Groups > linux.debian.maint.java > #8334

Re: Asking help for the picard-tools package

From	Vincent Danjean <vdanjean.ml@free.fr>
Newsgroups	linux.debian.maint.java
Subject	Re: Asking help for the picard-tools package
Date	2015-09-08 09:40 +0200
Message-ID	<q6lFw-63O-25@gated-at.bofh.it> (permalink)
References	<q6eE2-4tn-5@gated-at.bofh.it>
Organization	linux.* mail to news gateway

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On 08/09/2015 02:02, Vincent Danjean wrote:
>   I'm annoyed with the current package: the tests fail when the
> sources are in a directory containing a '+'. And, due to the repack
> and the +dfsg suffix, my sbuilder put the source into a
> «BUILDDIR»/picard-tools-1.138+dfsg.1 directory.

  In fact, the bug comes from the main program, at runtime:
vdanjean@atsina:~/picard-tools$ CLASSPATH=/usr/share/java/htsjdk.jar:/usr/share/java/guava.jar:dist/picard.jar java picard.cmdline.PicardCommandLine FilterVcf -h
USAGE: FilterVcf [options]
[... help text ...]
vdanjean@atsina:~/picard-tools$ cd ..
vdanjean@atsina:~$ mv picard-tools picard-tools+1
vdanjean@atsina:~$ cd picard-tools+1/
vdanjean@atsina:~/picard-tools+1$ CLASSPATH=/usr/share/java/htsjdk.jar:/usr/share/java/guava.jar:dist/picard.jar java picard.cmdline.PicardCommandLine FilterVcf -h
WARNING	2015-09-08 07:36:07	ClassFinder	could not read entriesjava.io.FileNotFoundException: /home/vdanjean/picard-tools 1/dist/picard.jar (No such file or directory)
USAGE: PicardCommandLine <program name> [-h]

Available Programs:
--------------------------------------------------------------------------------------

'FilterVcf' is not a valid command. See PicardCommandLine --help for more information.
vdanjean@atsina:~/picard-tools+1$

  :-(
  I will try to contact upstream.

  Regards,
    Vincent

-- 
Vincent Danjean       GPG key ID 0xD17897FA         vdanjean@debian.org
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Unofficial pkgs: http://moais.imag.fr/membres/vincent.danjean/deb.html
APT repo:  deb http://people.debian.org/~vdanjean/debian unstable main

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Asking help for the picard-tools package Vincent Danjean <vdanjean.ml@free.fr> - 2015-09-08 02:10 +0200
  Re: Asking help for the picard-tools package Vincent Danjean <vdanjean.ml@free.fr> - 2015-09-08 09:40 +0200
    Asking review for the picard-tools package Vincent Danjean <vdanjean.ml@free.fr> - 2015-09-08 11:50 +0200

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