| Patch | Description | Author | Forwarded | Bugs | Origin | Last update |
|---|---|---|---|---|---|---|
| Extract_version_from_BEDTools_properly.patch | Tests 8 and 26 in BEDTools.t failed because BEDTools.pm couldn't extract versions of tools properly. This patch fixes it. Related test 44 still fails due to an unknown error. |
Pranav Ballaney <ballaneypranav@gmail.com> | no | 2020-04-05 | ||
| skip_tests_for_RemoteBlast_rpsblast.patch | no | |||||
| skip_tests_for_RemoteBlast.patch | RemoteBlast.t needs internet access for some tests - disabled. | Pranav Ballaney <ballaneypranav@gmail.com> | no | 2020-04-05 | ||
| kalign-input-via-piping.patch | Kalign takes input via piping For some reason, input via the -i flag doesn't work inside a chroot. For this reason, Kalign.pm is modified to allow the program to take input via a pipe. |
Pranav Ballaney <ballaneypranav@gmail.com> | no | 2020-03-31 | ||
| kalign-version-regex.patch | Update regex to extract Kalign version Due to an update from v2 to v3, the output format of Kalign has changed. This patch changes the regex used to extract the version number from Kalign3. --show flag is added because otherwise Kalign3 throws an error, being run without an input file. |
Pranav Ballaney <ballaneypranav@gmail.com> | no | 2020-03-31 | ||
| skip_tests_for_wise.patch | Possibly incompatible wise versions - ignore these tests | Andreas Tille <tille@debian.org> | no | 2016-12-16 | ||
| skip_tests_for_phylip.patch | No idea why the number of tests is 8 instead of 9 | Andreas Tille <tille@debian.org> | no | 2016-12-16 | ||
| skip_tests_for_phyml.patch | Somehow there are issues to initialise openmpi, but beside these warnings there are also errors Warning messages from phyml: . beignet-opencl-icd: no supported GPU found, this is probably the wrong opencl-icd package for this hardware (If you have multiple ICDs installed and OpenCL works, you can ignore this message) -------------------------------------------------------------------------- . Probably we can ignore the GPU optimisation issue here. It seems also MPI initialisation is failing which whould be nice to solve (FIXME) . It looks like orte_init failed for some reason; your parallel process is likely to abort. There are many reasons that a parallel process can fail during orte_init; some of which are due to configuration or environment problems. This failure appears to be an internal failure; here's some additional information (which may only be relevant to an Open MPI developer): orte_ess_init failed --> Returned value Unable to start a daemon on the local node (-127) instead of ORTE_SUCCESS -------------------------------------------------------------------------- -------------------------------------------------------------------------- It looks like MPI_INIT failed for some reason; your parallel process is likely to abort. There are many reasons that a parallel process can fail during MPI_INIT; some of which are due to configuration or environment problems. This failure appears to be an internal failure; here's some additional information (which may only be relevant to an Open MPI developer): ompi_mpi_init: ompi_rte_init failed --> Returned "Unable to start a daemon on the local node" (-127) instead of "Success" (0) -------------------------------------------------------------------------- *** An error occurred in MPI_Init *** on a NULL communicator *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort, *** and potentially your MPI job) [hostname:2001] Local abort before MPI_INIT completed successfully, but am not able to aggregate error messages, and not able to guarantee that all other processes were killed! . |
Andreas Tille <tille@debian.org> | no | 2016-12-16 | ||
| skip_tests_for_infernal.patch | A lot of tests need to be skipped. BioPerl is spoorting only old infernal interface | Andreas Tille <tille@debian.org> | no | 2016-12-16 | ||
| skip_tests_for_ncbi-blast+.patch | Somehow tests are excluded automatically - adjust expected number of tests | Andreas Tille <tille@debian.org> | no | 2016-12-16 | ||
| hyphy.patch | Hyphy | no | ||||
| remove_tests_for_ensembl.patch | For some reason Ensembl.t test is executed in autopkgtest run even if it should be skipped due to missing preconditions (http://search.cpan.org/~cjfields/Bio-EUtilities-1.72/lib/Bio/DB/EUtilities.pm) The test will now be fully removed to make sure it is skipped. |
Andreas Tille <tille@debian.org> | no | 2017-01-14 | ||
| skip_tests_for_soap.patch | Somehow these tests are failing - no idea why | Andreas Tille <tille@debian.org> | no | 2019-02-11 | ||
| get-overlap.patch | change mapping of bedtools subcommand overlap This patch addresses the following test error: . # Failed test 'get version for 'overlap'' # at t/BEDTools.t line 212. . ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: No executable! STACK: Error::throw STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:449 STACK: Bio::Tools::Run::BEDTools::run /<<PKGBUILDDIR>>/blib/lib/Bio/Tools/Run/BEDTools.pm:278 STACK: t/BEDTools.t:275 ----------------------------------------------------------- . Config.pm assumes the subcommand of bedtools "overlap" is called "overlap", but it is actually "getOverlap". |
Étienne Mollier <etienne.mollier@mailoo.org> | no | debian | 2020-12-04 | |
| alternate-data.patch | use alternate rmsk dataset This patch solves the following test suite error, occurring even though BED tools are made available at build time testing: . ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: File '' not BED/GFF/VCF format. STACK: Error::throw STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:449 STACK: Bio::Tools::Run::BEDTools::run /<<PKGBUILDDIR>>/blib/lib/Bio/Tools/Run/BEDTools.pm:477 STACK: t/BEDTools.t:252 ----------------------------------------------------------- . Instead of using the default rmsk.hg18.chr21.bed file which is unavailable in the archive, let's use rmsk.hg18.chr21.small.bed, provided by the package python3-pybedtools, which seemingly does the job almost as well apparently. |
Étienne Mollier <etienne.mollier@mailoo.org> | no | debian | 2020-12-04 | |
| skip-test-for-kalign.patch | skip last Kalign test This test fails on armhf and ppc64el and prevents migration of bioperl-run to testing. This is either a Kalign bug on these architectures, or a side effect of working with qemu-user-static. Skipping that test buys us some time to investigate further, temporary hopefully. |
Étienne Mollier <etienne.mollier@mailoo.org> | not-needed | 2021-01-06 | ||
| fix-whatis-entries.patch | fix whatis entries in multiple Bio Perl modules | Étienne Mollier <emollier@debian.org> | no | 2021-07-14 | ||
| unscramble-erpin.patch | replace exotic character by seemingly correct plain old dash '-' A couple of ISO-8859 characters trigger the lintian warning national-encoding. Looking into details, it seems that a plain old dash '-' got replaced by a more exotic character 'Ð'. This patch brings the '-' in the description of the affected Perl module ERPIN.pm. |
Étienne Mollier <emollier@debian.org> | no | 2021-07-14 | ||
| fix-pod-conversion.patch | fix lintian warning about pod-conversion-message | Étienne Mollier <emollier@debian.org> | no | 2021-07-14 | ||
| adjust-muscle-test.patch | adjust skip count for Muscle test The initial count looks like upstream might have forgotten to update it. | Étienne Mollier <emollier@debian.org> | no | 2022-02-10 |