Date: Mon, 5 Jun 2006 21:46:13 -0300 (ART) From: Fernan Aguero <fernan@iib.unsam.edu.ar> To: FreeBSD-gnats-submit@FreeBSD.org Cc: Tony Maher <anthony.maher@uts.edu.au>, pav@FreeBSD.org Subject: ports/98570: [maintainer-update] biology/ncbi-toolkit 2006.05.07 (BLAST v2.2.14) Message-ID: <200606060046.k560kDJY069277@omega.iib.unsam.edu.ar> Resent-Message-ID: <200606060130.k561UOTP076213@freefall.freebsd.org>
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>Number: 98570 >Category: ports >Synopsis: [maintainer-update] biology/ncbi-toolkit 2006.05.07 (BLAST v2.2.14) >Confidential: no >Severity: non-critical >Priority: low >Responsible: freebsd-ports-bugs >State: open >Quarter: >Keywords: >Date-Required: >Class: maintainer-update >Submitter-Id: current-users >Arrival-Date: Tue Jun 06 01:30:19 GMT 2006 >Closed-Date: >Last-Modified: >Originator: Fernan Aguero >Release: FreeBSD 6.0-RELEASE-p4 i386 >Organization: IIB-UNSAM >Environment: System: FreeBSD omega.iib.unsam.edu.ar 6.0-RELEASE-p4 FreeBSD 6.0-RELEASE-p4 #0: Wed Jan 25 12:43:39 ART 2006 fernan@omega.iib.unsam.edu.ar:/usr/obj/usr/src/sys/OMEGA i386 >Description: Update biology/ncbi-toolkit to the latest release. Quoting from www.ncbi.nlm.nih.gov/blast/blast_whatsnew.shtml Major changes include: * blastall now uses the new engine by default, resulting in significant performance improvements and enabling query concatenation for all program types. * The Mac OS X build is now a universal binary. * Multithreaded searches now work properly under ia32-win32. * The sparc64-solaris build now requries Solaris 10. Support for axp64-tru64 will be discontinued. Pav was the committer of the last update to this port, so he gets the carbon copy :) And Tony Maher (the previous maintainer) also gets a CC, because he requested the update. Wellcome back! >How-To-Repeat: >Fix: --- ncbi-toolkit.diff begins here --- diff -ruN /usr/ports/biology/ncbi-toolkit/Makefile ncbi-toolkit/Makefile --- /usr/ports/biology/ncbi-toolkit/Makefile Sun Jan 15 12:12:51 2006 +++ ncbi-toolkit/Makefile Mon Jun 5 11:18:21 2006 @@ -7,7 +7,7 @@ # PORTNAME= ncbi-toolkit -PORTVERSION= 2005.12.06 +PORTVERSION= 2006.05.07 # containing BLAST v2.2.14 CATEGORIES= biology MASTER_SITES= ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/old/${PORTVERSION:S/.//g}/ DISTNAME= ncbi diff -ruN /usr/ports/biology/ncbi-toolkit/distinfo ncbi-toolkit/distinfo --- /usr/ports/biology/ncbi-toolkit/distinfo Sun Jan 15 12:12:51 2006 +++ ncbi-toolkit/distinfo Mon Jun 5 09:26:44 2006 @@ -1,3 +1,3 @@ -MD5 (ncbi-toolkit-2005.12.06/ncbi.tar.gz) = 50a83a509b67fd8f317b0da42703de1d -SHA256 (ncbi-toolkit-2005.12.06/ncbi.tar.gz) = 0b409557d6601b8703328cd1ae997985677416e9ad9375e57b298113ecaaeeda -SIZE (ncbi-toolkit-2005.12.06/ncbi.tar.gz) = 14693833 +MD5 (ncbi-toolkit-2006.05.07/ncbi.tar.gz) = 1c00462385fbf382c99ff65f34c0d09a +SHA256 (ncbi-toolkit-2006.05.07/ncbi.tar.gz) = b3cac971d552b2ad86ee7d82e77e6a425b98b33a7b6f1c77062aff133e34d129 +SIZE (ncbi-toolkit-2006.05.07/ncbi.tar.gz) = 15396356 diff -ruN /usr/ports/biology/ncbi-toolkit/pkg-plist ncbi-toolkit/pkg-plist --- /usr/ports/biology/ncbi-toolkit/pkg-plist Wed Jan 25 11:31:48 2006 +++ ncbi-toolkit/pkg-plist Mon Jun 5 11:04:37 2006 @@ -58,7 +58,9 @@ include/ncbi/connect/ncbi_host_info.h include/ncbi/connect/ncbi_host_infop.h include/ncbi/connect/ncbi_http_connector.h +include/ncbi/connect/ncbi_lb.h include/ncbi/connect/ncbi_lbsmd.h +include/ncbi/connect/ncbi_local.h include/ncbi/connect/ncbi_memory_connector.h include/ncbi/connect/ncbi_priv.h include/ncbi/connect/ncbi_sendmail.h @@ -438,6 +440,7 @@ include/ncbi/seqsub.h include/ncbi/sequtil.h include/ncbi/shim3d.h +include/ncbi/showalignwrap.h include/ncbi/simple.h include/ncbi/simutil.h include/ncbi/smith_waterman.h @@ -485,6 +488,7 @@ include/ncbi/udviewer.h include/ncbi/udvseq.h include/ncbi/undefwin.h +include/ncbi/unified_pvalues.h include/ncbi/urkbias.h include/ncbi/urkcnsrt.h include/ncbi/urkdust.h @@ -619,7 +623,6 @@ %%PORTDOCS%%%%DOCSDIR%%/man/Nentrez.1 %%PORTDOCS%%%%DOCSDIR%%/man/Psequin.1 %%PORTDOCS%%%%DOCSDIR%%/man/asn2asn.1 - %%PORTDOCS%%%%DOCSDIR%%/man/asn2gb.1 %%PORTDOCS%%%%DOCSDIR%%/man/asn2xml.1 %%PORTDOCS%%%%DOCSDIR%%/man/asndhuff.1 @@ -699,6 +702,9 @@ %%PORTDOCS%%%%DOCSDIR%%/seq_install/win-netscape.css %%PORTDOCS%%%%DOCSDIR%%/sequin.htm %%PORTDOCS%%%%DOCSDIR%%/tbl2asn.txt +%%DATADIR%%/16Score.nhr +%%DATADIR%%/16Score.nin +%%DATADIR%%/16Score.nsq %%DATADIR%%/BLOSUM45 %%DATADIR%%/BLOSUM62 %%DATADIR%%/BLOSUM80 --- ncbi-toolkit.diff ends here --- >Release-Note: >Audit-Trail: >Unformatted:
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