Hi again, On 11.09.20 00:01, Pierre Gruet wrote: > Hi, > > Le 10/09/2020 à 17:11, Andreas Tille a écrit : >> Hi Steffen, >> >> On Thu, Sep 10, 2020 at 03:32:49PM +0200, Steffen Möller wrote: >>> libpicard-java needs an argparse class from the barclay library. This >>> was found by the intense build-time testing of the PIGx-scRNAseq. >>> ... >>> How shall I/we proceed? My immediate plan was to just update locally to >>> vesion 4.0.0 (released a few days ago) and see if the two reverse >>> dependencies still build. >> From my naive point of view the migration to a recent libbarclay-java >> should be easy given that only two packages in our hands are rdepends >> of it. Thus I was running routine-update on barclay[1] but the build >> is running into: >> >> ... >> radle Test Executor 1 finished executing tests. >> Results: FAILURE (346 tests, 344 successes, 2 failures, 0 skipped) >> >> >> Pierre, can you help? ;-) >> > I have had a really hard time, but I finally found the issue (a > LinkedHashMap was wrongly iterated over in a Freemarker template), now > all build tests are passing and the .deb can be built :-) > I have pushed my changes to Salsa. > > Could someone do some final checks (maybe forward the patch I have written)?
https://github.com/broadinstitute/barclay/ You can expect to be listed as a contributor one your patch is accepted. That and an unpredictable exchange with upstream is what you earned. The submission to upstream is on you :) Should you feel a bit awkward with github then I happily help ... but since you are doing just fine with gitlab ... I added --- a/debian/pom-barclay.xml +++ b/debian/pom-barclay.xml @@ -5,7 +5,7 @@ <artifactId>barclay</artifactId> <packaging>jar</packaging> <description>barclay</description> - <version>2.1.0</version> + <version>4.0.0</version> <name>barclay</name> <organization> <name>org.broadinstitute</name> but otherwise left it and it looks good!?: $ dpkg -c ../libbarclay-java_4.0.0-1_all.deb drwxr-xr-x root/root 0 2020-09-10 23:55 ./ drwxr-xr-x root/root 0 2020-09-10 23:55 ./usr/ drwxr-xr-x root/root 0 2020-09-10 23:55 ./usr/share/ drwxr-xr-x root/root 0 2020-09-10 23:55 ./usr/share/doc/ drwxr-xr-x root/root 0 2020-09-10 23:55 ./usr/share/doc/libbarclay-java/ -rw-r--r-- root/root 709 2020-09-10 23:55 ./usr/share/doc/libbarclay-java/changelog.Debian.gz -rw-r--r-- root/root 3287 2020-09-10 23:55 ./usr/share/doc/libbarclay-java/copyright drwxr-xr-x root/root 0 2020-09-10 23:55 ./usr/share/java/ -rw-r--r-- root/root 147669 2020-09-10 23:55 ./usr/share/java/barclay-4.0.0.jar drwxr-xr-x root/root 0 2020-09-10 23:55 ./usr/share/maven-repo/ drwxr-xr-x root/root 0 2020-09-10 23:55 ./usr/share/maven-repo/org/ drwxr-xr-x root/root 0 2020-09-10 23:55 ./usr/share/maven-repo/org/broadinstitute/ drwxr-xr-x root/root 0 2020-09-10 23:55 ./usr/share/maven-repo/org/broadinstitute/barclay/ drwxr-xr-x root/root 0 2020-09-10 23:55 ./usr/share/maven-repo/org/broadinstitute/barclay/4.0.0/ -rw-r--r-- root/root 2246 2020-09-10 23:55 ./usr/share/maven-repo/org/broadinstitute/barclay/4.0.0/barclay-4.0.0.pom drwxr-xr-x root/root 0 2020-09-10 23:55 ./usr/share/maven-repo/org/broadinstitute/barclay/debian/ -rw-r--r-- root/root 2247 2020-09-10 23:55 ./usr/share/maven-repo/org/broadinstitute/barclay/debian/barclay-debian.pom lrwxrwxrwx root/root 0 2020-09-10 23:55 ./usr/share/java/barclay.jar -> barclay-4.0.0.jar lrwxrwxrwx root/root 0 2020-09-10 23:55 ./usr/share/maven-repo/org/broadinstitute/barclay/4.0.0/barclay-4.0.0.jar -> ../../../../../java/barclay.jar lrwxrwxrwx root/root 0 2020-09-10 23:55 ./usr/share/maven-repo/org/broadinstitute/barclay/debian/barclay-debian.jar -> ../../../../../java/barclay.jar > >>> If this update then then happens to also fix >>> the failed test of PIGx-scRNAseq, then this shall be it. Alternatively, >>> well, we would need versioned library packages, then, and I'll see how >>> far version 3 carries me. >> I do not think we should spent time on a version that just became >> outdated so version 4 should most probably be our target. >> >>> Right? If there is anyone out there who is a >>> bit closer to the barclay library, please direct me if there is any need >>> to keep the older version 2 in the archive. >> Libpicard-java needs an update as well - so I'd suggest to upgrade >> libbarclay-java first and than see how to continue (may be together >> with upstream). >> >> Disclaimer: All I said is probably absolutely naive and not based on >> any deeper knowledge about the software involved simply guided by my gut >> feeling about what usually was a sensible strategy. >> > I do not know barclay either but I would say the same. libpicard-java just finished building and testing (and it tested intensively), but pigx-scrnaseq will need to wait for another day. Will upload libbarclay-java - thank to tons! Steffen
