I would like all supporting arches to please stabilise sci-biology/emboss-3.0.0-r1. This will require stabilising sci-biology/rebase-601-r1. To test EMBOSS, use: $ wget pelican.rsvs.ulaval.ca/distfiles/seq/emboss-test.sh $ chmod + x emboss-test.sh $ ./emboss-test.sh This script will download a sequence from a server, do some manipulations, and finally compare the results with reference files. If the tests are sucessful (ie. the only differences shown are timestamps), the package is ready to be stabilised on your arch. (See the comments in the file for more details.) To test Rebase, use: $ wget pelican.rsvs.ulaval.ca/distfiles/seq/phikz-orf144.fasta $ wget pelican.rsvs.ulaval.ca/distfiles/seq/phikz-orf144-ref.restrict $ restrict -enzymes all -sitelen 4 phikz-orf144.fasta stdout | grep -v '#' | sort > phikz-orf144.restrict $ diff -u phikz-orf144-ref.restrict phikz-orf144.restrict If there are no differences, the package should be stabilised on your arch. Thanks in advance,
Created attachment 80194 [details] diff on ppc64 Hi, there is a difference on PPC64, when running the last command (diff -u phikz-orf144-ref.restrict phikz-orf144.restrict). What can I do?
doing a closer look it seems like the lines were just swaped. Unfortunaly I don't know if this makes a difference or not...
Same results here on x86. Please advise
Swaped entries are not a problem. (Although I wonder why we still have them now that the reference file and the restrict output are sorted.)
Stable on x86
stable on ppc64
Stable on ppc
emboss ok (including diffs), ppc-macos stable rebase ok (swapped lines), ppc-macos stable PS, your emboss-test.sh script lacks a 'j' in its tar command, that's why it doesn't run on OSX.
amd64, could you have a look at this please? (Last arch to stabilise.)
Can't mark emboss 3.0.0-r1 stable on amd64. Following the output of diff: dvandyk@phi gentoo $ diff -u phikz-orf144-ref.restrict phikz-orf144.restrict --- phikz-orf144-ref.restrict 2006-03-15 13:16:05.000000000 +0100 +++ phikz-orf144.restrict 2006-03-15 13:12:52.000000000 +0100 @@ -68,11 +68,11 @@ 369 372 AluI AGCT 370 370 . . 369 372 CviJI RGCY 370 370 . . 371 375 DdeI CTNAG 371 374 . . + 380 385 PstII CATCAG 410 412 . . 382 378 TspDTI ATGAA 368 366 . . 383 391 AlwNI CAGNNNCTG 388 385 . . 384 387 AluI AGCT 385 385 . . 384 387 CviJI RGCY 385 385 . . - 385 380 PstII CTGATG 352 354 . . 388 392 BsrI ACTGG 393 391 . . 395 400 NlaIV GGNNCC 397 397 . . 399 413 XcmI CCANNNNNNNNNTGG 406 405 . . Please advise.
(In reply to comment #10) > Can't mark emboss 3.0.0-r1 stable on amd64. Following the output of diff: If that is the only diff, you can mark it stable. This is a case where the restriction site was found correctly but on the reverse complement sequence (ie. 380-385 becomes 385-380, and CATCAG becomes CTGATG by reversing and swaping A/T and C/G).
amd64 team, can you look at this, please? (See comment 11).
we're finally done here, sorry for the delay
