Bug#1094729: java-comment-preprocessor: New upstream version injected into Git - help needed to build

Source: java-comment-preprocessor Version: 6.0.1-1.1 Severity: normal X-Debbugs-Cc: Debian Java List Hi, I had a look into java-comment-preprocessor and at least polished the packaging including setting Vcs fields properly. I also tried to work on the latest upstream version. Unfortunately I d

New upstream version injected into Git - help needed to build

Hi, I had a look into triplea and at least polished the packaging including setting Vcs fields properly. I also tried to work on the latest upstream version which includes fixing the CVE issue. Unfortunately I did not managed to build the package successfully. You can see the build result in Sa

Re: Bug#1081606: debian/maven.rules help needed for cdk

Hi Emmanuel, On 2024-09-28 00:51, Emmanuel Bourg wrote: Le 27/09/2024 à 14:47, Andrius Merkys a écrit : cdk-data is an artifact of the same project, however, I cannot make maven detect it. I am almost sure the problem is due to some misconfiguration in debian/maven.rules, but I cannot find wh

Re: Bug#1081606: debian/maven.rules help needed for cdk

Le 27/09/2024 à 14:47, Andrius Merkys a écrit : cdk-data is an artifact of the same project, however, I cannot make maven detect it. I am almost sure the problem is due to some misconfiguration in debian/maven.rules, but I cannot find where. I would be grateful if someone with better knowledge

debian/maven.rules help needed for cdk

Hello, I am trying to enable tests for cdk package on branch on salsa [1]. Build is failing with the following: [INFO] [INFO] BUILD FAILURE [INFO] ---

Re: [Debian-med-packaging] Bug#973070: 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:

Am 28.10.20 um 16:01 schrieb olivier sallou: [...] > *dumb* patch would be to simply remove those tests from code... Either this or you can keep the override for dh_auto_test-arch empty. The test creates a broken symlink but then FileUtils.deleteDirectory fails to delete the file, obviously bec

Re: [Debian-med-packaging] Bug#973070: 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:

On Wed, 2020-10-28 at 09:05 +0100, Andreas Tille wrote: > 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 th

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

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() > > https://issues.apache.org

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

Hi, 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() https://issues.apache.org/jira/browse/IO-610 Could it be related to this change? It is probably nec

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

On Tue, 27 Oct 2020, Andreas Tille wrote: > > > Caused by: java.io.IOException: Unable to delete file: > > > targets/unit-test-wd/ch.systemsx.cisd.base.unix.UnixTests/someDanglingLink > > > at org.apache.commons.io.FileUtils.forceDelete(FileUtils.java:1425) > > > at org.apache.commons.io.File

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

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: libsis-base-jav

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

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 ecos

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

Hi Sudip, On Wed, Jun 17, 2020, 13:38 Sudip Mukherjee wrote: > > That was easy. I have pushed my changes to "sudip" which now builds > only those two. > Great, thanks! And, just noticed (after pushing) that the Vcs in d/control is wrong. > It should be https://salsa.debian.org/java-team/google

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

On Wed, Jun 17, 2020 at 5:40 PM Olek Wojnar wrote: > > On Wed, Jun 17, 2020 at 12:19 PM Andreas Tille wrote: >> >> I have the feeling we are coming closer to a solution iteratively now >> but there are some remaining errors unfortunately: > > > If any of you have a moment, I recommend patching th

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

On Wed, Jun 17, 2020 at 12:19 PM Andreas Tille wrote: > I have the feeling we are coming closer to a solution iteratively now > but there are some remaining errors unfortunately: > If any of you have a moment, I recommend patching the main pom.xml to only build the two modules that we need (goog

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

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

On Wed, Jun 17, 2020 at 9:13 AM Andreas Tille wrote: > > 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. I have taken the liberty to push to "tmancill" branch and the issue with "c

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

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 a

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

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 implement

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

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 -Dmaven.multiModule

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

On Fri, 29 May 2020, Olek Wojnar wrote: > Ha! Figured it was something really simple. The trick is knowing which > simple thing it is, right? ;) Thanks again! Probably. You’re welcome ☻ bye, //mirabilos -- tarent solutions GmbH Rochusstraße 2-4, D-53123 Bonn • http://www.tarent.de/ Tel: +49 228

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

Perfect, thanks!! On Fri, May 29, 2020 at 4:04 PM Thorsten Glaser wrote: > > Took me eight minutes ☻ > Ha! Figured it was something really simple. The trick is knowing which simple thing it is, right? ;) Thanks again! -Olek

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

On Fri, 29 May 2020, Andreas Tille wrote: > Any help would be welcome u@h:/tmp/google-auto-common-java $ mvn -f build-pom.xml clean package Since maven-debian-helper pretty much hardcodes pom.xml as POM filename though, have at this: /tmp/google-auto-common-java/debian/patches/pom.patch After

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

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 problems

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

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 s

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 package looks weird. Where d

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

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 package looks weird. Where does the mix-up between libhdf5-java and libsis-jhdf5-java come from? T

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

Gilles Filippini a écrit le 30/04/2020 à 19:45 : > Pierre Gruet a écrit le 30/04/2020 à 17:40 : >> 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 Filippin

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

Pierre Gruet a écrit le 30/04/2020 à 17:40 : > 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

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

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 any test actually: >> >>debian/rules override_dh_auto_test >> make

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

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

Hi, Andreas Tille a écrit le 29/04/2020 à 11:59 : > 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

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

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 .

Re: Help needed for calling Java class from R

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", get.chem.object.builder()) : > java.lang.NoClassDefF

Re: Help needed for calling Java class from R

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

* 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-cran-rcdk-3

Re: Help needed for calling Java class from R

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-cran-rcdk-3.5.0/debian/r-cran-rcdk/us

Re: Help needed for calling Java class from R

* 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: > > > ** insta

Help needed for calling Java class from R

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 ins

Re: Help needed to upgrade cdk

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 w

Re: Help needed to upgrade cdk

Hi Andreas, and other Debian developers, 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. Egon On Tue, Nov 19, 2019 at 6:40 PM Andreas Tille wrote: > Hi, > > I've sat t

Re: Help needed to upgrade cdk

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 dependenci

Re: Help needed to upgrade cdk

Awesome! Plz let me know if I can answer any questions around dependencies, or impact of missing dependencies. Egon On Wed, Nov 20, 2019 at 9:35 PM Andrius Merkys wrote: > Hi Andreas, > > On Wed, 20 Nov 2019, 22:19 Andreas Tille, wrote: > >> I have no idea what restrictions the lack of cmlxom

Re: Help needed to upgrade cdk

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 an

Re: Help needed to upgrade cdk

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 k

Re: Help needed to upgrade cdk

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, b

Re: Help needed to upgrade cdk

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: Help needed to upgrade cdk

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

Am 19.11.19 um 18:40 schrieb 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 co

Help needed to upgrade cdk

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] cd

Re: Attempt to upgrade libjsonp-java - help needed

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: Attempt to upgrade libjsonp-java - help needed

On 1/25/19 9:45 AM, Andreas Tille wrote: > Hi Olivier, > > On Thu, Jan 24, 2019 at 10:59:33PM +0100, Olivier Sallou wrote: should be able to add in pom.xml     true >>> This works (Emmanuel, just leaving out the -doc package is not >>> sufficient in this case). >>> >>>

Re: Attempt to upgrade libjsonp-java - help needed

Hi Olivier, On Thu, Jan 24, 2019 at 10:59:33PM +0100, Olivier Sallou wrote: > > > > should be able to add in pom.xml > > > > > > > > >     true > > > > > > > This works (Emmanuel, just leaving out the -doc package is not > > sufficient in this case). > > > > Unfortunately I'm running into th

Re: Attempt to upgrade libjsonp-java - help needed

- Andreas Tille a écrit : > Hi Olivier, > > On Thu, Jan 24, 2019 at 05:54:54PM +0100, Olivier Sallou wrote: > > > > should be able to add in pom.xml > > > > > >     true > > > > This works (Emmanuel, just leaving out the -doc package is not > sufficient in this case). > > Unfortunatel

Re: Attempt to upgrade libjsonp-java - help needed

Hi Olivier, On Thu, Jan 24, 2019 at 05:54:54PM +0100, Olivier Sallou wrote: > > should be able to add in pom.xml > > >     true > This works (Emmanuel, just leaving out the -doc package is not sufficient in this case). Unfortunately I'm running into the next issue now: ... [WARNING] Failed

Re: Attempt to upgrade libjsonp-java - help needed

On 1/24/19 5:47 PM, Andreas Tille wrote: > Hi Markus, > > On Thu, Jan 24, 2019 at 12:27:35PM +0100, Markus Koschany wrote: >> If the documentation is not super important to you, I recommend to just >> drop the -doc package. > Doc is absolutely not important - its just a predependency of one of my

Re: Attempt to upgrade libjsonp-java - help needed

Am 24.01.19 um 17:47 schrieb Andreas Tille: > Hi Markus, > > On Thu, Jan 24, 2019 at 12:27:35PM +0100, Markus Koschany wrote: >> If the documentation is not super important to you, I recommend to just >> drop the -doc package. > > Doc is absolutely not important - its just a predependency of on

Re: Attempt to upgrade libjsonp-java - help needed

Le 24/01/2019 à 17:47, Andreas Tille a écrit : > Doc is absolutely not important - its just a predependency of one of my > packages. Do you have a hint where to poke to get rid of the doc > creation. I fiddled around a bit with the pom.xmls but failed. :-( Just remove the -java-doc package, and

Re: Attempt to upgrade libjsonp-java - help needed

Hi Markus, On Thu, Jan 24, 2019 at 12:27:35PM +0100, Markus Koschany wrote: > If the documentation is not super important to you, I recommend to just > drop the -doc package. Doc is absolutely not important - its just a predependency of one of my packages. Do you have a hint where to poke to get

Re: Attempt to upgrade libjsonp-java - help needed

Hi, Am 24.01.19 um 11:31 schrieb Andreas Tille: > [ERROR] Exit code: 1 - javadoc: error - The code being documented uses > modules but the packages defined in > https://docs.oracle.com/javase/8/docs/api/ are in the unnamed module. I believe this is Debian bug https://bugs.debian.org/919798 I

Attempt to upgrade libjsonp-java - help needed

Hi, I intend to update libjsonp-java but if I try to build the current state in Git[1] I get: ... Building index for all classes... Generating /build/libjsonp-java-1.1.2/api/target/apidocs/allclasses.html... Generating /build/libjsonp-java-1.1.2/api/target/apidocs/allclasses.html... Generating /b

Re: Help needed with morfologik

Hi Andrej, On 2018-12-30 02:57, Andrej Shadura wrote: > You can find the source here: > https://salsa.debian.org/java-team/morfologik-stemming the packaging repository lacks pristine-tar branch, is this intentional? Also, 'make -f debian/rules get-orig-source' fails with: uscan --download-versi

Re: Help needed with morfologik

Hi, On 2019-01-02 09:31, Andrej Shadura wrote: > In fact, > just to build the package, you don’t need the tarball, you can > `fakeroot debian/rules clean binary` directly. ah, indeed, I need only this part. With package libmorfologik-stemming-java installed I was able to reproduce your problem.

Re: Test failure in libsis-base-java 18.08.0 (Was: Bug#842815: Help needed for HDF5 1.10 transition of libsis-jhdf5-java)

Hi Andreas, I figured it out: JRE 10.0 last modified time with milli-second resolution while JRE 8.0 and earlier provide it with second resolution (though it provides it in milli-seconds). I can confirm that the change fixes the test with JRE 10.0. All the best, Bernd On 08/21/2018 03:23 PM, Ber

Re: Test failure in libsis-base-java 18.08.0 (Was: Bug#842815: Help needed for HDF5 1.10 transition of libsis-jhdf5-java)

Hi Andreas, On 08/21/2018 10:11 AM, Andreas Tille wrote: > Hi Bernd, > > On Sun, Aug 19, 2018 at 03:25:46PM +0200, Bernd Rinn wrote: >> Yes, sis-base needs to be updated to 18.08.0. This library is in the GIT >> repository in directory >> >> https://sissource.ethz.ch/sispub/jhdf5/tree/master/libs

Test failure in libsis-base-java 18.08.0 (Was: Bug#842815: Help needed for HDF5 1.10 transition of libsis-jhdf5-java)

Hi Bernd, On Sun, Aug 19, 2018 at 03:25:46PM +0200, Bernd Rinn wrote: > Yes, sis-base needs to be updated to 18.08.0. This library is in the GIT > repository in directory > > https://sissource.ethz.ch/sispub/jhdf5/tree/master/libs/prod > > You can find the version also at: > > https://sissource

Re: Help needed for change of build system to gradle of package libsis-jhdf5-java

Le dim. 19 août 2018 à 16:17, Bernd Rinn a écrit : > On 08/19/2018 04:02 PM, olivier sallou wrote: > > > > > > Le dim. 19 août 2018 à 15:23, Bernd Rinn > > a écrit : > > > > Hi Andreas, > > > > I have no idea why the classes are missing for you as they are all > >

Re: Help needed for change of build system to gradle of package libsis-jhdf5-java

On 08/19/2018 04:02 PM, olivier sallou wrote: > > > Le dim. 19 août 2018 à 15:23, Bernd Rinn > a écrit : > > Hi Andreas, > > I have no idea why the classes are missing for you as they are all > present in our ivy-repository which we use for dependency resoluti

Re: Help needed for change of build system to gradle of package libsis-jhdf5-java

Le dim. 19 août 2018 à 15:23, Bernd Rinn a écrit : > Hi Andreas, > > I have no idea why the classes are missing for you as they are all > present in our ivy-repository which we use for dependency resolution. > Maybe there is an issue with your gradle build environment? > In debian, all deps must

Re: Help needed for change of build system to gradle of package libsis-jhdf5-java

Hi Andreas, I have no idea why the classes are missing for you as they are all present in our ivy-repository which we use for dependency resolution. Maybe there is an issue with your gradle build environment? Anyway, I have now simplified the build process by removing automatic dependency resolut

Re: Help needed for change of build system to gradle of package libsis-jhdf5-java

Hi Bernd, could you give some hints about the missing classes? On Tue, Aug 14, 2018 at 12:23:22PM +0200, olivier sallou wrote: > Le mar. 14 août 2018 à 11:32, Andreas Tille a écrit : > > > A problem occurred evaluating root project 'libsis-jhdf5-java'. > > > Could not resolve all dependencies f

Re: Help needed for change of build system to gradle of package libsis-jhdf5-java

Le mar. 14 août 2018 à 11:32, Andreas Tille a écrit : > Hi, > > upstream of libsis-jhdf5-java[1] has switched to gradle in its new > version that is compatible with HDF5 1.10. I tried to adapt debian/rules > from previous manual build to buildsystem=gradle but got: > > ... > Parallel execution i

Help needed for change of build system to gradle of package libsis-jhdf5-java

Hi, upstream of libsis-jhdf5-java[1] has switched to gradle in its new version that is compatible with HDF5 1.10. I tried to adapt debian/rules from previous manual build to buildsystem=gradle but got: ... Parallel execution is an incubating feature. Evaluating root project 'libsis-jhdf5-java' u

Re: Help needed for Artemis

Hi, Am 05.08.2018 um 13:48 schrieb Andreas Tille: [...] > > Is there any clever way to solve this instead of doing a lot of copying or > symlinking? To me it looks like the jar-rules.patch is responsible for this build failure. Some files and directories don't exist in your upstream sources. It

Re: Help needed for Artemis

Hi Markus, after fixing the patch I've build all class files successfully but when it comes to generating the JAR it switches to a subdirectory which leads to ... cd jar_build/build; \ rm -rf META-INF/MANIFEST.MF; \ echo "Main-Class: uk.ac.sanger.artemis.components.ArtemisMain\nPermissions: all-

Help needed for Artemis

Hi, I try to build the latest version of Artemis[1] but when I try to build the current state in Git I get: ... CLASSPATH=/usr/share/java/biojava.jar:/usr/share/java/j2ssh-core.jar:/usr/share/java/ibatis.jar:/usr/share/java/log4j-1.2.jar:/usr/share/java/postgresql-jdbc3.jar:/usr/share/java/picard

Re: Help needed to build prottest

On Fri, Jul 13, 2018 at 01:12:07PM +0200, Markus Koschany wrote: > It turned out that the import statement must be adapted to the new > location. Patch is attached. Thanks a lot Andreas. -- http://fam-tille.de

Re: Help needed to build prottest

Am 13.07.2018 um 11:02 schrieb Andreas Tille: [...] > > Hmmm, not sure whether this is the same question. I always have trouble > to find out in what package the respective JAR can be found. In the > current case when browsing the alter.jar content the respective classes > are just moved to a sb

Re: Help needed to build prottest

Hi Markus, On Thu, Jul 12, 2018 at 10:56:19PM +0200, Markus Koschany wrote: > > Any idea how to fix this? > > Some of those class files are in alter.jar [1] but I don't know the > corresponding upstream project. It is alter-sequence-alignment and I've just updated this to the new upstream versio

Re: Help needed to build prottest

Hi, Am 11.07.2018 um 23:02 schrieb Andreas Tille: [...] > > Any idea how to fix this? Some of those class files are in alter.jar [1] but I don't know the corresponding upstream project. If you get "package X does not exist or cannot find symbol" errors, you have to build-depend on the respective

Help needed to build prottest

Hi, when migrating prottest to Salsa[1] I was running into a FTBFS: ... Buildfile: /build/prottest-3.4.2+dfsg/build.xml compile: [mkdir] Created dir: /build/prottest-3.4.2+dfsg/build/classes [javac] Using javac -source 1.6 is no longer supported, switching to 7 [javac] Using javac -t

Re: Help with encoding issue needed for libjscience-java (Was: Help needed for libapfloat-java)

Hi, Markus Koschany wrote: > In this case you need to override the default iso8851 encoding and pass > --javacopts="-encoding UTF-8" to jh_build. I have pushed this change > already Cool. That's very welcome. > but the build fails because of missing build-dependencies now. I started working on

Re: Help with encoding issue needed for libjscience-java (Was: Help needed for libapfloat-java)

Hallo Andreas, Am 25.05.2018 um 15:32 schrieb Andreas Tille: [...] > Any hint how to fix this? In this case you need to override the default iso8851 encoding and pass --javacopts="-encoding UTF-8" to jh_build. I have pushed this change already but the build fails because of missing build-dependen

Help with encoding issue needed for libjscience-java (Was: Help needed for libapfloat-java)

Hi, On Wed, May 16, 2018 at 05:21:44PM +0200, Olivier Sallou wrote: > missing dependency com.aparpi.aparapi:1.3.4 (for apfloat-aparapi) and > org.jscience.jscience:4.3.1 (for apfloat-jscience) I tried to start with the latter and have committed some initial packaging to. Unfortunately I get lots

Re: Help needed for libapfloat-java

On Thu, May 17, 2018 at 08:02:33AM +0200, Olivier Sallou wrote: > > I wonder whether we start with a packaging attempt anyway and if > > ftpmaster considers this a blocker we could try to negotiate with > > the authors about this part of the license. > > > For me it is blocking with the 'you will

Re: Help needed for libapfloat-java

- Andreas Tille a écrit : > On Wed, May 16, 2018 at 05:21:44PM +0200, Olivier Sallou wrote: > > > > I updated repo with a few fixes, but lib needs additional external > > dependencies not in Debian. I added info to d/changelog > > > > missing dependency com.aparpi.aparapi:1.3.4 (for apfloat

Re: Help needed for libapfloat-java

On Wed, May 16, 2018 at 05:21:44PM +0200, Olivier Sallou wrote: > > I updated repo with a few fixes, but lib needs additional external > dependencies not in Debian. I added info to d/changelog > > missing dependency com.aparpi.aparapi:1.3.4 (for apfloat-aparapi) and > org.jscience.jscience:4.3.1

Re: Help needed for libapfloat-java

On 05/16/2018 05:04 PM, Olivier Sallou wrote: > > On 05/16/2018 03:34 PM, Andreas Tille wrote: >> On Wed, May 16, 2018 at 02:40:31PM +0200, Emmanuel Bourg wrote: >>> Le 16/05/2018 à 14:30, Andreas Tille a écrit : >>> but my naive attempt to fire up mh_make and expect that it results in

Re: Help needed for libapfloat-java

On 05/16/2018 03:34 PM, Andreas Tille wrote: > On Wed, May 16, 2018 at 02:40:31PM +0200, Emmanuel Bourg wrote: >> Le 16/05/2018 à 14:30, Andreas Tille a écrit : >> >>> but my naive attempt to fire up mh_make and expect that it results >>> in something that builds was again to naive to work. you

Re: Help needed for libapfloat-java

Le 16/05/2018 à 15:34, Andreas Tille a écrit : > No error but javac is not fired up at all and thus no JARs are created. Probably because the package depends on maven-repo-helper instead of maven-debian-helper. maven-debian-helper is for projects using Maven as the build system. maven-repo-help

Re: Help needed for libapfloat-java

On Wed, May 16, 2018 at 02:40:31PM +0200, Emmanuel Bourg wrote: > Le 16/05/2018 à 14:30, Andreas Tille a écrit : > > > but my naive attempt to fire up mh_make and expect that it results > > in something that builds was again to naive to work. > What error did you get? No error but javac is not fi

Re: Help needed for libapfloat-java

Le 16/05/2018 à 14:30, Andreas Tille a écrit : > but my naive attempt to fire up mh_make and expect that it results > in something that builds was again to naive to work. What error did you get? Emmanuel Bourg

Help needed for libapfloat-java

Hi, I intend to package libapfloat-java[1] which is needed by some Debian Med target package (snpeff) but my naive attempt to fire up mh_make and expect that it results in something that builds was again to naive to work. Any hint how to get the JARs build in the preliminary Git repository[1] wou

Re: Help needed to port beast2-mcmc to Java 9

On Fri, Apr 06, 2018 at 01:50:39PM +0200, Emmanuel Bourg wrote: > Le 06/04/2018 à 13:45, Andreas Tille a écrit : > > > [javac] error: package org.fest.util does not exist > > fest-util.jar? Better, but not solved: ... compile-all: [echo] Building BEAST 2 [mkdir] Created dir: /buil

Re: Help needed to port beast2-mcmc to Java 9

Le 06/04/2018 à 13:45, Andreas Tille a écrit : > [javac] error: package org.fest.util does not exist fest-util.jar?

Re: Help needed to port beast2-mcmc to Java 9

Hi Emmanuel, On Fri, Apr 06, 2018 at 10:25:07AM +0200, Emmanuel Bourg wrote: > > error: package org.antlr.v4.runtime.dfa does not exist > > I think you have to add antlr4-runtime.jar to the classpath. That's way better now. The remaining issues are: [javac] Compiling 468 source files

Re: Help needed to port beast2-mcmc to Java 9

Hi Andreas, Le 06/04/2018 à 09:35, Andreas Tille a écrit : > error: package org.antlr.v4.runtime.dfa does not exist I think you have to add antlr4-runtime.jar to the classpath. Emmanuel Bourg

Help needed to port beast2-mcmc to Java 9

Control: tags -1 help Hi, I have pushed the latest upstream version including the proposed fix of the Build-Depends to default-jdk to Git[1]. Unfortunately when trying to build the package I get lots of errors, starting with: ... [javac] /build/beast2-mcmc-2.4.8+dfsg/src/beast/util/XMLPars

  1   2   3   >