Bug#961347: sra-sdk: autopktest failure
Sebastian Ramacher writes: > | 2020-05-22T21:52:08 fastq-load.2.10.6 err: > libs/vdb/wtable.c:204:VTableOpenUpdate: schema not found while creating > manager within virtual database module - failed to create table with schema > NCBI:SRA:Illumina:tbl:phred:v2 Thanks for the report. FTR, libncbi-vdb2 does already install the schemas; the problem is getting it to acknowledge our differences from upstream's layout preferences. I already saw this failure and am working on a proper fix. -- Aaron M. Ucko, KB1CJC (amu at alum.mit.edu, ucko at debian.org) http://www.mit.edu/~amu/ | http://stuff.mit.edu/cgi/finger/?a...@monk.mit.edu
Bug#961347: sra-sdk: autopktest failure
Source: sra-sdk Version: 2.10.6+dfsg-4 Severity: serious The autopkgtests of sra-sdk currently fail in unstable: | >Running fastq-load... | 2020-05-22T21:52:08 fastq-load.2.10.6 warn: file="SRR6650398_1.fastq" offset="0" | 2020-05-22T21:52:08 fastq-load.2.10.6 warn: quality_scoring_system attribute not set for this file, using Phred as default | 2020-05-22T21:52:08 fastq-load.2.10.6 err: libs/vdb/wtable.c:204:VTableOpenUpdate: schema not found while creating manager within virtual database module - failed to create table with schema NCBI:SRA:Illumina:tbl:phred:v2 | 2020-05-22T21:52:08 fastq-load.2.10.6 err: libs/kproc/queue.c:365:KQueuePop: schema not found while creating manager within virtual database module - accession="SRR6650398" status="failure" | 2020-05-22T21:52:08 fastq-load.2.10.6 err: libs/kproc/queue.c:365:KQueuePop: schema not found while creating manager within virtual database module - load failed: libs/kproc/queue.c:365:KQueuePop: schema not found | autopkgtest [21:52:08]: test run-unit-test: ---] | autopkgtest [21:52:08]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - | run-unit-testFAIL non-zero exit status 3 | autopkgtest [21:52:08]: summary | run-unit-testFAIL non-zero exit status 3 See also https://ci.debian.net/data/autopkgtest/unstable/amd64/s/sra-sdk/5608930/log.gz Cheers -- Sebastian Ramacher signature.asc Description: PGP signature
