Re: libitext5-java: FTBFS with bouncycastle 1.77

2023-12-09 Thread Andreas Tille
Hi, I tried the latest upstream version of libitext5-java and commited the change to Git. Unfortunately the problem persists. Some Debian Med packages are depending from this package so I'd be happy if someone could have a look. You can find the latest log in Salsa CI[1]. Kind regards

Re: beauti2 fails to start

2023-12-07 Thread Andreas Tille
Hi, Am Sun, Dec 18, 2022 at 03:15:28PM +0100 schrieb Pierre Gruet: > Control: tags -1 help > > Hello, > > I tried to investigate further, I feel a window should appear and the action > of the user is expected, yet I don't see anything except the initial > "Initializing BEAUti..." GUI. > My

Re: jblas update to 1.2.5?

2021-12-09 Thread Andreas Tille
Hi Tony and Debian Science Am Thu, Dec 09, 2021 at 09:31:31AM -0800 schrieb tony mancill: > Hello Debian Med, > > jblas (http://jblas.org/) is a Debian Java team package, but I think it > is more appropriate to ask about users here. ... well, better Debian Science IMHO (which I'm keeping in the

Re: May be its rather a "java.io.IOException: No such file or directory" issue (Was: Calling sbt inside d/rules)

2021-05-27 Thread Andreas Tille
Hi Thorsten, On Thu, May 27, 2021 at 05:55:20PM +0200, Thorsten Glaser wrote: > > pbuilder@tglase:~/b/r-cran-epitweetr/java$ sbt -no-share package A, that was helpful! > … is the key to success, at least until… > > [warn] :: > [warn] ::

Re: May be its rather a "java.io.IOException: No such file or directory" issue (Was: Calling sbt inside d/rules)

2021-05-27 Thread Andreas Tille
On Thu, May 27, 2021 at 02:57:41PM +0200, Thorsten Glaser wrote: > On Thu, 27 May 2021, Andreas Tille wrote: > > > I tried again without any clue - may be it is simply some missing > > directory inside pbuilder - but I have no idea which one. :-( > > Shoot into the blue

May be its rather a "java.io.IOException: No such file or directory" issue (Was: Calling sbt inside d/rules)

2021-05-27 Thread Andreas Tille
Hi again, I tried again without any clue - may be it is simply some missing directory inside pbuilder - but I have no idea which one. :-( Any hint would be welcome Andreas. On Tue, May 25, 2021 at 11:29:52AM +0200, Andreas Tille wrote: > Hi, > > the source of r-cran-ep

Calling sbt inside d/rules

2021-05-25 Thread Andreas Tille
Hi, the source of r-cran-epitweetr[1] contains a JAR and the corresponding scala code. I tried to sneak in a sbt call into debian/rules. I tried several different things to at least get sbt running but I always get: java.io.IOException: No such file or directory at

Re: Bug#988650: logol: broken symlink: /usr/share/logol/lib/xml-apis.jar -> ../../java/xml-apis.jar

2021-05-17 Thread Andreas Tille
Hi, I'd like to forward this to Debian Java list for comments. Kind regards Andreas. On Mon, May 17, 2021 at 01:50:01PM +0200, olivier sallou wrote: > Issue seems to be related to xml-apis.jar not being symlinked itself > > /usr/share/java# ls *xml-api* > xml-apis-1.4.01.jar

Re: No CI/CD settings in packages of Debian Java team?

2021-04-16 Thread Andreas Tille
Hi Emmanuel, On Fri, Apr 16, 2021 at 09:41:11PM +0200, Emmanuel Bourg wrote: > > Is there any good reason for this setting? > > When Salsa was set up we were instructed no to overuse the CI system, I > don't know how this has evolved now. As far as I know this has settled now. > Personally I

Re: No CI/CD settings in packages of Debian Java team?

2021-04-16 Thread Andreas Tille
Hi Sudip, On Fri, Apr 16, 2021 at 10:48:51AM +0100, Sudip Mukherjee wrote: > > This entry can be found in the menu between Repository and Operations. > > I intended to do this setting for packages (for instance cronometer and > > cdk). However, the whole menu entry is missing. I have no idea

Re: Packaging OpenRefine

2021-04-16 Thread Andreas Tille
On Fri, Mar 12, 2021 at 08:35:59PM -0500, Olek Wojnar wrote: > > Good news, we came to an agreement to package OpenRefine and to support its > > maintenance for the foreseeable future. I intend to introduce the core > > That looks really exciting, thanks for working on that! I imagine that the >

No CI/CD settings in packages of Debian Java team?

2021-04-16 Thread Andreas Tille
Hi, in Debian Med we are activating Salsa-CI by adding debian/salsa-ci.yml to all packages and set this in -> Settings -> CI/CD This entry can be found in the menu between Repository and Operations. I intended to do this setting for packages (for instance cronometer and cdk). However, the

Re: Help with libjsonp-java needed

2021-01-17 Thread Andreas Tille
On Sat, Jan 16, 2021 at 10:52:21PM +0100, Pierre Gruet wrote: > > Yes, the issue is the version number of the dependency javax.json-api was > hardcoded in the patch 03-bundle-dependencies -- this thus broke when the > last upstream version was adopted. I have pushed a correction to Salsa. > > To

Help with libjsonp-java needed

2021-01-16 Thread Andreas Tille
Hi, I'm not sure whether this is the right moment to update libjsonp-java but I just stumbled upon it on the "stinks" page[1] and I'd love to make those packages I'm responsible for non-stinky. ;-) Thus I refreshed the packaging in Git[2] but the build time test issue I observed some time ago

Salsa repository permissions of gsoc-kotlin-blog

2021-01-09 Thread Andreas Tille
Hi, when I'm running the teammetrics gatherer of team commits I stumbled upon https://salsa.debian.org/java-team/gsoc-kotlin-blog/edit which states that this repository is only visible for project members. Usually repositories should be public. The gatherer will ignore this project as long

Re: libsis-base-java: unaligned access on armhf

2020-12-02 Thread Andreas Tille
Control: tags -1 help Hi, I wonder whether some Java expert might be able to clarify the situation in bug #929530. Any help would be appreciated Andreas. -- http://fam-tille.de

Re: [RFS] libapfloat-java

2020-11-09 Thread Andreas Tille
Hi, On Tue, Nov 03, 2020 at 10:30:23AM +0100, Pierre Gruet wrote: > > There is a minor mistake with the email address of the Java team in > > debian/control: > > > > pkg-java-maintain...@alioth-lists.debian.net > > > > should be replaced by: > > > >

Re: Bug#973070: libsis-base-java: FTBFS: Could not delete the directory targets/unit-test-wd/ch.syst

2020-10-29 Thread Andreas Tille
Hi, here is a suggested patch for commons-io that would prevent making the test in libsis-base-java fail. Kind regards Andreas. - Forwarded message from Bernd Rinn - Date: Wed, 28 Oct 2020 21:40:29 +0100 From: Bernd Rinn To: Andreas Tille CC: 973...@bugs.debian.org Subject

Re: Help needed: Bug#973070: libsis-base-java: FTBFS: Could not delete the directory targets/unit-test-wd/ch.systemsx.cisd.base.unix.UnixTests because: 1 exceptions: [java.io.IOException: Unable to de

2020-10-28 Thread Andreas Tille
Hi, On Tue, Oct 27, 2020 at 10:55:43PM +0100, Markus Koschany wrote: > This appears to be caused by the recent upgrade of Apache commons-io to > version 2.8.0 (we had 2.6), see also #973135. In version 2.7 they > removed a throws IOException in the method isSymlink() > >

Help needed: Bug#973070: libsis-base-java: FTBFS: Could not delete the directory targets/unit-test-wd/ch.systemsx.cisd.base.unix.UnixTests because: 1 exceptions: [java.io.IOException: Unable to delete

2020-10-27 Thread Andreas Tille
Control: tags -1 help Hi, I checked out the latest upstream commit and pushed it to Salsa. Its the same with this. Any idea why this test has worked before but is failing now? Kind regards Andreas. On Tue, Oct 27, 2020 at 06:06:55PM +0100, Lucas Nussbaum wrote: > Source:

Re: [RFS] libreflections-java

2020-09-12 Thread Andreas Tille
Hi Pierre, On Wed, Sep 02, 2020 at 12:32:49PM +0200, Pierre Gruet wrote: > > > > in the source package. While its definitely primitive and just contains > > "pack/empty.class" as binary content my bet is ftpmaster will stumble > > upon this. > > > > What do you think? > > > > Thanks for

Re: src:cgview: fails to migrate to testing for too long: autopkgtest failure

2020-09-09 Thread Andreas Tille
Control: tags -1 help Hi, I wonder why this ... autopkgtest [16:10:05]: test run-unit-test: [--- [warning] /usr/bin/cgview: No java runtime was found autopkgtest [16:10:06]: test run-unit-test: ---] autopkgtest [16:10:06]: test run-unit-test: - - - - - -

Re: [RFS] libreflections-java

2020-09-02 Thread Andreas Tille
Hi Pierre, On Sat, Aug 29, 2020 at 01:22:41PM +0200, Pierre Gruet wrote: > I have worked on the initial packaging of libreflections-java, which > lies in the Salsa repository > > https://salsa.debian.org/java-team/libreflections-java > > Could someone please review and sponsor it when time

Re: [RFS] libdsiutils-java

2020-09-02 Thread Andreas Tille
Hi Pierre, On Sat, Aug 29, 2020 at 12:46:22PM +0200, Pierre Gruet wrote: > Hi, > > I have worked on the initial packaging of libdsiutils-java, which lies > in the Salsa repository > > https://salsa.debian.org/java-team/libdsiutils-java > > Could someone please review and sponsor it when time

Re: jimfs: FTBFS: [ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.8.1:compile (default-compile) on project jimfs: Compilation failure

2020-08-08 Thread Andreas Tille
On Sat, Aug 08, 2020 at 12:07:17AM +0200, Thorsten Glaser wrote: > > Gimme a bit, I’ll build it locally, now I found the Debian packaging. > > Heh, it was as easy as build targetting Java 8… patch and log attached. Ahhh, that was simple. :-) Thanks a lot. BTW, I'd consider it more

Re: jimfs: FTBFS: [ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.8.1:compile (default-compile) on project jimfs: Compilation failure

2020-08-07 Thread Andreas Tille
Hi Thorsten, On Thu, Aug 06, 2020 at 04:04:22PM +0200, Thorsten Glaser wrote: > On Thu, 6 Aug 2020, Andreas Tille wrote: > > > [ERROR] > > /build/jimfs-1.1/jimfs/src/main/java/com/google/common/jimfs/PathService.java:[290,30] > > error: is not abstract > >

Re: jimfs: FTBFS: [ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.8.1:compile (default-compile) on project jimfs: Compilation failure

2020-08-06 Thread Andreas Tille
Control: tags -1 help Hi, I was running routine-update on jimfs repository since it seems to lack some love (not even Salsa URLs in VCS-fields) but the build error remains (for sure since I did not changed the code). I've checked upstream[1] which says: 1.1 @cgdecker released this on Feb

Re: [Help] Re: Bug#966878: figtree: FTBFS: [javac] /<>/src/figtree/application/JSONTreeExporter.java:56: error: JSONTreeExporter is not abstract and does not override abstract method clos

2020-08-05 Thread Andreas Tille
Uploaded. Thanks a lot, Andreas. On Mon, Aug 03, 2020 at 01:29:28PM +0100, Sudip Mukherjee wrote: > Hi Andreas, > > On Mon, Aug 3, 2020 at 10:25 AM Andreas Tille wrote: > > > > Control: tags -1 help > > > > Hi Java team > > > > I admit I hav

[Help] Re: Bug#966878: figtree: FTBFS: [javac] /<>/src/figtree/application/JSONTreeExporter.java:56: error: JSONTreeExporter is not abstract and does not override abstract method close()

2020-08-03 Thread Andreas Tille
Control: tags -1 help Hi Java team I admit I have no idea how to tackle this. Any help would be really appreciated. Kind regards Andreas. On Mon, Aug 03, 2020 at 10:01:35AM +0200, Lucas Nussbaum wrote: > Source: figtree > Version: 1.4.4-4 > Severity: serious > Justification: FTBFS on

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

2020-07-29 Thread Andreas Tille
Hi Tony & Andrius, On Wed, Jul 29, 2020 at 09:18:52AM +0300, mer...@debian.org wrote: > > [1] https://salsa.debian.org/java-team/cdk/-/merge_requests/4 > > The MR looks good to me. Thanks a lot for you both working on it. > I posted a tiny suggestion to depend on > jgrapht0.6 with a version to

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

2020-07-26 Thread Andreas Tille
Hi Andrius, On Fri, Jul 24, 2020 at 08:11:29AM +0300, mer...@debian.org wrote: > 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-depic

Re: RFS : libcharts4j-java

2020-07-26 Thread Andreas Tille
Hi Emmanuel, On Sat, Jul 25, 2020 at 11:36:08PM +0200, Emmanuel Bourg wrote: > On 25/07/2020 08:39, Emmanuel Bourg wrote: > > >> Could someone please review and sponsor it when time permits? > > > > Hi Pierre, I'll take care of it. > > The package has been uploaded and is now in the NEW queue.

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

2020-07-23 Thread Andreas Tille
Hi Andrius, On Thu, Jul 23, 2020 at 04:42:20PM +0300, mer...@debian.org wrote: > Hello, > > On 2020-07-22 22:00, Giovanni Mascellani wrote: > > Thanks, I just pushed geogebra. > > Thanks! Would you mind to update cdk package (which was the original issue I stumbled upon freehep)? Kind regards

Help for package sepp needed: error: incompatible types: JSONArray cannot be converted to Collection

2020-07-23 Thread Andreas Tille
Hi, the Debian Med team wants to package sepp[1] as a COVID-19 relevant package. It contains some Java code which fails to build with: ... [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. [javac]

Help with oncofuse needed

2020-07-22 Thread Andreas Tille
Hi, I had a look at oncofuse[1] again. The new version now has a different reason to fail - hopefully it is easier to fix: ... [INFO] Scanning for projects... [INFO] [INFO] --< es.unav:oncofuse >-- [INFO] Building oncofuse 1.1.1 [INFO]

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

2020-07-15 Thread Andreas Tille
On Fri, Jul 10, 2020 at 04:06:03PM +0300, mer...@debian.org wrote: > 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

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

2020-07-01 Thread Andreas Tille
Hi Andrius, On Wed, Jul 01, 2020 at 11:09:54AM +0300, mer...@debian.org wrote: > > 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 clear NEW. Thanks for this. I've added

Re: Bug#959829: [covid-19] Help needed to finalise bazel predependency google-api-client-java

2020-06-17 Thread Andreas Tille
Hi, On Wed, Jun 17, 2020 at 02:12:09PM -0400, Olek Wojnar wrote: > > That was easy. I have pushed my changes to "sudip" which now builds > > only those two. > > Great, thanks! Yep. > Good catch, thanks! The repo should be named google-api-client-java for > consistency with the rest of the

Re: Bug#959829: [covid-19] Help needed to finalise bazel predependency google-api-client-java

2020-06-17 Thread Andreas Tille
Hi Sudip, On Wed, Jun 17, 2020 at 11:42:52AM +0100, Sudip Mukherjee wrote: > > I have taken the liberty to push to "tmancill" branch and the issue As I tried to express: I wished you all would take the freedom to simply push to the master branch which is perfectly fine for me. ;-) Thanks a lot

Re: Bug#959829: [covid-19] Help needed to finalise bazel predependency google-api-client-java

2020-06-17 Thread Andreas Tille
Hi Tony, On Tue, Jun 16, 2020 at 09:34:20PM -0700, tony mancill wrote: > > I've pushed a "tmancill" branch to the Salsa repo that gets us further > along. Thanks a lot for your great help. I've merged your branch to master. Feel free to push right to master in future since I feel unable to do

Re: Bug#959829: [covid-19] Help needed to finalise bazel predependency google-api-client-java

2020-06-16 Thread Andreas Tille
Hi Olek, On Tue, Jun 16, 2020 at 05:01:37AM -0400, Olek Wojnar wrote: > > Good question! Due to some dependency issues, the bom artifacts are not > packaged. OK, that explains the issue ... > But you should be able to just depend on the non-bom pom files. ... but I'm to uneducated to

[covid-19] Help needed to finalise bazel predependency google-api-client-java

2020-06-16 Thread Andreas Tille
Hi, I have injected some preliminary packaging for google-api-client-java into salsa[1]. When trying to build I get: ... dh_auto_build /usr/lib/jvm/default-java/bin/java -noverify -cp /usr/share/maven/boot/plexus-classworlds-2.x.jar -Dmaven.home=/usr/share/maven

Re: Issue about mutual dependencies for aparapi

2020-06-04 Thread Andreas Tille
[add debian-java to CC] Hi Pierre, thanks a lot for your continuous work to get snpeff packaged finally. This is extremely welcome. On Thu, Jun 04, 2020 at 05:49:23PM +0200, Pierre Gruet wrote: > Hello everyone, > > I am currently beginning packaging aparapi, which is a Java API to > execute

ITP: google-http-client-java -- Google HTTP Client Library for Java

2020-06-01 Thread Andreas Tille
Control: retitle -1 ITP: google-http-client-java -- Google HTTP Client Library for Java Control: owner -1 Andreas Tille Control: tags -1 help Hi, in the COVID-19 sprint of Debian Med we spotted the bazel packaging system as important target to finally get tensorflow packaged for Debian

Help needed to create jar in maven project (auto-common - predependency for bazel)

2020-05-29 Thread Andreas Tille
Hi Java team, I'm working together with Olek to get all predependencies for bazel which will finally enable us to build tensorflow for Debian. We both have no clue to build a jar in the following project: On Fri, May 29, 2020 at 12:54:52PM -0400, Olek Wojnar wrote: > > I've been having

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

2020-05-21 Thread Andreas Tille
Hi, On Wed, May 20, 2020 at 10:07:48PM +0200, Andreas Tille wrote: > > Thanks. This was pretty helpful. Now I need to package the > remaining JAR which is not yet packaged from > >http://la4j.org/ I made some progress and also uploaded libla4j-java[1] to new. With this I

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

2020-05-20 Thread Andreas Tille
HI Felix, On Wed, May 20, 2020 at 06:12:54PM +0200, Felix Natter wrote: > > Since the upstream jars were in ${lib}, you need to point ${lib} to > /usr/share/java/: > > diff --git a/debian/patches/debian_packaged_libs.patch > b/debian/patches/debian_packaged_libs.patch > index 1d3790c..4fc1ed9

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

2020-05-20 Thread Andreas Tille
Hi, I've started packaging of drop-seq[1] and replaced those JARs that are replacable by Debian packaged versions. I also have set CLASS_PATH in d/rules, but it seems to be ignored. I have dealt with similar cases by patching it into build.xml but here I have not found the relevant place to do

Re: Maven packages in Debian (was Re: Progress in preparing the Bazel Build System for Debian (COVID-19 Biohackathon follow-up))

2020-05-13 Thread Andreas Tille
On Wed, May 13, 2020 at 08:33:07PM +0200, Thorsten Glaser wrote: > > I remember times when such a web page (actually some autogenerated text > > file) existed which was **extremely** helpful. I wished this would be > > back! > > > > > … I just volunteerd, didn’t I? > > Here you are: > >

ITP: opencensus-java -- Stats collection and distributed tracing framework

2020-05-12 Thread Andreas Tille
Control: retitle -1 ITP: opencensus-java -- Stats collection and distributed tracing framework Control: owner -1 Andreas Tille Control: tags -1 help I've started packaging in https://salsa.debian.org/java-team/opencensus-java to support bazel packaging. Unfortunately I have no idea how

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

2020-05-06 Thread Andreas Tille
Hi Pierre, On Fri, May 01, 2020 at 07:48:14AM +0200, Pierre Gruet wrote: > > I was planning to consider a full refresh of debian/rules, including > dh_auto_clean. Since I realised your changelog that all tests are passing I decided to upload the current status in Git. That's really great work

Re: Progress in preparing the Bazel Build System for Debian (COVID-19 Biohackathon follow-up)

2020-05-06 Thread Andreas Tille
Hi Thorsten, On Wed, May 06, 2020 at 05:15:04PM +0200, Thorsten Glaser wrote: > > Provides or something to make it clear? I saw changes to packages adding > > Or perhaps we need a webpage or wiki page generated by parsing the > Contents file and listing the matching Debian package for each class

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

2020-04-30 Thread Andreas Tille
On Thu, Apr 30, 2020 at 01:10:34PM +0200, Andreas Tille wrote: > For the moment I did this. I delay the hint for the gradle dependencies > given by Benedict in the other mail since for the moment I think I have > spotted a real dependency that needs to be packaged: > > A p

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

2020-04-30 Thread Andreas Tille
Hi Andrius and Benedict, thanks to you both for your answers! On Thu, Apr 30, 2020 at 06:01:45AM +0300, mer...@debian.org wrote: > > 8< > plugins { >     id "io.codearte.nexus-staging" version "0.21.2" > } >

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

2020-04-29 Thread Andreas Tille
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 any test actually: > >debian/rules override_dh_auto_test > make[1]: Entering directory > ... >

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

2020-04-29 Thread Andreas Tille
Hi Pierre, On Tue, Apr 28, 2020 at 10:40:31PM +0200, Pierre Gruet wrote: > 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

[covid-19] Gradle help for nextflow needed

2020-04-28 Thread Andreas Tille
Hi, in our COVID-19 effort the Debian Med team intends to package some workflows that are useful to detect viruses. A common workflow tool is nextflow which I in injected into Salsa[1]. The build system uses gradle where I do not have any experience in. The build log of my weak attempt is

Re: Changes to get tomcat8 security fixes into Debian 9?

2020-04-28 Thread Andreas Tille
On Fri, Mar 06, 2020 at 03:17:09PM +0100, Andreas Tille wrote: > On Fri, Mar 06, 2020 at 12:24:56AM +0100, Markus Koschany wrote: > > Hi Andreas, > > > > Am 05.03.20 um 09:34 schrieb Andreas Tille: > > > Hi, > > > > > > I was wondering, whet

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

2020-04-28 Thread Andreas Tille
Hi Andrius, thanks a lot for your work on this - also thanks to Giovanni for your comments. I'd be really happy to get FreeHEP updated. Kind regards Andreas. On Fri, Apr 24, 2020 at 08:03:20AM +0300, mer...@debian.org wrote: > Hello, > > On 2020-04-21 10:40, Giovanni Mascellani wrote:

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

2020-04-20 Thread Andreas Tille
Hi Andrius, On Sat, Apr 18, 2020 at 10:18:04AM +0300, mer...@debian.org wrote: > Some time ago I had attempted packaging new freehep-vectorgraphics, with > considerable success. However, I dropped the ball and did not upload it. > I have pushed my packaging to salsa [1]. Thanks a lot for the

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

2020-04-15 Thread Andreas Tille
Hi, I was digging through CDK to get the R interface running (see my other mails here on this list). I just found another clue that cdk-depict is missing. When inspecting cdk source I've found: libcdk-java.poms:# depict requires freehep-graphicsio-* 2.4 (Debian has older) This made me

Re: Help needed for calling Java class from R

2020-04-15 Thread Andreas Tille
Hi again, On Tue, Apr 14, 2020 at 10:50:28PM +0200, Andreas Tille wrote: > 1 Test Suite : > rcdk rcdk Unit Tests - 31 test functions, 31 errors, 0 failures > ERROR in test.charges: Error in > .jnew("org/openscience/cdk/smiles/SmilesParser", g

Re: Help needed for calling Java class from R

2020-04-14 Thread Andreas Tille
Hi Florian, On Tue, Apr 14, 2020 at 08:49:44PM +0200, Florian Weimer wrote: > > Meh. Does R have exceptions? It would be nice to translate the > underlying exception from > > if (clnam) > cls = findClass(env, clnam, oClassLoader); > else > cls = objectClass(env,o); > if (!cls) >

Re: Help needed for calling Java class from R

2020-04-14 Thread Andreas Tille
On Tue, Apr 14, 2020 at 06:52:56PM +0200, Florian Weimer wrote: > * Andreas Tille: > > ERROR: loading failed > > * removing > > '/build/r-cran-rcdk-3.5.0/debian/r-cran-rcdk/usr/lib/R/site-library/rcdk' > > dh_auto_install: error: R CMD INSTALL -l > > /build/r-c

Help needed for calling Java class from R

2020-04-14 Thread Andreas Tille
Hi, in the COVID-19 packaging effort I need r-cran-rcdk as a predependency. I have injected it into r-pkg-team Git[1]. It is using the rjava interface and depends from r-cran-rcdklibs (which has a dependency from libcdk-java). When I try to build I get: ** installing vignettes ** testing if

Re: Changes to get tomcat8 security fixes into Debian 9?

2020-03-06 Thread Andreas Tille
On Fri, Mar 06, 2020 at 12:24:56AM +0100, Markus Koschany wrote: > Hi Andreas, > > Am 05.03.20 um 09:34 schrieb Andreas Tille: > > Hi, > > > > I was wondering, whether there is a chance to get CVE-2020-1938 fixed in > > Tomcat8 in Stretch? If the chances are

Changes to get tomcat8 security fixes into Debian 9?

2020-03-05 Thread Andreas Tille
Hi, I was wondering, whether there is a chance to get CVE-2020-1938 fixed in Tomcat8 in Stretch? If the chances are low possibly backporting Tomcat9 to stretch-backports-sloppy would be a feasible way to go for me. What would you recomment? Kind regards Andreas. -- http://fam-tille.de

Re: freehep-graphicsio update

2019-11-28 Thread Andreas Tille
Hi, On Sat, Nov 23, 2019 at 11:30:11AM +0100, Giovanni Mascellani wrote: > Il 21/11/19 12:18, mer...@debian.org ha scritto: > > 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

Re: Help needed to upgrade cdk

2019-11-20 Thread Andreas Tille
On Wed, Nov 20, 2019 at 10:35:11PM +0200, Andrius Merkys 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

Re: Help needed to upgrade cdk

2019-11-20 Thread Andreas Tille
Hi Andrius, On Wed, Nov 20, 2019 at 10:56:52AM +0200, mer...@debian.org wrote: > 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,

Help needed to upgrade cdk

2019-11-19 Thread Andreas Tille
Hi, 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 sequence and thus we are running into: [INFO]

Any hints about maven libs from Debian Java team (Was: IGV update - any takers?)

2019-11-14 Thread Andreas Tille
Hi, I'd be very happy if Debian Java team could comment on the analysis of libs done by Olivier to enable us upgrading IGV. On Thu, Nov 14, 2019 at 09:34:51AM +0100, Olivier Sallou wrote: > > I had a quick look at latest version. It seems to be have been rewritten > a lot, a lots of dependency

Re: Bug#940606: new upstream (2.6.3)

2019-09-17 Thread Andreas Tille
Control: tags -1 help On Tue, Sep 17, 2019 at 08:01:53PM +0200, Daniel Baumann wrote: > it would be nice if you could upgrade to current igv version 2.6.3. the > current version in unstable is (apart from the other issues) so old, > it's hardly usable. I agree and its work in progress

Help with gradle needed (Was: Bug#923731: Any volunteer to fix the "usual" issues when upgrading to new version of igv?)

2019-09-16 Thread Andreas Tille
Hi, any comment from Debian Java team? Kind regards Andreas. On Mon, Sep 16, 2019 at 09:57:58AM +0200, Olivier Sallou wrote: > > On 9/13/19 3:43 PM, Andreas Tille wrote: > > Hi, > > > > I upgraded the igv packaging Git[1] to the latest upstream version. I > &

Re: Oncofuse: Is there any way to avoid groovy-eclipse-compiler

2019-06-26 Thread Andreas Tille
On Wed, Jun 26, 2019 at 10:03:03PM +0200, Thorsten Glaser wrote: > On Wed, 26 Jun 2019, Mykola Nikishov wrote: > > > Seems the only option is to use Ant tasks directly [1] as GMaven is not > > an option any more [2]: > > What about gmavenplus? It seems you are refering to the package

Oncofuse: Is there any way to avoid groovy-eclipse-compiler

2019-06-26 Thread Andreas Tille
Hi, I'm trying to package oncofuse[1]. I used mh-make to create the packaging skeleton. I asked mh-make to ignore the dependency groovy-eclipse-compiler since I was hoping that its not urgently needed (and I do not have the slightest idea what this is and how hard it is to package it as

Re: jTDS driver horribly out of date

2019-06-13 Thread Andreas Tille
Hi Ryan, On Tue, Jun 11, 2019 at 11:55:59PM +, Ryan Morillo wrote: > Hi guys, > The jTDS driver has been at version 1.3.1 for a few years and we still > have 1.2.5 in the testing repo (libjtds-java) Can we get the newer > version packaged up and included? > The biggest benefit is it makes it

Is anybody able to reproduce this issue (help urgently needed) (Was: Potential bug in jh_build (Was: fannj: FTBFS in buster/sid))

2019-04-23 Thread Andreas Tille
. On Fri, Apr 12, 2019 at 10:21:46AM +0200, Andreas Tille wrote: > Hi, > > I'd like to make some noise again about this issue. I'm concerned > about the fact that > > jh_build --javadoc-opts='-link /usr/share/doc/default-jdk-doc/api' > > was creating a JAR file

Potential bug in jh_build (Was: fannj: FTBFS in buster/sid)

2019-04-12 Thread Andreas Tille
. On Thu, Apr 04, 2019 at 01:36:18PM +0200, Andreas Tille wrote: > Hi, > > On Tue, Apr 02, 2019 at 03:35:58PM +0200, Andreas Tille wrote: > > Daniel, if I do not hear from you I assume you agree that I inject > > fannj into Debian Science Git and do a team upload. > > As

Re: Looking on how to contribute to the Debian Java Packaging Team

2019-04-09 Thread Andreas Tille
Hi, On Sat, Apr 06, 2019 at 01:23:49PM +0200, Hans-Christoph Steiner wrote: > Hey Armando, > > Thanks for your interest and welcome! +1 > There are many ways to jump into > Java packaging. One way is to go through the bug reports and try > confirming them and fixing them. Right now

Re: fannj: FTBFS in buster/sid

2019-04-04 Thread Andreas Tille
Hi, On Tue, Apr 02, 2019 at 03:35:58PM +0200, Andreas Tille wrote: > Daniel, if I do not hear from you I assume you agree that I inject > fannj into Debian Science Git and do a team upload. As I said I assumed agreement and have moved fannj to Salsa[1]. Unfortunately the build is no

Re: fannj: FTBFS in buster/sid

2019-04-02 Thread Andreas Tille
Hi again, Daniel, if I do not hear from you I assume you agree that I inject fannj into Debian Science Git and do a team upload. Kind regards Andreas. On Wed, Mar 27, 2019 at 03:08:17PM +0100, Andreas Tille wrote: > Hi, > > as far as I understood the Debian Java team agreed tha

Re: fannj: FTBFS in buster/sid

2019-03-27 Thread Andreas Tille
Hi, as far as I understood the Debian Java team agreed that droping the documentation is an appropriate way to deal with errors like this: Creating destination directory: "debian/_jh_build.javadoc/api/" javadoc: error - The code being documented uses packages in the unnamed module, but the

Re: One step ahead but compile errors (Was: netlib-java contains nealy empty jar)

2019-03-26 Thread Andreas Tille
Hi Markus, thanks a lot! On Mon, Mar 25, 2019 at 03:49:52PM +0100, Markus Koschany wrote: > > Thinking about it, the patch could be much simpler. Actually all you > need is the list of URLs. They are hardcoded but those jar files and > your build directory probably will never change again.

Re: One step ahead but compile errors (Was: netlib-java contains nealy empty jar)

2019-03-25 Thread Andreas Tille
is the compile target that seems to be "hidden" in nbproject/build-impl.xml not executed any more and how can I get back the status of 0.9.3-3 which was building nicely? I seriously need help on this matter. Kind regards Andreas. On Thu, Mar 21, 2019 at 01:55:46PM +0100, Andreas T

One step ahead but compile errors (Was: netlib-java contains nealy empty jar)

2019-03-21 Thread Andreas Tille
Hi, On Tue, Mar 12, 2019 at 10:58:33AM +0100, Andreas Tille wrote: > I realised that > > /usr/share/java/netlib-java-0.9.3.jar > > is nearly empty, specifically > > /org/netlib/arpack > /org/netlib/blas > /org/netlib/lapack >

Re: icedtea-web FTBFS with OpenJDK 11

2019-03-14 Thread Andreas Tille
On Wed, Mar 13, 2019 at 10:25:06PM +0100, Emmanuel Bourg wrote: > On 13/03/2019 21:30, Markus Koschany wrote: > > >> please look at the new upstream 1.7.2 and 1.8 releases. May be that's sensible for Buster+1 > > In https://bugs.debian.org/855686 Emmanuel wrote that icedtea-web will > > be

Re: icedtea-web FTBFS with OpenJDK 11

2019-03-13 Thread Andreas Tille
On Tue, Mar 12, 2019 at 11:41:22AM +0100, Andreas Tille wrote: > Michael Crusoe has suggested a workaround[1]. What do you think about > this? In case there is no answer to this question I assume it is OK to upload the workaround. Hope you agree with this. Kind regards A

Re: icedtea-web FTBFS with OpenJDK 11

2019-03-12 Thread Andreas Tille
Hi, Michael Crusoe has suggested a workaround[1]. What do you think about this? Kind regards, Andreas. [1] https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=912549#10 -- http://fam-tille.de

netlib-java contains nealy empty jar (Was: mtj: FTBFS in buster/sid)

2019-03-12 Thread Andreas Tille
ally want to package the new versions * debhelper 12 * Point Vcs fields to salsa.debian.org * Standards-Version: 4.3.0 * Secure URI in copyright format -- Andreas Tille Sun, 13 Jan 2019 21:11:05 +0100 and the previous version on snapshots[1] contains a proper jar file with all classes I su

Re: Bug#923756: libhac-java: FTBFS in buster/sid

2019-03-05 Thread Andreas Tille
On Tue, Mar 05, 2019 at 02:02:05PM +0100, Markus Koschany wrote: > ... > Maybe we should change our javadoc policy too. Developers shall not > build-depend on other -doc packages by default and override jh_build if > they wish to link against external packages. This way they have more > fine

Re: Bug#923756: libhac-java: FTBFS in buster/sid

2019-03-05 Thread Andreas Tille
On Tue, Mar 05, 2019 at 09:41:53AM +0100, Andreas Tille wrote: > On the other hand: It seems this is not needed by any rdepends any more > and popcon data are looking as if we should rather remove than fix this > package ... Sorry for the noise but this is really needed for

Re: Bug#923756: libhac-java: FTBFS in buster/sid

2019-03-05 Thread Andreas Tille
On Tue, Mar 05, 2019 at 06:11:32AM +0100, Andreas Tille wrote: > Hi Debian Java team, > > On Tue, Mar 05, 2019 at 12:19:40AM +, Santiago Vila wrote: > > jh_build -J hac.jar src > > find src -name *.java -and -type f -print0 | xargs -s 512000 -0 > > /usr/lib/jvm/de

Re: Bug#923756: libhac-java: FTBFS in buster/sid

2019-03-04 Thread Andreas Tille
Hi Debian Java team, On Tue, Mar 05, 2019 at 12:19:40AM +, Santiago Vila wrote: > jh_build -J hac.jar src > find src -name *.java -and -type f -print0 | xargs -s 512000 -0 > /usr/lib/jvm/default-java/bin/javac -g -cp :debian/_jh_build.hac -d > debian/_jh_build.hac -source 1.7 -target 1.7

libmilib-java depends libredberry-pipe-java (>= 1.0.0-alpha0) but should rather libredberry-pipe-java (>= 1.0.0~alpha0)

2019-02-19 Thread Andreas Tille
Hi, I realised that libmilib-java is not installable[1] since ${maven:Depends}[2] is resolved into libredberry-pipe-java (>= 1.0.0-alpha0) rather than the existing libredberry-pipe-java (>= 1.0.0~alpha0) (see difference between '-' and '~' before 'alpha0'). How can I make sure that the correct

Please remove repository the now outdated java-team/milib (package was moved to med-team)

2019-02-12 Thread Andreas Tille
Hi, the description of milib is bioinformatics related and a clear target of Debian Med team. "Hiding" the package in Debian Java is escaping the QA measures we have in our team and thus I realised bug #920839 very late and only by chance. Thus I have moved the package to Debian Med[1] in my

Re: Attempt to upgrade libjsonp-java - help needed

2019-01-30 Thread Andreas Tille
On Fri, Jan 25, 2019 at 10:03:44AM +0100, Olivier Sallou wrote: > >>> [INFO] > >>> > >>> [INFO] Reactor Summary for JSR 374 (JSON Processing) RI 1.1.2: > >>> [INFO] > >>> [INFO] JSR 374 (JSON Processing) RI

Re: New version has switched build system to Maven - any hint how to resolve dependencies?

2019-01-30 Thread Andreas Tille
On Tue, Jan 29, 2019 at 11:59:04AM +0100, Olivier Sallou wrote: > > > which are less issues but the according JARs are definitely inside Debian: > > > > com.ibatis:ibatis:jar:debian -> libibatis-java > > com.sshtools:j2ssh-core:jar:debian -> libj2ssh-java > >

Re: New version has switched build system to Maven - any hint how to resolve dependencies?

2019-01-29 Thread Andreas Tille
Hi Emmanuel, On Mon, Jan 28, 2019 at 09:15:49PM +0100, Emmanuel Bourg wrote: > No no no it has to work, otherwise you'll run into many other issues... Ahhh, another very helpful hint. I was running mh_make now and was merging its results in. That was very enlightening and saved me some stupid

Re: New version has switched build system to Maven - any hint how to resolve dependencies?

2019-01-28 Thread Andreas Tille
Hi Emmanuel, as always thanks a lot for your quick help. On Mon, Jan 28, 2019 at 02:26:27PM +0100, Emmanuel Bourg wrote: > You don't need jacoco, that's a test coverage tool that can be safely > disabled when building Debian packages. > > Just add this to debian/maven.ignoreRules: > >

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