Obviously it shouldn't download anything. One of the failures is due to: [testng] FAILED: testRemoteQuery [testng] java.io.FileNotFoundException: http://data.broadinstitute.org/igvdata/test/tabix/trioDup.vcf.gz.tbi ... The other 3 failures look like: [testng] FAILED: testFailingRScript [testng] net.sf.picard.PicardException: Unexpected exception executing [Rscript /tmp/script2502320441721673396.R] [testng] at net.sf.picard.util.ProcessExecutor.execute(ProcessExecutor.java:103) [testng] at net.sf.picard.util.ProcessExecutor.execute(ProcessExecutor.java:79) [testng] at net.sf.picard.util.RExecutor.executeFromFile(RExecutor.java:76) ... On the plus side, there are 21997 passes! I tried this with icedtea-bin-7.
https://bugs.gentoo.org/580176#c1
The bug has been referenced in the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=1aa6122f56334850d1168c1da91af91af58175b3 commit 1aa6122f56334850d1168c1da91af91af58175b3 Author: David Seifert <soap@gentoo.org> AuthorDate: 2021-12-06 11:40:53 +0000 Commit: David Seifert <soap@gentoo.org> CommitDate: 2021-12-06 11:40:53 +0000 profiles: last-rite sci-biology/picard Bug: https://bugs.gentoo.org/572142 Bug: https://bugs.gentoo.org/580176 Bug: https://bugs.gentoo.org/776298 Signed-off-by: David Seifert <soap@gentoo.org> profiles/package.mask | 6 ++++++ 1 file changed, 6 insertions(+)
The bug has been closed via the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=8c4dc835b136a9585d825da398339774c16b7c43 commit 8c4dc835b136a9585d825da398339774c16b7c43 Author: Jakov Smolić <jsmolic@gentoo.org> AuthorDate: 2022-01-08 10:28:27 +0000 Commit: Jakov Smolić <jsmolic@gentoo.org> CommitDate: 2022-01-08 10:32:29 +0000 sci-biology/picard: treeclean Closes: https://bugs.gentoo.org/776298 Closes: https://bugs.gentoo.org/580176 Closes: https://bugs.gentoo.org/572142 Signed-off-by: Jakov Smolić <jsmolic@gentoo.org> profiles/package.mask | 6 -- sci-biology/picard/Manifest | 1 - sci-biology/picard/files/1.103-gentoo.patch | 131 ---------------------------- sci-biology/picard/metadata.xml | 11 --- sci-biology/picard/picard-1.103.ebuild | 69 --------------- 5 files changed, 218 deletions(-)
