|Summary:||[maintainer-update] update biology/fasta3|
|Product:||Ports & Packages||Reporter:||Fernan Aguero <fernan>|
|Component:||Individual Port(s)||Assignee:||freebsd-ports-bugs (Nobody) <ports-bugs>|
|Severity:||Affects Only Me||CC:||sem|
Description Fernan Aguero 2006-05-15 18:10:15 UTC
fasta3 has just been updated by the author. Quoting Bill Pearson (the author): o This version corrects a but in the display of alignment coordinates in some cases (only for fasta34(_t) and ssearch34(_t). o It also provides new functions for reading the ASN.1 binary blastpgp checkpoint files: blastpgp -J T -C checkpoint_file -u 2 ... o This code was designed to allow users of the NCBI BLAST WWW site to independently evaluate statistical estimates by downloading the encoded PSSM data. Unfortunately, last week, just as I finished the code, NCBI changed their ASN.1 binary structure with the introduction of blast2.2.14. Unfortunately, blast2.2.14 is only available over the web, not from their FTP site. When the new version of the program (and perhaps an updated toolkit) is available, I hope to support their new format. Notes from the port maintainer -- that's me :) o fasta34t25d7 now includes the 'Makefile.freebsd' that was part of the FreeBSD port, so I removed it from files/ and removed the post-extract target accordingly. As a future reference -- just in case future maintainers are fond of reading old PRs :) -- please notify the author (Bill Pearson) of changes in the Makefile.freebsd file, so that the changes are included in the next fasta3 release. o note to self: the next fasta3 version should be done in sync with the ncbi-toolkit once the NCBI releases a toolkit that includes blast2.2.14 o CCed sem, who committed the last fasta3 update a week ago :)
Comment 1 Sergey Matveychuk 2006-05-16 07:59:00 UTC
fetch: ftp://ftp.virginia.edu/pub/fasta/fasta34t25d7.shar.Z: size mismatch: expected 812709, actual 811798 -- Sem.
Comment 2 Sergey Matveychuk 2006-05-16 07:59:33 UTC
State Changed From-To: open->feedback Ask for maintainer fix.
Comment 3 Fernan Aguero 2006-05-16 14:25:39 UTC
+----[ Sergey Matveychuk <sem@FreeBSD.org> (16.May.2006 04:04): | | fetch: ftp://ftp.virginia.edu/pub/fasta/fasta34t25d7.shar.Z: size | mismatch: expected 812709, actual 811798 | | -- | Sem. | +----] Seems like they re-rolled the distfile yesterday ... attached is a new diff. Fernan
Comment 4 Sergey Matveychuk 2006-05-24 17:56:57 UTC
State Changed From-To: feedback->closed Committed. Thanks!