Bug#1042769: provean: incompatible with cd-hit >= 4.8.1-4

Control: tags -1 + patch pending On Wed, 2 Apr 2025 10:05:52 +0300 Andrius Merkys wrote: I finally managed to isolate the difference in cdhit output which causes segfaults in provean. It seems that cdhit >= 4.8.1-4 replaced full FASTA headers in its output with partial IDs: diff -r /home/and

Bug#1042769: provean: incompatible with cd-hit >= 4.8.1-4

A note for posterity: I solved this bug by comparing the outputs of each tool used in provean (cdhit and blastdbcmd) between last known working environment (Ubuntu Xenial) and Ubuntu Focal (where it is broken). After preparing a patch, I checked it on Debian Sid as well. Correct output with

Bug#1042769: provean: incompatible with cd-hit >= 4.8.1-4

Hello, I finally managed to isolate the difference in cdhit output which causes segfaults in provean. It seems that cdhit >= 4.8.1-4 replaced full FASTA headers in its output with partial IDs: diff -r /home/andrius/provean/good/cdhit.cluster /home/andrius/provean/bad/cdhit.cluster 1c1 < >gi

Bug#1042769: provean: incompatible with cd-hit >= 4.8.1-4

Hi Andrius, trying to find more readers on Debian Med list to possibly reach some cd-hit users. Am Fri, Aug 18, 2023 at 07:01:08AM +0300 schrieb Andrius Merkys: > Hi Andreas, > > On 2023-08-17 10:49, Andreas Tille wrote: > > thanks for reporting this issue. You were mentioning you want to come

Bug#1042769: provean: incompatible with cd-hit >= 4.8.1-4

Hi Andreas, On 2023-08-17 10:49, Andreas Tille wrote: thanks for reporting this issue. You were mentioning you want to come up with a patch. Since you seem to have dived into this issue deeper I assume you will care for this bug. If not please clarify the status (or may be set the "help" tag)

Bug#1042769: provean: incompatible with cd-hit >= 4.8.1-4

Hi Andrius, thanks for reporting this issue. You were mentioning you want to come up with a patch. Since you seem to have dived into this issue deeper I assume you will care for this bug. If not please clarify the status (or may be set the "help" tag). Kind regards Andreas. -- http://fam-

Bug#1042769: provean: incompatible with cd-hit >= 4.8.1-4

Package: provean Version: 1.1.5+ds-2 Severity: serious Hello, Current provean package is broken: it segfaults while parsing the output of cd-hit. The most recent compatible version of cd-hit seems to be 4.6.4-1. I hope to come up with a patch sooner or later. Andrius