Re: Now we have antlr 4.6 - any chance to get 4.7 soon (Was: beast-mcmc2: Cannot find symbol CharStreams.fromString(newick))
On Fri, Oct 19, 2018 at 05:33:44PM +0200, Emmanuel Bourg wrote: > >https://salsa.debian.org/merkys-guest/mojo-executor > > > > to > > > >https://salsa.debian.org/java-team/mojo-executor > > > > where it should reside when maintained in Java Team. :-) > > @Andreas: We have a script [1] to create the repositories on Salsa. It's > important to use it because it configures the IRC/BTS/mail hooks properly. Thanks for the hint - I'll do this in future. However, in this case I simply used the Gitlab web interface to create a clone which I considered more sensible to connect it to the repository of Andrius. Kind regards Andreas. > [1] > https://salsa.debian.org/java-team/pkg-java-scripts/blob/master/setup-salsa-repository > -- http://fam-tille.de
Re: Now we have antlr 4.6 - any chance to get 4.7 soon (Was: beast-mcmc2: Cannot find symbol CharStreams.fromString(newick))
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: Now we have antlr 4.6 - any chance to get 4.7 soon (Was: beast-mcmc2: Cannot find symbol CharStreams.fromString(newick))
Control: tags 911286 + pending Control: tags 911302 + pending Le 19/10/2018 à 16:42, Andrius Merkys a écrit : > updating antlr4 to 4.7 requires two new Debian packages, > libmojo-executor-java (ITP #911286) and libstring-template-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 possible, sponsor them. 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. Emmanuel Bourg
Re: Now we have antlr 4.6 - any chance to get 4.7 soon (Was: beast-mcmc2: Cannot find symbol CharStreams.fromString(newick))
Am 19.10.18 um 17:33 schrieb Emmanuel Bourg: [...] > @Andreas: We have a script [1] to create the repositories on Salsa. It's > important to use it because it configures the IRC/BTS/mail hooks properly. > > [1] > https://salsa.debian.org/java-team/pkg-java-scripts/blob/master/setup-salsa-repository Would it be possible to execute this script via the "official" Salsa/Gitlab interface or is there another way to configure hooks? I find it somehow backwards if we have to configure hooks this way and not via the "Create repository" feature of Gitlab. Regards, Markus signature.asc Description: OpenPGP digital signature
Re: Now we have antlr 4.6 - any chance to get 4.7 soon (Was: beast-mcmc2: Cannot find symbol CharStreams.fromString(newick))
Le 19/10/2018 à 17:14, Andreas Tille a écrit : > I have cloned > >https://salsa.debian.org/merkys-guest/mojo-executor > > to > >https://salsa.debian.org/java-team/mojo-executor > > where it should reside when maintained in Java Team. :-) @Andreas: We have a script [1] to create the repositories on Salsa. It's important to use it because it configures the IRC/BTS/mail hooks properly. [1] https://salsa.debian.org/java-team/pkg-java-scripts/blob/master/setup-salsa-repository
Re: Now we have antlr 4.6 - any chance to get 4.7 soon (Was: beast-mcmc2: Cannot find symbol CharStreams.fromString(newick))
Le 19/10/2018 à 17:14, Andreas Tille a écrit : > Moreover there are some lintian issues: > > I: mojo-executor-parent source: quilt-patch-missing-description > sonatype-to-eclipse.patch > W: libmojo-executor-java-doc: embedded-javascript-library > usr/share/doc/libmojo-executor-java/mojo-executor-maven-plugin/jquery/jquery-ui.structure.css > please use libjs-jquery-ui Thanks a lot for the packages Andrius, I'll review them. Two things: * We don't build the javadoc for the Maven plugins, because nobody calls the plugin API directly. * The jquery warnings can be ignored, this is a javadoc issue to be fixed at the openjdk level (if ever fixed). Emmanuel Bourg
Re: Now we have antlr 4.6 - any chance to get 4.7 soon (Was: beast-mcmc2: Cannot find symbol CharStreams.fromString(newick))
Hi Andrius, On Fri, Oct 19, 2018 at 05:42:34PM +0300, Andrius Merkys wrote: > Hi Andreas, > > On 2018-10-16 17:03, Andreas Tille wrote: > > Very good. Let me know if I could be of any help (which basically would > > boil down to testing and if needed sponsoring). > > updating antlr4 to 4.7 requires two new Debian packages, > libmojo-executor-java (ITP #911286) and libstring-template-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 possible, sponsor them. > Meanwhile I will work on splitting antlr4 Java and Cpp source packages, as > suggested by Emmanuel in #911371. I have cloned https://salsa.debian.org/merkys-guest/mojo-executor to https://salsa.debian.org/java-team/mojo-executor where it should reside when maintained in Java Team. :-) Something that looks suspicious to me is: ... mh_resolve_dependencies --non-interactive --offline --build -plibmojo-executor-java --javadoc --base-directory=/build/mojo-executor-parent-2.3.0 --non-explore Analysing pom.xml... Analysing mojo-executor/pom.xml... Checking the parent dependency in the sub project mojo-executor/pom.xml Analysing mojo-executor-maven-plugin/pom.xml... Checking the parent dependency in the sub project mojo-executor-maven-plugin/pom.xml Checking dependencies for documentation packages... > dpkg --search /usr/share/doc/libcommons-lang-java/api/index.html Found libcommons-lang-java-doc > dpkg --search /usr/share/doc/libmaven3-core-java/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libmaven3-core-java/api/index.html > dpkg --search /usr/share/doc/libmaven3-core-java-doc/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libmaven3-core-java-doc/api/index.html > dpkg --search /usr/share/doc/libmaven3-core-java/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libmaven3-core-java/apidocs/index.html > dpkg --search /usr/share/doc/libmaven3-core-java-doc/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libmaven3-core-java-doc/apidocs/index.html > dpkg --search /usr/share/doc/libplexus-utils2-java/api/index.html Found libplexus-utils2-java-doc > dpkg --search /usr/share/doc/libslf4j-java/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libslf4j-java/api/index.html > dpkg --search /usr/share/doc/libslf4j-java-doc/api/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libslf4j-java-doc/api/index.html > dpkg --search /usr/share/doc/libslf4j-java/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libslf4j-java/apidocs/index.html > dpkg --search /usr/share/doc/libslf4j-java-doc/apidocs/index.html dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/doc/libslf4j-java-doc/apidocs/index.html bash -c "rm -f target/apidocs/*.sh target/apidocs/options" mh_unpatchpoms -plibmojo-executor-java ... I have no idea about maven but I have never seen any dpkg --search calls in a build log before. Moreover there are some lintian issues: I: mojo-executor-parent source: quilt-patch-missing-description sonatype-to-eclipse.patch W: libmojo-executor-java-doc: embedded-javascript-library usr/share/doc/libmojo-executor-java/mojo-executor-maven-plugin/jquery/jquery-ui.structure.css please use libjs-jquery-ui Thanks a lot for working on this Andreas. -- http://fam-tille.de
Re: Now we have antlr 4.6 - any chance to get 4.7 soon (Was: beast-mcmc2: Cannot find symbol CharStreams.fromString(newick))
Hi Andreas, On 2018-10-16 17:03, Andreas Tille wrote: > Very good. Let me know if I could be of any help (which basically would > boil down to testing and if needed sponsoring). updating antlr4 to 4.7 requires two new Debian packages, libmojo-executor-java (ITP #911286) and libstring-template-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 possible, sponsor them. Meanwhile I will work on splitting antlr4 Java and Cpp source packages, as suggested by Emmanuel in #911371. Best wishes, Andrius [#911286] https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=911286 [#911302] https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=911302 [#911371] https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=911371 -- 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))
Hi Andrius, On Wed, Oct 17, 2018 at 01:57:29PM +0300, Andrius Merkys wrote: > On 10/16/18 5:03 PM, Andreas Tille wrote: > > Very good. Let me know if I could be of any help (which basically would > > boil down to testing and if needed sponsoring). > > Many thanks! I will turn to you once I get the updated package build. Fine. > > Interesting. You might like to join the Debian Med sprint in March 2019 > > which will happen in Vilnius[1] (no better details yet). > > Thanks, I will be there. Meanwile the Wiki page is setup and you (and for sure everybody else reading this list) can add your name to the list of participants: https://wiki.debian.org/Sprints/2019/DebianMed2019 Looking forward to meed you in Vilnius Andreas. -- http://fam-tille.de
Re: Now we have antlr 4.6 - any chance to get 4.7 soon (Was: beast-mcmc2: Cannot find symbol CharStreams.fromString(newick))
Hi Andreas, On 10/16/18 5:03 PM, Andreas Tille wrote: > Very good. Let me know if I could be of any help (which basically would > boil down to testing and if needed sponsoring). Many thanks! I will turn to you once I get the updated package build. > Interesting. You might like 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))
Hi Andrius, On Mon, Oct 15, 2018 at 01:01:04PM +0300, Andrius Merkys wrote: > On 10/15/2018 12:54 PM, Andreas Tille wrote: > > when I tried last time we had antlr 4.5. I now tried with 4.6 but it > > seems 4.7 is really needed. Any chance to get this soon? > > I am interested in packaging antlr 4.7 (with Cpp support, needed for > #902798), I am working on it right now. Very good. Let me know if I could be of any help (which basically would boil down to testing and if needed sponsoring). > Andrius Merkys > Vilnius University Institute of Biotechnology, Saulėtekio al. 7, room V325 > LT-10257 Vilnius, Lithuania Interesting. You might like to join the Debian Med sprint in March 2019 which will happen in Vilnius[1] (no better details yet). Kind regards Andreas. [1] https://lists.debian.org/debian-med/2018/10/msg0.html -- http://fam-tille.de
Re: Now we have antlr 4.6 - any chance to get 4.7 soon (Was: beast-mcmc2: Cannot find symbol CharStreams.fromString(newick))
Hi Andreas, On 10/15/2018 12:54 PM, Andreas Tille wrote: > when I tried last time we had antlr 4.5. I now tried with 4.6 but it > seems 4.7 is really needed. Any chance to get this soon? I am interested in packaging antlr 4.7 (with Cpp support, needed for #902798), I am working on it right now. Best, Andrius -- Andrius Merkys Vilnius University Institute of Biotechnology, Saulėtekio al. 7, room V325 LT-10257 Vilnius, Lithuania
Now we have antlr 4.6 - any chance to get 4.7 soon (Was: beast-mcmc2: Cannot find symbol CharStreams.fromString(newick))
Hi, when I tried last time we had antlr 4.5. I now tried with 4.6 but it seems 4.7 is really needed. Any chance to get this soon? Kind regards Andreas. On Sat, Aug 04, 2018 at 11:23:42AM +0200, Andreas Tille wrote: > On Thu, Jul 19, 2018 at 09:44:30AM +0200, Emmanuel Bourg wrote: > > Hi Andreas, > > > > Le 19/07/2018 à 08:56, Andreas Tille a écrit : > > > > > [javac] > > > /build/beast2-mcmc-2.5.0+dfsg/src/beast/util/TreeParser.java:353: error: > > > cannot find symbol > > > [javac] CharStream charStream = > > > CharStreams.fromString(newick); > > > [javac] ^ > > > [javac] symbol: variable CharStreams > > > [javac] location: class TreeParser > > > [javac] > > > /build/beast2-mcmc-2.5.0+dfsg/src/beast/util/treeparser/NewickLexer.java:98: > > > error: method does not override or implement a method from a supertype > > > [javac] @Override > > > [javac] ^ > > > > It looks like these errors are related to ANTLR [1]. > > You'll need the version 4.7. > > Upstream confirmed this[2] - and suggests to use antlr 4.7. > So my question is: Can we expect this version of antlr in Debian > in the foreseeable future? > > Kind regards > > Andreas. > > > [1] https://github.com/CompEvol/beast2/commit/deacdc96 > [2] https://github.com/CompEvol/beast2/issues/797 > > -- > http://fam-tille.de -- http://fam-tille.de
Re: beast-mcmc2: Cannot find symbol CharStreams.fromString(newick)
Le 04/08/2018 à 11:23, Andreas Tille a écrit : > Upstream confirmed this[2] - and suggests to use antlr 4.7. > So my question is: Can we expect this version of antlr in Debian > in the foreseeable future? I tried after you email but failed. The best I could do for now was upgrading to 4.6. Emmanuel Bourg
Re: beast-mcmc2: Cannot find symbol CharStreams.fromString(newick)
On Thu, Jul 19, 2018 at 09:44:30AM +0200, Emmanuel Bourg wrote: > Hi Andreas, > > Le 19/07/2018 à 08:56, Andreas Tille a écrit : > > > [javac] > > /build/beast2-mcmc-2.5.0+dfsg/src/beast/util/TreeParser.java:353: error: > > cannot find symbol > > [javac] CharStream charStream = CharStreams.fromString(newick); > > [javac] ^ > > [javac] symbol: variable CharStreams > > [javac] location: class TreeParser > > [javac] > > /build/beast2-mcmc-2.5.0+dfsg/src/beast/util/treeparser/NewickLexer.java:98: > > error: method does not override or implement a method from a supertype > > [javac] @Override > > [javac] ^ > > It looks like these errors are related to ANTLR [1]. > You'll need the version 4.7. Upstream confirmed this[2] - and suggests to use antlr 4.7. So my question is: Can we expect this version of antlr in Debian in the foreseeable future? Kind regards Andreas. > [1] https://github.com/CompEvol/beast2/commit/deacdc96 [2] https://github.com/CompEvol/beast2/issues/797 -- http://fam-tille.de
Re: beast-mcmc2: Cannot find symbol CharStreams.fromString(newick)
Hi Andreas, Le 19/07/2018 à 08:56, Andreas Tille a écrit : > [javac] /build/beast2-mcmc-2.5.0+dfsg/src/beast/util/TreeParser.java:353: > error: cannot find symbol > [javac] CharStream charStream = CharStreams.fromString(newick); > [javac] ^ > [javac] symbol: variable CharStreams > [javac] location: class TreeParser > [javac] > /build/beast2-mcmc-2.5.0+dfsg/src/beast/util/treeparser/NewickLexer.java:98: > error: method does not override or implement a method from a supertype > [javac] @Override > [javac] ^ It looks like these errors are related to ANTLR [1]. You'll need the version 4.7. Emmanuel Bourg [1] https://github.com/CompEvol/beast2/commit/deacdc96
beast-mcmc2: Cannot find symbol CharStreams.fromString(newick)
Hi, I think I came very close with beast-mcmc2 package[1] but there are two remaining errors: compile-all: [echo] Building BEAST 2 [mkdir] Created dir: /build/beast2-mcmc-2.5.0+dfsg/build [javac] Compiling 470 source files to /build/beast2-mcmc-2.5.0+dfsg/build [javac] warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] /build/beast2-mcmc-2.5.0+dfsg/src/beast/util/TreeParser.java:353: error: cannot find symbol [javac] CharStream charStream = CharStreams.fromString(newick); [javac] ^ [javac] symbol: variable CharStreams [javac] location: class TreeParser [javac] /build/beast2-mcmc-2.5.0+dfsg/src/beast/util/treeparser/NewickLexer.java:98: error: method does not override or implement a method from a supertype [javac] @Override [javac] ^ [javac] Note: Some input files use or override a deprecated API. [javac] Note: Recompile with -Xlint:deprecation for details. [javac] Note: Some input files use unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [javac] 2 errors [javac] 1 warning Any hint how to fix this? Kind regards Andreas. [1] https://salsa.debian.org/med-team/beast2-mcmc -- http://fam-tille.de
