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's not a Java specific issue and you can most likely solve it by updating this patch. Regards, Markus signature.asc Description: OpenPGP digital signature
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-permissions" > manifest-art; \ jar cmf manifest-art ../artemis.jar META-INF/services images/Wellcome_Sanger_Institute_Logo_Landscape_Digital_RGB_Full_Colour.jpg images/icon.gif README.md etc \ artemis_sqlmap org uk com net htsjdk picard gov joptsimple ngs freemarker ; \ echo "Main-Class: uk.ac.sanger.artemis.circular.DNADraw\nPermissions: all-permissions" > manifest-circular; \ jar cmf manifest-circular ../DNAPlotter.jar images/Wellcome_Sanger_Institute_Logo_Landscape_Digital_RGB_Full_Colour.jpg README.md etc \ org uk com net htsjdk picard gov joptsimple ngs freemarker ; \ echo "Main-Class: uk.ac.sanger.artemis.components.alignment.BamView\nPermissions: all-permissions" > manifest-bamview; \ jar cmf manifest-bamview ../bamview.jar META-INF/services etc org uk com net htsjdk picard gov joptsimple ngs freemarker ; \ echo "Main-Class: uk.ac.sanger.artemis.components.ActMain\nPermissions: all-permissions" > manifest-act; \ jar cmf manifest-act ../act.jar META-INF/services images/Wellcome_Sanger_Institute_Logo_Landscape_Digital_RGB_Full_Colour.jpg images/icon.gif README.md etc \ artemis_sqlmap org uk com net htsjdk picard gov joptsimple ngs freemarker ; \ META-INF/services : no such file or directory images/Wellcome_Sanger_Institute_Logo_Landscape_Digital_RGB_Full_Colour.jpg : no such file or directory images/icon.gif : no such file or directory README.md : no such file or directory ... Is there any clever way to solve this instead of doing a lot of copying or symlinking? Kind regards Andreas. [1] https://salsa.debian.org/med-team/artemis -- http://fam-tille.de
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.jar:/usr/share/java/htsjdk.jar:/usr/share/java/commons-net.jar:/usr/share/java/commons-lang3.jar:/usr/share/java/batik-all.jar:/usr/share/java/batik-awt-util.jar:/usr/share/java/batik-dom.jar:/usr/share/java/batik-ext.jar:/usr/share/java/batik-svggen.jar:/usr/share/java/batik-util.jar:/usr/share/java/batik-xml.jar:/usr/share/EMBOSS/jemboss/lib/jemboss.jar:/build/artemis-17.0.1+dfsg javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/MegaBlastComparisonData.java warning: [options] bootstrap class path not set in conjunction with -source 8 /build/artemis-17.0.1+dfsg/uk/ac/sanger/artemis/j2ssh/SshFileManager.java:437: warning: [removal] destroy() in Thread has been deprecated and marked for removal public void destroy() ^ /build/artemis-17.0.1+dfsg/uk/ac/sanger/artemis/components/alignment/BamView.java:565: error: cannot find symbol FTPSeekableStream fss = new FTPSeekableStream(new URL(alignmentFile), ftpSocketTimeout); ^ symbol: class FTPSeekableStream location: class BamView /build/artemis-17.0.1+dfsg/uk/ac/sanger/artemis/components/alignment/BamView.java:565: error: cannot find symbol FTPSeekableStream fss = new FTPSeekableStream(new URL(alignmentFile), ftpSocketTimeout); ^ symbol: class FTPSeekableStream location: class BamView Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 2 errors 2 warnings ... Any help would be welcome. Kind regards Andreas. [1] https://salsa.debian.org/med-team/artemis -- http://fam-tille.de
