Hi Steffen, Le 11/09/2020 à 02:23, Steffen Möller a écrit : > 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 ... >
Thanks! :-) I have just forwarded the patch. I was too lazy (or it was too late) to do it yesterday night. Thanks for your words! > > 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! > Thanks for the upload and for the information that libpicard-java is also fine! > > Steffen > > Best, Pierre
