Bug 281533 – sci-biology/repeatmasker-3.2.7: sh: /usr/share/repeatmasker/ProcessRepeats: No such file or directory

• Product: Gentoo Linux
• Status: RESOLVED FIXED

[Description Martin Mokrejš 2009-08-15 00:44:47 UTC]

$ /usr/bin/RepeatMasker -species human -nolow blah.dna
RepeatMasker version open-3.2.7
Search engine: Crossmatch
Using Master Database: /usr/share/repeatmasker/Libraries/RepeatMaskerLib.embl
Building general libraries in: /home/mmokrejs/.RepeatMaskerCache/20090120/general
Building species libraries in: /home/mmokrejs/.RepeatMaskerCache/20090120/homo_sapiens

analyzing file blah.dna

Checking for E. coli insertion elements
identifying full-length ALUs in batch 1 of 1
identifying full-length interspersed repeats in batch 1 of 1
identifying remaining ALUs in batch 1 of 1
identifying most interspersed repeats in batch 1 of 1
identifying long interspersed repeats in batch 1 of 1
identifying ancient repeats in batch 1 of 1
identifying retrovirus-like sequences in batch 1 of 1
identifying tough LINE1s in batch 1 of 1
refining SINE/Alu elements in batch 1 of 1
sh: /usr/share/repeatmasker/ProcessRepeats: No such file or directory
$

[Comment 1 Martin Mokrejš 2009-08-15 01:03:11 UTC]

# equery files repeatmasker
 * Searching for repeatmasker ...
 * Contents of sci-biology/repeatmasker-3.2.7:
/usr
/usr/bin
/usr/bin/DateRepeats
/usr/bin/DupMasker
/usr/bin/ProcessRepeats
^^^^^^^^^

I guess in Gentoo REPEATMASKER_DIR is "/usr/share/repeatmasker/" and will never be "/usr/bin". I suspect you will have to create symlinks from the original place or let them be in the default place or patch the real perl code to use another variable for executables.

[Comment 2 Andrey Kislyuk (RETIRED) 2009-08-17 19:42:36 UTC]

Thanks for pointing that out, Martin. Fix committed to main tree, please re-merge and test.

[Comment 3 Martin Mokrejš 2009-08-18 10:58:52 UTC]

fixed, thanks.