Re: Update of the Integrative Genomics Viewer to version 2.0 ?
On 25 July 2011 17:13, Charles Plessy ple...@debian.org wrote: Le Mon, Jul 25, 2011 at 05:03:55PM -0700, Shaun Jackman a écrit : I used git-import-orig from git-buildpackage 0.5.26, but it didn't update the pristine-tar branch by default. I'll read the man page tomorrow and see if I can get it working. git-import-orig --pristine-tar :) Also, it can be made the default using a debian/gbp.conf file (example in /etc/gbp.conf). I actually recommend this, since the presence of the file reminds that the package uses git-buildpackage. Do you know how I can generate the pristine-tar data now, after I've already committed upstream/2.0.6? Trying git-import-orig --pristine-tar makes a mess of it: $ git-import-orig --pristine-tar ../2.0.6/igv_2.0.6.orig.tar.bz2 What is the upstream version? [2.0.6] gbp:info: Importing '../2.0.6/igv_2.0.6.orig.tar.bz2' to branch 'upstream'... gbp:info: Source package is igv gbp:info: Upstream version is 2.0.6 pristine-tar: committed igv_2.0.6.orig.tar.bz2.delta to branch pristine-tar fatal: tag 'upstream/2.0.6' already exists gbp:error: git returned 128 gbp:error: Couldn't tag upstream/2.0.6 gbp:error: Import of ../2.0.6/igv_2.0.6.orig.tar.bz2 failed Cheers, Shaun -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/CADX6M3r1jXCAuXeVN-LV+u9Lds=Zy+T1TT=q80mudrpd+wm...@mail.gmail.com
Re: Update of the Integrative Genomics Viewer to version 2.0 ?
On 26 July 2011 10:02, Shaun Jackman sjack...@gmail.com wrote: On 25 July 2011 17:13, Charles Plessy ple...@debian.org wrote: Le Mon, Jul 25, 2011 at 05:03:55PM -0700, Shaun Jackman a écrit : I used git-import-orig from git-buildpackage 0.5.26, but it didn't update the pristine-tar branch by default. I'll read the man page tomorrow and see if I can get it working. git-import-orig --pristine-tar :) Also, it can be made the default using a debian/gbp.conf file (example in /etc/gbp.conf). I actually recommend this, since the presence of the file reminds that the package uses git-buildpackage. Do you know how I can generate the pristine-tar data now, after I've already committed upstream/2.0.6? Trying git-import-orig --pristine-tar makes a mess of it: $ git-import-orig --pristine-tar ../2.0.6/igv_2.0.6.orig.tar.bz2 What is the upstream version? [2.0.6] gbp:info: Importing '../2.0.6/igv_2.0.6.orig.tar.bz2' to branch 'upstream'... gbp:info: Source package is igv gbp:info: Upstream version is 2.0.6 pristine-tar: committed igv_2.0.6.orig.tar.bz2.delta to branch pristine-tar fatal: tag 'upstream/2.0.6' already exists gbp:error: git returned 128 gbp:error: Couldn't tag upstream/2.0.6 gbp:error: Import of ../2.0.6/igv_2.0.6.orig.tar.bz2 failed Figured it out: pristine-tar commit ../igv_2.0.6.orig.tar.bz2 Cheers, Shaun -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/cadx6m3qceml7jti7w8ootujseg6ry5rjcuijnzjczpv6aqb...@mail.gmail.com
Re: Update of the Integrative Genomics Viewer to version 2.0 ?
Hi Charles, I've just uploaded IGV 2.0.6-1. What do I do with the pristine-tar and meta branches? These branches are new to me. Cheers, Shaun On 28 June 2011 10:38, Shaun Jackman sjack...@gmail.com wrote: Hi Charles, I'm going to be pretty busy for about two weeks. I probably won't have time to look into this until then. If 1.5.65 compiles cleanly and works, there's no harm in uploading that in the mean time. I can take a look into the 2.0 log4j issue two weeks from now. The RollingFileAppender class is at least present in the jar: $ strings /usr/share/java/log4j-1.2-1.2.15.jar |grep /RollingFileAppender.class$ org/apache/log4j/RollingFileAppender.class Cheers, Shaun On 27 June 2011 23:17, Charles Plessy ple...@debian.org wrote: Dear Shaun and everybody, There is a major update of the IGV, which may be interesting to follow. Unfortunately, I have tried to build it from source but could not produce a JAR file that can be executed. I have been reluctant to modify the master branch of the Git repository where we manage the igv package, as there is a version 1.5.65 on the upstream download area, but not in their changelog, which suggests that there may be some maintainance. What shall I do: share work on version 2.0 in our master branch, make a separate branch for the moment, or provide a temporary fork separately ? For the record, the error I get is: log4j:ERROR Could not find value for key log4j.appender.R log4j:ERROR Could not instantiate appender named R. ERROR [2011-06-28 15:16:26,637] [DefaultExceptionHandler.java:42] [main] Unhandled exception java.lang.NoClassDefFoundError: org/apache/log4j/RollingFileAppender at org.broad.igv.ui.Main.initializeLog(Main.java:225) at org.broad.igv.ui.Main.initApplication(Main.java:94) at org.broad.igv.ui.Main.main(Main.java:70) Caused by: java.lang.ClassNotFoundException: org.apache.log4j.RollingFileAppender at java.net.URLClassLoader$1.run(URLClassLoader.java:217) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(URLClassLoader.java:205) at java.lang.ClassLoader.loadClass(ClassLoader.java:321) at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:294) at java.lang.ClassLoader.loadClass(ClassLoader.java:266) at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:334) ... 3 more Have a nice day, -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/CADX6M3rG7Mb0-qErugTjCZgqTd1H4u4BmSzKLWPFP3WYFO9D=q...@mail.gmail.com
Re: Update of the Integrative Genomics Viewer to version 2.0 ?
Le Mon, Jul 25, 2011 at 12:56:01PM -0700, Shaun Jackman a écrit : Hi Charles, I've just uploaded IGV 2.0.6-1. What do I do with the pristine-tar and meta branches? These branches are new to me. Hi Shaun, thanks a lot for bringing us IGV 2.0 ! the pristine-tar is a convenience branch that stores information necessary to re-create a bit-by-bit identical upstream archive (‘.orig.tar.gz’), so that it avoids problems of hashsum mismatches when uploading Debian revisions (perhaps you have seen these rejection emails on our maintainer mailing list). For some reasons, just doing ‘tar xfvz’ from the upstream branch (ignoring .git, of course) will not produce exactly the same file on different systems. The main helper tool we use to register an ‘upstream’ tarball (in the case of IGV, that is what the get-orig-source script produces) is ‘git-import-orig’ from the git-buildpackage toolkit. The meta branch is more of a personal experiment. Feel free to ignore it if it bothers you. In this branch I store mainly the build logs for each uploaded versions. In some cases, I found it very convenient for troubleshooting. I also store the signed .changes and .dsc files, but I am less sure how useful they are. Have a nice day, -- Charles -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20110725231225.gb24...@merveille.plessy.net
Re: Update of the Integrative Genomics Viewer to version 2.0 ?
On 25 July 2011 16:12, Charles Plessy ple...@debian.org wrote: Le Mon, Jul 25, 2011 at 12:56:01PM -0700, Shaun Jackman a écrit : Hi Charles, I've just uploaded IGV 2.0.6-1. What do I do with the pristine-tar and meta branches? These branches are new to me. Hi Shaun, thanks a lot for bringing us IGV 2.0 ! the pristine-tar is a convenience branch that stores information necessary to re-create a bit-by-bit identical upstream archive (‘.orig.tar.gz’), so that it avoids problems of hashsum mismatches when uploading Debian revisions (perhaps you have seen these rejection emails on our maintainer mailing list). For some reasons, just doing ‘tar xfvz’ from the upstream branch (ignoring .git, of course) will not produce exactly the same file on different systems. The main helper tool we use to register an ‘upstream’ tarball (in the case of IGV, that is what the get-orig-source script produces) is ‘git-import-orig’ from the git-buildpackage toolkit. Hi Charles, I used git-import-orig from git-buildpackage 0.5.26, but it didn't update the pristine-tar branch by default. I'll read the man page tomorrow and see if I can get it working. Cheers, Shaun -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/CADX6M3qSPyK-rC1kU9vcNcYMy=x4me_81rg_mfnqgwjtgjm...@mail.gmail.com
Re: Update of the Integrative Genomics Viewer to version 2.0 ?
Le Mon, Jul 25, 2011 at 05:03:55PM -0700, Shaun Jackman a écrit : I used git-import-orig from git-buildpackage 0.5.26, but it didn't update the pristine-tar branch by default. I'll read the man page tomorrow and see if I can get it working. git-import-orig --pristine-tar :) Also, it can be made the default using a debian/gbp.conf file (example in /etc/gbp.conf). I actually recommend this, since the presence of the file reminds that the package uses git-buildpackage. Cheers, -- Charles Plessy -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20110726001329.ge24...@merveille.plessy.net
Update of the Integrative Genomics Viewer to version 2.0 ?
Dear Shaun and everybody, There is a major update of the IGV, which may be interesting to follow. Unfortunately, I have tried to build it from source but could not produce a JAR file that can be executed. I have been reluctant to modify the master branch of the Git repository where we manage the igv package, as there is a version 1.5.65 on the upstream download area, but not in their changelog, which suggests that there may be some maintainance. What shall I do: share work on version 2.0 in our master branch, make a separate branch for the moment, or provide a temporary fork separately ? For the record, the error I get is: log4j:ERROR Could not find value for key log4j.appender.R log4j:ERROR Could not instantiate appender named R. ERROR [2011-06-28 15:16:26,637] [DefaultExceptionHandler.java:42] [main] Unhandled exception java.lang.NoClassDefFoundError: org/apache/log4j/RollingFileAppender at org.broad.igv.ui.Main.initializeLog(Main.java:225) at org.broad.igv.ui.Main.initApplication(Main.java:94) at org.broad.igv.ui.Main.main(Main.java:70) Caused by: java.lang.ClassNotFoundException: org.apache.log4j.RollingFileAppender at java.net.URLClassLoader$1.run(URLClassLoader.java:217) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(URLClassLoader.java:205) at java.lang.ClassLoader.loadClass(ClassLoader.java:321) at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:294) at java.lang.ClassLoader.loadClass(ClassLoader.java:266) at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:334) ... 3 more Have a nice day, -- Charles Plessy Debian Med packaging team, http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20110628061749.gb32...@merveille.plessy.net
Re: Update of the Integrative Genomics Viewer to version 2.0 ?
Hi Charles, I'm going to be pretty busy for about two weeks. I probably won't have time to look into this until then. If 1.5.65 compiles cleanly and works, there's no harm in uploading that in the mean time. I can take a look into the 2.0 log4j issue two weeks from now. The RollingFileAppender class is at least present in the jar: $ strings /usr/share/java/log4j-1.2-1.2.15.jar |grep /RollingFileAppender.class$ org/apache/log4j/RollingFileAppender.class Cheers, Shaun On 27 June 2011 23:17, Charles Plessy ple...@debian.org wrote: Dear Shaun and everybody, There is a major update of the IGV, which may be interesting to follow. Unfortunately, I have tried to build it from source but could not produce a JAR file that can be executed. I have been reluctant to modify the master branch of the Git repository where we manage the igv package, as there is a version 1.5.65 on the upstream download area, but not in their changelog, which suggests that there may be some maintainance. What shall I do: share work on version 2.0 in our master branch, make a separate branch for the moment, or provide a temporary fork separately ? For the record, the error I get is: log4j:ERROR Could not find value for key log4j.appender.R log4j:ERROR Could not instantiate appender named R. ERROR [2011-06-28 15:16:26,637] [DefaultExceptionHandler.java:42] [main] Unhandled exception java.lang.NoClassDefFoundError: org/apache/log4j/RollingFileAppender at org.broad.igv.ui.Main.initializeLog(Main.java:225) at org.broad.igv.ui.Main.initApplication(Main.java:94) at org.broad.igv.ui.Main.main(Main.java:70) Caused by: java.lang.ClassNotFoundException: org.apache.log4j.RollingFileAppender at java.net.URLClassLoader$1.run(URLClassLoader.java:217) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(URLClassLoader.java:205) at java.lang.ClassLoader.loadClass(ClassLoader.java:321) at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:294) at java.lang.ClassLoader.loadClass(ClassLoader.java:266) at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:334) ... 3 more Have a nice day, -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/banlktik0_a4s8kkp_fs_r6wyh2ehpkb...@mail.gmail.com
