-21 11:27, Egon Willighagen wrote: > Awesome! Plz let me know if I can answer any questions around > dependencies, or impact of missing dependencies. I have made it to a successful cdk build today! I had to exclude three artifacts due to compilation problems (mostly

freehep-graphicsio update

2019-11-21 Thread merkys
Hello, New version of freehep-graphicsio is out (in 2014 [1]), and I would like to see it packaged. However, packaging of freehep-graphicsio is split in a dozen of source packages, and update maintaining this split would be tedious. Maybe merging the source packages (retaining the upstream

Re: Help needed to upgrade cdk

2019-11-19 Thread merkys
Hi, On 2019-11-19 19:40, Andreas Tille wrote: > I've sat together with Egon Willighagen who is member of CDK upstream > team to update the cdk package[1]. So far the switch from ant to maven > seems to have basically succeeded. However, for some reason it does not > build modules in the correct

Re: Help needed to upgrade cdk

2019-11-20 Thread merkys
Hi, I have managed to get around the most of the build problems. However, a lot of the artifacts depend (transitively) on org.xml-cml.cmlxom, which is not packaged yet. For the time being I can skip these artifacts, but in the long run it would be great to have cmlxom packaged. Best, Andrius

Re: freehep-graphicsio update

2019-11-28 Thread merkys
Hello, On 2019-11-23 12:30, Giovanni Mascellani wrote: > I am not against this, but I think I would happily give away maintenance > of these packages. I never used them directly, just needed them as > GeoGebra dependencies. > > That said, before updating I would suggest to consider exactly what

Java packages and autopkgtest

2019-10-09 Thread merkys
Hello, Java Team's page [1] states that some help/information is needed regarding the autopkgtest. I haven't seen much Java packages having autopkgtests, but to me it seems possible at least for packages using maven-debian-helper. Maybe there are gotchas that I am not aware of? Workflow of an

Re: Help needed to upgrade cdk

2019-12-31 Thread merkys
Hi Egon, On 2019-12-31 16:02, Egon Willighagen wrote: > I saw that CDK 2.3 is now in unstable! Great news! Many thanks for > your time during the BioHackathon, and others for their effort to make > this happen. Very much appreciated. Yes, it's finally in! :) Hope to get the CDK's depiction part

Re: Upgrading freehep to latest upstream (needed by cdk and probably others)

2020-04-18 Thread merkys
Hi Andreas, On 2020-04-15 15:53, Andreas Tille wrote: > This made me wonder about the status of the freehep-* packages that did > not had a new upload since the move from Alioth. It seems the new version > of freehep can be found at > > https://github.com/freehep > > and the structure of the

Re: Upgrading freehep to latest upstream (needed by cdk and probably others)

2020-04-23 Thread merkys
Hello, On 2020-04-21 10:40, Giovanni Mascellani wrote: > So I have no problems in removing GeoGebra to allow FreeHEP to be > updated (maybe it turns out that GeoGebra also works with FreeHEP's new > version, but I believe it is unlikely), but then at the same time I give > up as FreeHEP

Re: [covid-19] Gradle help for nextflow needed

2020-04-30 Thread merkys
Hi Andreas, On 2020-04-30 15:27, Andreas Tille wrote: > I wonder whether this fits into Debian packaging policy at all and > whether I need to avoid this in favour of packaging proper JARs? I believe it is the latter. Capsules seem to embed all their dependencies, and this is something to avoid.

Re: Upgrading freehep to latest upstream (needed by cdk and probably others)

2020-05-02 Thread merkys
Hi Giovanni, On 2020-04-21 10:40, Giovanni Mascellani wrote: > So I have no problems in removing GeoGebra to allow FreeHEP to be > updated (maybe it turns out that GeoGebra also works with FreeHEP's new > version, but I believe it is unlikely), but then at the same time I give > up as FreeHEP

Re: [covid-19] Gradle help for nextflow needed

2020-04-29 Thread merkys
Hi Andreas, On 2020-04-28 12:05, Andreas Tille wrote: > Any help for a kickstart would be really appreciated. I have almost no idea what nexus-staging plugin does, but it may be not essential for building the package. You can try to patch it out by removing the following lines from build.gradle:

Re: Looking for advice about json-simple 3 transition

2020-05-13 Thread merkys
Hello, On 2020-05-13 16:46, Gilles Filippini wrote: > I'd like to push json-simple 3.1.1 into unstable, but I'm not sure how I > should handle the transition. The 3.x releases are not backward > compatible with 2.x. > > A whole set of deprecated classes has been removed: >> * Deprecated JSONParse

Re: Looking for advice about json-simple 3 transition

2020-05-14 Thread merkys
Hello, On 2020-05-14 10:07, Gilles Filippini wrote: > I won't maintain 2 source packages. The deprecated one (version 2.x) > should be dropped. The 'Conflicts' field is needed during the transition > only. The new package would have: > * 'json-simple' as source package name (unchanged) > *

Re: Looking for advice about json-simple 3 transition

2020-05-14 Thread merkys
On 2020-05-14 11:27, Gilles Filippini wrote: > I think I could try this indeed. Would a versioned 'Breaks' field > listing the few reverse dependencies be useful then? No, this is not needed, libsimple-json-java upload for v3.0.0 shouldn't be any different from the other uploads. However, please

Re: Upgrading freehep to latest upstream (needed by cdk and probably others)

2020-07-22 Thread merkys
Hello, On 2020-07-19 15:40, Giovanni Mascellani wrote: > I have no problem with your changes, but since merkys should be back > shortly we can leave it to him to do the upload. Once that is done, I > will push geogebra with the updated patches. I have uploaded freehep to unstable toda

Re: Upgrading freehep to latest upstream (needed by cdk and probably others)

2020-07-01 Thread merkys
Hi Andreas, On 2020-07-01 12:30, Andreas Tille wrote: > Thanks for this. I've added it to the COVID-19 relevant list of packages > in new[1] > [1] > https://salsa.debian.org/med-team/community/2020-covid19-hackathon/-/wikis/NEW-Requests > Thanks for doing so! Best, Andrius

Re: Upgrading freehep to latest upstream (needed by cdk and probably others)

2020-07-10 Thread merkys
Hi, On 2020-07-10 09:49, Giovanni Mascellani wrote: > There is no need for this step. I have already a patched version that > compiles with the new FreeHEP. The thing I ask you is to add this patch > to freehep-vectorgraphics: [snip] Glad to hear that, and thanks for the patch. I have added it

Re: Upgrading freehep to latest upstream (needed by cdk and probably others)

2020-07-10 Thread merkys
Hi, On 2020-07-10 15:59, Giovanni Mascellani wrote: > Great, then I revoke the intention of RMing geogebra and close the > corresponding bug. As soon as freehep-vectographics is available, I will > bump patches and dependencies on geogebra and everything should be find. Sure, I will ping you

Re: Upgrading freehep to latest upstream (needed by cdk and probably others)

2020-07-01 Thread merkys
Hi, On 2020-07-01 10:46, Giovanni Mascellani wrote: > Sorry, I completely lost track of this thread. Here is the RM bug: > > https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=964070 Thanks a lot for the information. I have uploaded freehep-vectorgraphics to experimental, waiting for it to

Re: Upgrading freehep to latest upstream (needed by cdk and probably others)

2020-07-09 Thread merkys
Hello, On 2020-07-02 18:40, Giovanni Mascellani wrote: > On second thought, it seems that it would not be too difficult to port > GeoGebra to the new FreeHEP, so maybe we can consider this a little bit > more carefully. I agree that porting GeoGebra is much better than removing it altogether. I

Re: Building r-cran-rcdk with cdk [Was: Re: Upgrading freehep to latest upstream (needed by cdk and probably others)]

2020-07-29 Thread merkys
Hi Tony, On 2020-07-29 06:41, tony mancill wrote: > Fair enough... In the long run, it is likely that porting r-cran-rcdk > is a better use of time. However, I got interested in it and here is > the status so far: > > 1) I updated jgrapht0.6 to install a pom file and uploaded a new > package

Re: Building r-cran-rcdk with cdk [Was: Re: Upgrading freehep to latest upstream (needed by cdk and probably others)]

2020-07-28 Thread merkys
Hi Tony, On 2020-07-27 16:50, tony mancill wrote: > On Mon, Jul 27, 2020 at 08:51:49AM +0300, mer...@debian.org wrote: >> What is more, the subtree tool/smsd/ contains only pom.xml, what might >> be the reason of codeless jar. It seems to me that cdk-smsd is legacy >> now, and I would suggest

Building r-cran-rcdk with cdk [Was: Re: Upgrading freehep to latest upstream (needed by cdk and probably others)]

2020-07-26 Thread merkys
Hello, On 2020-07-27 08:38, tony mancill wrote: >> It actually seems that org/openscience/cdk/smsd/Isomorphism is not >> part of the currently packaged CDK. Any idea how to solve this? > I am just starting to take a look a this, but I think we need to spend > some more time with CDK. That class

Re: Upgrading freehep to latest upstream (needed by cdk and probably others)

2020-07-23 Thread merkys
Hello, On 2020-07-22 22:00, Giovanni Mascellani wrote: > Thanks, I just pushed geogebra. Thanks! By the way, could you please also initiate removals of obsolete freehep source packages? They are the following: freehep-graphics2d freehep-graphicsio freehep-graphicsio-emf freehep-graphicsio-java

Re: Upgrading freehep to latest upstream (needed by cdk and probably others)

2020-07-23 Thread merkys
Hi Andreas, On 2020-07-23 17:55, Andreas Tille wrote: > Would you mind to update cdk package (which was the original issue > I stumbled upon freehep)? I have updated cdk yesterday. The cdk-depict module is built now. Best, Andrius

Re: Now we have antlr 4.6 - any chance to get 4.7 soon (Was: beast-mcmc2: Cannot find symbol CharStreams.fromString(newick))

2018-10-15 Thread Andrius Merkys
right now. Best, Andrius -- Andrius Merkys Vilnius University Institute of Biotechnology, Saulėtekio al. 7, room V325 LT-10257 Vilnius, Lithuania

Re: Now we have antlr 4.6 - any chance to get 4.7 soon (Was: beast-mcmc2: Cannot find symbol CharStreams.fromString(newick))

2018-10-19 Thread Andrius Merkys
mplate-maven-plugin-java (ITP #911302). I have pushed their packaging to Salsa: * https://salsa.debian.org/merkys-guest/mojo-executor * https://salsa.debian.org/merkys-guest/string-template-maven-plugin (build-depends on libmojo-executor-java) It would be great if you could review and, if po

Re: Now we have antlr 4.6 - any chance to get 4.7 soon (Was: beast-mcmc2: Cannot find symbol CharStreams.fromString(newick))

2018-10-17 Thread Andrius Merkys
e to join the Debian Med sprint in March 2019 > which will happen in Vilnius[1] (no better details yet). Thanks, I will be there. Best, Andrius -- Andrius Merkys Vilnius University Institute of Biotechnology, Saulėtekio al. 7, room V325 LT-10257 Vilnius, Lithuania

Re: Now we have antlr 4.6 - any chance to get 4.7 soon (Was: beast-mcmc2: Cannot find symbol CharStreams.fromString(newick))

2018-10-24 Thread Andrius Merkys
On 10/24/18 1:40 PM, Emmanuel Bourg wrote: > I've uploaded mojo-executor and string-template-maven-plugin, they are > awaiting in the NEW queue for the FTP masters approval. Thanks a lot > Andrius. Many thanks for reviewing and uploading the packages! Best, Andrius

Re: java: building interdependent artifacts with maven

2018-12-30 Thread Andrius Merkys
10:30, Andrius Merkys > wrote: > > I am preparing a package for apache-opennlp [1]. Building it results in > six artifacts, one of them, > org.apache.opennlp:opennlp-morfologik-addon:jar:1.9.0, depends on another > artifact org.apache.opennlp:opennlp-tools:jar:debian which is b

Re: Help needed with morfologik

2019-01-02 Thread Andrius Merkys
drius 40 Jan  2 03:17 morfologik-fsa-debian.pom -> ../../../../../../morfologik-fsa/pom.xml Thus this might be used to solve the interdependency problem. However, this method looks more like a hack and I expect maven-debian-helper to have some built-ins for this. Best, Andrius -- Andr

Re: Help needed with morfologik

2019-01-02 Thread Andrius Merkys
to fix this? I would like to investigate the issue myself, but cannot figure out how to get to the build. Best, Andrius -- Andrius Merkys Vilnius University Institute of Biotechnology, Saulėtekio al. 7, room V325 LT-10257 Vilnius, Lithuania

Request to join Debian Java Packaging Project

2019-04-01 Thread Andrius Merkys
Hello, I have recently been granted Developer rights in Debian Java Project on Salsa (as 'merkys'). However, I am unable to create new repositories there, and I am willing to upload a couple of new packages. Are there additional requirements for repo creation rights? I have read and I accept

Re: Request to join Debian Java Packaging Project

2019-04-01 Thread Andrius Merkys
ndrius -- Andrius Merkys Vilnius University Institute of Biotechnology, Saulėtekio al. 7, room V325 LT-10257 Vilnius, Lithuania

Re: Request to join Debian Java Packaging Project

2019-04-01 Thread Andrius Merkys
Dear Markus, On 2019-04-01 16:39, Markus Koschany wrote: > You just needed the "maintainer" status. I've granted it a minute ago. > Welcome on board! Thanks a lot for adding me! Best wishes, Andrius -- Andrius Merkys Vilnius University Institute of Biotechnology, Saulėtekio

Re: [OT] Cannot use the Java offline utility given at https://www.incometaxindiaefiling.gov.in/downloads/offlineUtilities?lang=eng

2019-04-17 Thread Andrius Merkys
On 2019-04-17 09:52, shirish शिरीष wrote: > ~/Documents/ITR-1_2019_170419$ cat ITR.sh > java -jar ITR-1_AY201920_PR1.jar OK, this means that all required classes should be there in the JAR file. Could you check what does 'jar -tvf ITR-1_AY201920_PR1.jar | grep ThreeRedLightsIlluminate' say?

Re: [OT] Cannot use the Java offline utility given at https://www.incometaxindiaefiling.gov.in/downloads/offlineUtilities?lang=eng

2019-04-17 Thread Andrius Merkys
Hello, On 2019-04-17 09:35, shirish शिरीष wrote: > I don't think it's just an openjdk issue, it's probably something to > do with the class as it shows - > > com.itd.efiling.offline.common.player.ctrl.ThreeRedLightsIlluminate to me this looks like a problem with the CLASSPATH. Does

Re: [OT] Cannot use the Java offline utility given at https://www.incometaxindiaefiling.gov.in/downloads/offlineUtilities?lang=eng

2019-04-17 Thread Andrius Merkys
Dear Shirish, On 2019-04-17 10:19, shirish शिरीष wrote: > ~/Documents/ITR-1_2019_170419$ jar -tvf ITR-1_AY201920_PR1.jar | grep > ThreeRedLightsIlluminate > 1699 Mon Apr 15 19:26:26 IST 2019 > com/itd/efiling/offline/common/player/ctrl/ThreeRedLightsIlluminate$1.class > 3599 Mon Apr 15

Re: Help needed to upgrade cdk

2019-11-20 Thread Andrius Merkys
Hi Andreas, On Wed, 20 Nov 2019, 22:19 Andreas Tille, wrote: > I have no idea what restrictions the lack of cmlxom might imply. > I have packaged and uploaded cmlxom today. Will do so with the rest of dependencies. Would you take over and upload your changes? If not please push and > let me

Re: Help to detect java classes in drop-seq (covid-19 relevant) needed

2020-05-20 Thread Andrius Merkys
Hi Andreas, On 2020-05-20 14:20, Andreas Tille wrote: > Any hint how to take this hurdle would be welcome. Try setting the CLASSPATH in your d/rules like this: export CLASSPATH := $(DEBJAR)/htsjdk.jar:$(DEBJAR)/picard.jar:$(DEBJAR)/commons-collections4.jar I did this in one of packages and it

Re: Java packages and autopkgtest

2020-12-07 Thread Andrius Merkys
https://salsa.debian.org/java-team/maven-debian-helper/-/merge_requests/2 [2] https://salsa.debian.org/merkys/maven-debian-helper/-/blob/autopkgtest-pkg-maven/share/maven-debian-helper/autopkgtest-runner Hope this helps, Andrius

Divergence in salsa.debian.org/java-team/xom

2021-08-25 Thread Andrius Merkys
Hello, I want to make an upload for xom package with a couple of fixes. I want to use its packaging repository on salsa [1], but it is in somewhat diverged state. The newest Debian version of xom is 1.2.10-1.1, but repository on salsa has 1.2.10-1 (note incorrect git tag) plus a pair of commits

Re: Divergence in salsa.debian.org/java-team/xom

2021-08-25 Thread Andrius Merkys
Hi Sebastiaan, On 2021-08-25 12:32, Sebastiaan Couwenberg wrote: > Import the changes from the NMU: > > gbp import-dsc /tmp/xom_1.2.10-1.1.dsc > > Review the changes since -1: > > git diff debian/1.2.10-1{,.1} debian/ > > Restore changes that were reverted by the NMU import. Thanks, I will

Re: Old Gradle version

2021-09-14 Thread Andrius Merkys
Hi, On 2021-09-15 00:59, Philippe De Neve wrote: > I was wondering why the Gradle version in buster/bullseye/bookworm/sid > is 4.4.1. Latest release is 7.2. Please see these bug reports for reference: https://bugs.debian.org/926714 https://bugs.debian.org/933264 Best, Andrius

Re: packaging Go runtime for ANTLR4

2021-07-29 Thread Andrius Merkys
Hello, Maintainer of antlr4-cpp-runtime here. On 2021-07-28 22:36, Nilesh Patra wrote: > 2) Do "$something-else" for all these packages to stay in sync - again, > probably bumping versions only when needed. > With this approach, I do not see a problem in introducing a Go runtime > source package

maven-*-helper JAR placement seems to contradict Java policy

2021-10-15 Thread Andrius Merkys
Hello, Java policy on Java libraries (Ch. 2.4.) reads [1]: Their classes must be in jar archive(s) in the directory /usr/ share/java, with the name packagename[-extraname] -fullversion.jar. The extraname is optional and used internally within the package to separate the different

Re: maven-*-helper JAR placement seems to contradict Java policy

2021-10-18 Thread Andrius Merkys
Hi, On 2021-10-18 10:31, Alexandre Rossi wrote: >>> Not sure though what is the impact of this policy inversion. Most of >>> Java-related software seems to read both regular files and symbolic >>> links transparently. >> >> There isn't much impact, both styles are fine in my opinion. > > This

Bug#996727: ITP: ciftools-java -- Java library to read and write CIF files

2021-10-17 Thread Andrius Merkys
Hi Pierre, On 2021-10-17 22:18, Pierre Gruet wrote: > * Package name: ciftools-java > Version : 3.0.0 > Upstream Author : Sebastian Bittrich > * URL : https://github.com/rcsb/ciftools-java > * License : Expat > Programming Lang: Java > Description :

Re: maven-*-helper JAR placement seems to contradict Java policy

2021-10-15 Thread Andrius Merkys
Hi Markus, On 2021-10-15 14:34, Markus Koschany wrote: > Indeed, that looks like a bug in libcommons-lang3-java or rather maven-debian- > helper to me. I have just checked some other Maven packages and there the > policy is implemented correctly. The bug in libcommons-lang3-java could be >

Re: maven-*-helper JAR placement seems to contradict Java policy

2022-03-28 Thread Andrius Merkys
Hi Alexandre, On 2022-03-23 16:33, Alexandre Rossi wrote: > Seems to work: > > $ ls -la /usr/share/java/htmlcleaner* > lrwxrwxrwx 1 root root 15 18 mars 18:20 > /usr/share/java/htmlcleaner-2.26.jar -> htmlcleaner.jar > -rw-r--r-- 1 root root 176219 18 mars 18:20

antlr 4.10 released [Was: Re: packaging Go runtime for ANTLR4]

2022-04-13 Thread Andrius Merkys
Hello, Some time ago there was a discussion about the need to coordinate uploads of antlr and its runtime packages, as in Debian they are split into several source packages across several teams: On 2021-07-29 10:09, Andrius Merkys wrote: > Maybe an antlr4 packaging team could be set

Re: Gradle problems when building adql-java package

2023-12-08 Thread Andrius Merkys
Hi Ole, On 2023-12-08 13:03, Ole Streicher wrote: I am trying to update the adql-java package to the newest upstream (beta) version. As it is my first project using gradle, I sumbled upon a number of problems: One is that the plugin org.javacc.javacc is not available. I guess this is because