Hi Shruti,
Le 21/07/2021 à 17:18, Andreas Tille a écrit :
Hi Shruti,
On Wed, Jul 21, 2021 at 01:32:35PM +0530, Shruti Sridhar wrote:
I am working on writing autopkgtests for logol [1] and the test passes in
my chroot but fails the pipeline
I could reproduce this locally with autopkgtest-virt-lxc run with the
"-B" option (otherwise it passes).
Hmmm, this
+ JAVA_OPTS=' -Xms512m -Xmx4096m'
+ java -Xms512m -Xmx1024m
-Dlogol.install=/tmp/autopkgtest-lxc.kjfgq_8m/downtmp/build.yfB/src
-Dlogol.conf=/tmp/autopkgtest-lxc.kjfgq_8m/downtmp/build.yfB/src/prolog/logol.properties
-Dlog4j.configuration=file:///tmp/autopkgtest-lxc.kjfgq_8m/downtmp/build.yfB/src/log4j.properties
-classpath
/tmp/autopkgtest-lxc.kjfgq_8m/downtmp/build.yfB/src/lib/biojava.jar:/tmp/autopkgtest-lxc.kjfgq_8m/downtmp/build.yfB/src/lib/bytecode:/tmp/autopkgtest-lxc.kjfgq_8m/downtmp/build.yfB/src/lib/mail.jar:/tmp/autopkgtest-lxc.kjfgq_8m/downtmp/build.yfB/src/lib/activation.jar:/tmp/autopkgtest-lxc.kjfgq_8m/downtmp/build.yfB/src/lib/xalan.jar:/tmp/autopkgtest-lxc.kjfgq_8m/downtmp/build.yfB/src/lib/xercesImpl.jar:/tmp/autopkgtest-lxc.kjfgq_8m/downtmp/build.yfB/src/lib/xml-apis.jar:/tmp/autopkgtest-lxc.kjfgq_8m/downtmp/build.yfB/src/lib/serializer.jar:/tmp/autopkgtest-lxc.kjfgq_8m/downtmp/build.yfB/src/lib/commons-configuration.jar:/tmp/autopkgtest-lxc.kjfgq_8m/downtmp/build.yfB/src/lib/LogolExec.jar:/tmp/autopkgtest-lxc.kjfgq_8m/downtmp/build.yfB/src/lib/commons-cli.jar:/tmp/autopkgtest-lxc.kjfgq_8m/downtmp/build.yfB/src/lib/commons-collections.jar:/tmp/autopkgtest-lxc.kjfgq_8m/downtmp/build.yfB/src/lib/commons-lang.jar:/tmp/autopkgtest-lxc.kjfgq_8m/downtmp/build.yfB/src/lib/commons-logging.jar:/tmp/autopkgtest-lxc.kjfgq_8m/downtmp/build.yfB/src/lib/log4j-1.2.jar:/tmp/autopkgtest-lxc.kjfgq_8m/downtmp/build.yfB/src/lib/antlr.jar
org.irisa.genouest.logol.Logol -g 1799.logol -s 1799.fasta -dna
Error: Could not find or load main class org.irisa.genouest.logol.Logol
Caused by: java.lang.ClassNotFoundException: org.irisa.genouest.logol.Logol
autopkgtest [06:49:18]: test run-unit-test: -----------------------]
looks tricky. Olivier, do you have some idea?
I think the problem is the invocation in the test you wrote:
bash -ex ${CUR_DIR}/LogolExec.sh -g 1799.logol -s 1799.fasta -dna
(and the same afterwards with LogolMultiExec.sh) : as LogolExec.sh and
LogolMultiExec.sh are located in the source tree, LOGOL_HOME in
LogolExec.sh points to the source tree and not to /usr/share/logol/,
which is what we want.
Replacing the invitations in your test with
LogolExec -g 1799.logol -s 1799.fasta -dna
solves the issue, and moreover it is perhaps more natural as I think
this is the typical invocation one would expect from an user.
Kind regards
Andreas.
[1] https://salsa.debian.org/med-team/logol
ᐧ
Warm regards,
--
Pierre
