Date: Mon, 15 May 2006 14:05:32 -0300 (ART) From: Fernan Aguero <fernan@iib.unsam.edu.ar> To: FreeBSD-gnats-submit@FreeBSD.org Cc: Sergey Matveychuk <sem@FreeBSD.org> Subject: ports/97310: [maintainer-update] update biology/fasta3 Message-ID: <200605151705.k4FH5VaM031572@omega.iib.unsam.edu.ar> Resent-Message-ID: <200605151710.k4FHATep004618@freefall.freebsd.org>
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>Number: 97310 >Category: ports >Synopsis: [maintainer-update] update biology/fasta3 >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: Mon May 15 17:10:15 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: 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 :) >How-To-Repeat: >Fix: --- fasta3.diff begins here --- diff -ruN /usr/ports/biology/fasta3/Makefile fasta3/Makefile --- /usr/ports/biology/fasta3/Makefile Wed May 10 14:31:51 2006 +++ fasta3/Makefile Mon May 15 13:17:30 2006 @@ -7,7 +7,7 @@ # PORTNAME= fasta3 -PORTVERSION= 34.t25.d6 +PORTVERSION= 34.t25.d7 CATEGORIES= biology MASTER_SITES= ftp://ftp.virginia.edu/pub/fasta/ DISTNAME= fasta${PORTVERSION:S/.//g} @@ -43,9 +43,6 @@ @ for file in ${EXTRACT_ONLY}; do \ cd ${WRKSRC} && (${GZCAT} ${DISTDIR}/$${file} | ${SH} >/dev/null); \ done - -post-extract: - @ cp ${FILESDIR}/Makefile.freebsd ${WRKSRC} post-install: ${INSTALL_DATA} ${WRKSRC}/fastlibs ${PREFIX}/etc/fastlibs.sample diff -ruN /usr/ports/biology/fasta3/distinfo fasta3/distinfo --- /usr/ports/biology/fasta3/distinfo Wed May 10 14:31:51 2006 +++ fasta3/distinfo Mon May 15 13:12:07 2006 @@ -1,3 +1,3 @@ -MD5 (fasta34t25d6.shar.Z) = 462419371d55afd787043d2104c461cc -SHA256 (fasta34t25d6.shar.Z) = 409abdf657931cb07ea2ae38587d9387d418436662f1c1b889a3829302656449 -SIZE (fasta34t25d6.shar.Z) = 798483 +MD5 (fasta34t25d7.shar.Z) = 9361050336f7b20cace9b65f14eb8f68 +SHA256 (fasta34t25d7.shar.Z) = c5d813760bc9cad91388a3bebf4fd12ced23caf39fd600cb14dedf3a1edd09ae +SIZE (fasta34t25d7.shar.Z) = 812709 diff -ruN /usr/ports/biology/fasta3/files/Makefile.freebsd fasta3/files/Makefile.freebsd --- /usr/ports/biology/fasta3/files/Makefile.freebsd Sun May 7 13:52:33 2006 +++ fasta3/files/Makefile.freebsd Wed Dec 31 21:00:00 1969 @@ -1,67 +0,0 @@ -# -# Makefile for building fasta3 on FreeBSD -# -# Fernan Aguero - <fernan@iib.unsam.edu.ar> - -# we take care of doing variable assignment using the '?=' and '+=' -# operators to preserve the value of variables if they are already -# defined. In FreeBSD this happens when fasta3 is build from the port or -# when the user has set these variables -- most notably CC and/or CFLAGS -# -- in /etc/make.conf - -# Compiler executable, and optional flags -CC?= gcc -CFLAGS?= -g -O2 - -# your FASTA host -FASTA_HOST?= "your_fasta_host" - -# common CFLAGS. These are the set of CFLAGS that are always used -COMMON_CFLAGS= -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -c -DMAX_WORKERS=2 \ - -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT \ - -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO \ - -DHAS_INTTYPES -DSAMP_STATS - -# standard options, these will be added to the common CFLAGS if -# selected below -STANDARD_CFLAGS= -DSFCHAR="':'" -DFASTA_HOST='${FASTA_HOST}' \ - -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC - -# options for superfamily validations, these will be added to the common -# CFLAGS if selected below -SUPERFAMILY_CFLAGS= -DSFCHAR="'|'" -DSUPERFAMNUM -DBIG_LIB64 - -# here we define CFLAGS to be the sum of common flags plus a subset of -# optional flags that define our intended use. -# The default standard flags are selected by default, although the user -# can override this if s/he wants -CFLAGS+= ${COMMON_CFLAGS} ${STANDARD_CFLAGS} - -XDIR?= /usr/local/bin - -LIB_M+= -lm - -HFLAGS+= -o -NFLAGS+= -o - - - -# FreeBSD users BEWARE! Different threading models ahead! - -# The threading model has changed along the way from FreeBSD-4 to -# FreeBSD-6. If you're building fasta3 on your own, you will need to -# adjust this accordingly. The default works in FreeBSD-6x (currently -# the recommended major version for use in production). Or better yet, -# use the biology/fasta3 port from the ports collection, which will use -# the correct threading library for your OSVERSION - -THR_SUBS?= pthr_subs2 -THR_LIBS?= -lpthread -THR_CC?= - -DROPNFA_O = drop_nfa.o -DROPGSW_O = dropgsw.o -DROPRSS_O = dropnsw.o -DROPTFA_O = drop_tfa.o - -include Makefile34m.common --- fasta3.diff ends here --- >Release-Note: >Audit-Trail: >Unformatted:
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