Re: Could not build picard-tools version 1.100
On 21/10/13 07:45, Olivier Sallou wrote:
>
> On 10/20/2013 05:32 PM, Andreas Tille wrote:
>> Hi,
>>
>> it smells like it might be that the changes are explicitly about java6
>> but we are now building with Java 7. Unfurtunately I have no idea how
>> to turn this suspicion into code.
>>
>> Kind regards
>>
>> Andreas.
Hi,
I'm using picard-tools 1.96-0ubuntu2 under Bio-Linux 7 and had problems
because the CLASSPATH was not set, and the wrapper script does not set
-cp for the sam and bzip2 jars. It works if I set the java -cp paths
explicity in the wrapper. Tim Booth has updated the package in Bio-Linux:
root@beluga:~# apt-cache policy picard-tools
picard-tools:
Installed: 1.96-0ubuntu2
Candidate: 1.96-0ubuntu2
Version table:
*** 1.96-0ubuntu2 0
500 http://ppa.launchpad.net/nebc/bio-linux/ubuntu/ precise/main
amd64 Packages
100 /var/lib/dpkg/status
1.46-1build1 0
500 http://gb.archive.ubuntu.com/ubuntu/ precise/universe amd64
Packages
Here is my work-around:
Tony.
> rwt017@wildcat:~$ diff -Naur /usr/bin/picard-tools
/usr/local/bin/test-picard-tools
> --- /usr/bin/picard-tools 2013-08-16 14:45:04.000000000 +0100
> +++ /usr/local/bin/test-picard-tools 2013-10-16 14:44:44.347312505 +0100
> @@ -1,6 +1,6 @@
> #!/bin/sh
> set -eu
> -if [ `basename -- $0` = picard-tools ]; then
> +if [ `basename -- $0` = test-picard-tools ]; then
> if [ $# = 0 ]; then
> cat 1>&2 <<EOF
> picard-tools: missing command argument
> @@ -56,4 +56,4 @@
>
> # Note, jbzip2.jar and sam.jar etc. should now be added to cp implicitly
> p=/usr/share/java
> -exec java -XX:MaxPermSize=256m -cp $p/picard.jar $main "$@"
> +exec java -XX:MaxPermSize=256m -cp
$p/picard.jar:sam.jar:$p/jbzip2.jar $main "$@"
>> On Sun, Oct 20, 2013 at 11:06:17AM +0900, Charles Plessy wrote:
>>> Hello everybody,
>>>
>>> I tried to update picard-tools to version 1.100, unfortunately, it makes an
>>> error. It may be trivial for people knowing Java, so please let me know of a
>>> workaround (or commit it directly).
>>>
>>> The update made the following change in the build.xml file.
>>>
>>> <property environment="env"/>
>>> + <property name="java6.home" value="${env.JAVA6_HOME}"/>
> Hi,
> you indeed explicitly set a property with JAVA6_HOME, taken from
> environment.
> We are, as Andreas said, in Java7. Furthermore, is JAVA6_HOME set in
> debian/rules ? I think we usually have JAVA_HOME (not specifically
> related to a version).
> Maybe you should only set:
>
> + <property name="java6.home" value="${env.JAVA_HOME}"/>
>
>
> I wonder why however they need Java libs directly.
>
> Olivier
>>>
>>> <condition property="isUnix">
>>> <os family="unix"/>
>>> @@ -75,6 +77,10 @@
>>> <pathelement path="${classpath}"/>
>>> <pathelement location="${classes}"/>
>>> </path>
>>> +
>>> + <path id="java6.lib.ref">
>>> + <fileset dir="${java6.home}/lib" includes="*.jar"/>
>>> + </path>
>>> </target>
>>>
>>> And it leads to the following error.
>>>
>>> compile-sam-jdk:
>>> [mkdir] Created dir: /«PKGBUILDDIR»/classes
>>>
>>> BUILD FAILED
>>> /«PKGBUILDDIR»/build.xml:109: The following error occurred while executing this line:
>>> /«PKGBUILDDIR»/build.xml:476: /«PKGBUILDDIR»/${env.JAVA6_HOME}/lib does not exist.
>>>
>>> Cheers,
>>>
>>> Charles
>>>
>>> --
>>> Charles Plessy
>>> Debian Med packaging team,
>>> http://www.debian.org/devel/debian-med
>>> Tsurumi, Kanagawa, Japan
>>>
>>>
>>> --
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>>>
>>>
>
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