Re: Finishing ncbi-vdb and sra-sdk
Am Sun, Aug 07, 2022 at 11:24:02PM -0400 schrieb Aaron M. Ucko: > Andreas Tille writes: > > > CMake Error at test/sharq/CMakeLists.txt:42 (add_dependencies): > > The dependency target "RE2_" of target "test-sharq-parser" does not exist. > > I'll try to take a look soon, but most likely your patch didn't go quite > far enough. Thanks for having a look. > Meanwhile, I have made more (local) progress on ncbi-vdb; I'm pleased to > report that we should be able to drop its NGS build dependencies as of > version 3.0, so there won't be a cycle to contend with after all. Also, > I'm going to want to split out a small -data package to allow > (temporary) coinstallation of libncbi-vdb2 and libncbi-vdb3. This would mean another trip through new. I think it would be good to upload this quickly sinnce the package is currently hanging in new and ftpmaster can inspect your changed package. Kind regards Andreas. -- http://fam-tille.de
Re: zalign: autopkgtest failure on 32 bit architectures: Segmentation fault
On Sat, 6 Aug 2022 15:45:55 +0200 Paul Gevers wrote: Source: zalign Version: 0.9.1-6 Severity: serious User: debian...@lists.debian.org Usertags: fails-always Dear maintainer(s), You recently added an autopkgtest to your package zalign, great. However, it fails. Currently this failure is blocking the migration to testing [1]. Can you please investigate the situation and fix it? I copied some of the output at the bottom of this report. More information about this bug and the reason for filing it can be found on https://wiki.debian.org/ContinuousIntegration/RegressionEmailInformation Paul [1] https://qa.debian.org/excuses.php?package=zalign https://ci.debian.net/data/autopkgtest/testing/armhf/z/zalign/23914703/log.gz [93m[1mRunning Tests[0m [93m[1mTest 1[0m Stage 1: Distribute data to all nodes - # File parameters S sequence: 104 characters Filename: dd T sequence: 104 characters Filename: rt # Performance parameters Number of 'split' submatrices: 1 Available nodes:1 Horizontal block divisions:10 Vertical block divisions: 10 # Scoring parameters Match: 1 Mismatch: -3 Gap Opening: -5 Gap Extension: > Stage 3: Gather best scores --- 0: local_Count=1 score=32286916 local_BufferSize=32 [ci-203-97b45286:02642] *** Process received signal *** [ci-203-97b45286:02642] Signal: Segmentation fault (11) [ci-203-97b45286:02642] Signal code: Address not mapped (1) [ci-203-97b45286:02642] Failing at address: 0xeabc4e74 [ci-203-97b45286:02642] *** End of error message *** /tmp/autopkgtest-lxc.6k2utcwh/downtmp/build.a3p/src/debian/tests/run-unit-test: line 20: 2642 Segmentation fault mpialign dd rt autopkgtest [04:02:32]: test run-unit-test Hello Team, I took a look at this and it seems the upstream[1] is not active anymore and Ubuntu already has a long standing bug report[2] regarding the same issue which hasn't seen any progress yet. So can we skip the tests for the failing architectures ? [1] - https://code.launchpad.net/zalign [2] - https://bugs.launchpad.net/zalign/+bug/1174235 Thanks -- ╭───╮ │ Mohammed Bilal│ │ 2D65 BC1E B966 5A6E 97F9 730A B3F5 9452 8521 9E1F │ ╰───╯ OpenPGP_signature Description: OpenPGP digital signature
Re: zalign: autopkgtest failure on 32 bit architectures: Segmentation fault
On 8/8/22 5:50 PM, Mohd Bilal wrote: On Sat, 6 Aug 2022 15:45:55 +0200 Paul Gevers wrote: Source: zalign Version: 0.9.1-6 Severity: serious User: debian...@lists.debian.org Usertags: fails-always Dear maintainer(s), You recently added an autopkgtest to your package zalign, great. However, it fails. Currently this failure is blocking the migration to testing [1]. Can you please investigate the situation and fix it? I copied some of the output at the bottom of this report. More information about this bug and the reason for filing it can be found on https://wiki.debian.org/ContinuousIntegration/RegressionEmailInformation Paul [1] https://qa.debian.org/excuses.php?package=zalign https://ci.debian.net/data/autopkgtest/testing/armhf/z/zalign/23914703/log.gz [93m[1mRunning Tests[0m [93m[1mTest 1[0m Stage 1: Distribute data to all nodes - # File parameters S sequence: 104 characters Filename: dd T sequence: 104 characters Filename: rt # Performance parameters Number of 'split' submatrices: 1 Available nodes: 1 Horizontal block divisions: 10 Vertical block divisions: 10 # Scoring parameters Match: 1 Mismatch: -3 Gap Opening: -5 Gap Extension: > Stage 3: Gather best scores --- 0: local_Count=1 score=32286916 local_BufferSize=32 [ci-203-97b45286:02642] *** Process received signal *** [ci-203-97b45286:02642] Signal: Segmentation fault (11) [ci-203-97b45286:02642] Signal code: Address not mapped (1) [ci-203-97b45286:02642] Failing at address: 0xeabc4e74 [ci-203-97b45286:02642] *** End of error message *** /tmp/autopkgtest-lxc.6k2utcwh/downtmp/build.a3p/src/debian/tests/run-unit-test: line 20: 2642 Segmentation fault mpialign dd rt autopkgtest [04:02:32]: test run-unit-test Hello Team, I took a look at this and it seems the upstream[1] is not active anymore and Ubuntu already has a long standing bug report[2] regarding the same issue which hasn't seen any progress yet. I tried to add autopkgtests to zalign long ago, and if I remember correctly it was segfaulting on some data on amd64 itself. So can we skip the tests for the failing architectures ? We should instead ask for _removal of this package_. Same version since 9 years and upstream is dead too. [1] - https://code.launchpad.net/zalign [2] - https://bugs.launchpad.net/zalign/+bug/1174235 -- Best, Nilesh OpenPGP_signature Description: OpenPGP digital signature
Re: zalign: autopkgtest failure on 32 bit architectures: Segmentation fault
On 8/8/22 18:05, Nilesh Patra wrote: On 8/8/22 5:50 PM, Mohd Bilal wrote: Hello Team, I took a look at this and it seems the upstream[1] is not active anymore and Ubuntu already has a long standing bug report[2] regarding the same issue which hasn't seen any progress yet. I tried to add autopkgtests to zalign long ago, and if I remember correctly it was segfaulting on some data on amd64 itself. So can we skip the tests for the failing architectures ? We should instead ask for _removal of this package_. Same version since 9 years and upstream is dead too. Makes sense. So shall I file a removal request for this package ? [1] - https://code.launchpad.net/zalign [2] - https://bugs.launchpad.net/zalign/+bug/1174235 -- ╭╮ │ Mohammed Bilal │ │ 2D65 BC1E B966 5A6E 97F9 730A B3F5 9452 8521 9E1F │ ╰╯ OpenPGP_0xB3F5945285219E1F.asc Description: OpenPGP public key OpenPGP_signature Description: OpenPGP digital signature
Re: zalign: autopkgtest failure on 32 bit architectures: Segmentation fault
On 8/8/22 6:20 PM, Mohd Bilal wrote: On 8/8/22 18:05, Nilesh Patra wrote: On 8/8/22 5:50 PM, Mohd Bilal wrote: Hello Team, I took a look at this and it seems the upstream[1] is not active anymore and Ubuntu already has a long standing bug report[2] regarding the same issue which hasn't seen any progress yet. I tried to add autopkgtests to zalign long ago, and if I remember correctly it was segfaulting on some data on amd64 itself. So can we skip the tests for the failing architectures ? We should instead ask for _removal of this package_. Same version since 9 years and upstream is dead too. Makes sense. So shall I file a removal request for this package ? Yes. @Andreas, any objections? -- Best, Nilesh
