Date: Sat, 21 Jun 2008 04:47:45 +0300 From: "QA Tindy (Ion-Mihai Tetcu)" <itetcu@FreeBSD.org> To: Felippe de Meirelles Motta <lippe@FreeBSD.org> Cc: cvs-ports@FreeBSD.org, Mark Linimon <linimon@FreeBSD.org>, cvs-all@FreeBSD.org, ports-committers@FreeBSD.org Subject: Re: cvs commit: ports/biology Makefile ports/biology/ssaha Makefile distinfo pkg-descr pkg-plist ports/biology/ssaha/files patch-GlobalDefinitions.cpp patch-GlobalDefinitions.h patch-HashTable.cpp patch-HashTableGeneric.cpp patch-HashTablePacked.cpp patch-HashTablePacked.h ... Message-ID: <20080621044745.7a0c6ebc@it.buh.tecnik93.com> In-Reply-To: <200806210001.m5L01vHj017020@repoman.freebsd.org> References: <200806210001.m5L01vHj017020@repoman.freebsd.org>
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On Sat, 21 Jun 2008 00:01:57 +0000 (UTC) Felippe de Meirelles Motta <lippe@FreeBSD.org> wrote: > lippe 2008-06-21 00:01:57 UTC > > FreeBSD ports repository > > Modified files: > biology Makefile > Added files: > biology/ssaha Makefile distinfo pkg-descr pkg-plist > biology/ssaha/files patch-GlobalDefinitions.cpp > patch-GlobalDefinitions.h > patch-HashTable.cpp > patch-HashTableGeneric.cpp > patch-HashTablePacked.cpp > patch-HashTablePacked.h > patch-HashTableTranslated.cpp > patch-MatchAligner.cpp > patch-MatchAligner.h patch-MatchStore.h > patch-MatchStoreGapped.h > patch-MatchStoreUngapped.h > patch-QueryManager.cpp > patch-QueryManager.h patch-README > patch-SSAHAMain.cpp patch-SSAHAMain.h > patch-SequenceEncoder.cpp > patch-SequenceReader.cpp > patch-SequenceReader.h > patch-SequenceReaderFasta.cpp > patch-SequenceReaderFasta.h > patch-SequenceReaderFilter.h > patch-SequenceReaderLocal.cpp > patch-SequenceReaderMulti.cpp > patch-SequenceReaderMulti.h > patch-SequenceReaderString.h > patch-makefile > patch-testHashTableNoOverlap.cpp > patch-testQueryManager.cpp > patch-testSequenceReaderFasta.cpp > Log: > SSAHA is a software tool for very fast matching and alignment of DNA > sequences. It stands for Sequence Search and Alignment by Hashing > Algorithm. It achieves its fast search speed by converting sequence > information into a `hash table' data structure, which can then be > searched very rapidly for matches. > > WWW: http://www.sanger.ac.uk/Software/analysis/SSAHA/ > > PR: ports/124525 > Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> > Approved by: gabor (mentor, implicit) > > Revision Changes Path > 1.102 +1 -0 ports/biology/Makefile > 1.1 +33 -0 ports/biology/ssaha/Makefile (new) > 1.1 +3 -0 ports/biology/ssaha/distinfo (new) > 1.1 +11 -0 ports/biology/ssaha/files/patch-GlobalDefinitions.cpp (new) > 1.1 +82 -0 ports/biology/ssaha/files/patch-GlobalDefinitions.h (new) > 1.1 +20 -0 ports/biology/ssaha/files/patch-HashTable.cpp (new) > 1.1 +48 -0 ports/biology/ssaha/files/patch-HashTableGeneric.cpp (new) > 1.1 +29 -0 ports/biology/ssaha/files/patch-HashTablePacked.cpp (new) > 1.1 +16 -0 ports/biology/ssaha/files/patch-HashTablePacked.h (new) > 1.1 +77 -0 ports/biology/ssaha/files/patch-HashTableTranslated.cpp (new) > 1.1 +94 -0 ports/biology/ssaha/files/patch-MatchAligner.cpp (new) > 1.1 +33 -0 ports/biology/ssaha/files/patch-MatchAligner.h (new) > 1.1 +54 -0 ports/biology/ssaha/files/patch-MatchStore.h (new) > 1.1 +25 -0 ports/biology/ssaha/files/patch-MatchStoreGapped.h (new) > 1.1 +13 -0 ports/biology/ssaha/files/patch-MatchStoreUngapped.h (new) > 1.1 +54 -0 ports/biology/ssaha/files/patch-QueryManager.cpp (new) > 1.1 +19 -0 ports/biology/ssaha/files/patch-QueryManager.h (new) > 1.1 +13 -0 ports/biology/ssaha/files/patch-README (new) > 1.1 +48 -0 ports/biology/ssaha/files/patch-SSAHAMain.cpp (new) > 1.1 +19 -0 ports/biology/ssaha/files/patch-SSAHAMain.h (new) > 1.1 +75 -0 ports/biology/ssaha/files/patch-SequenceEncoder.cpp (new) > 1.1 +20 -0 ports/biology/ssaha/files/patch-SequenceReader.cpp (new) > 1.1 +11 -0 ports/biology/ssaha/files/patch-SequenceReader.h (new) > 1.1 +32 -0 ports/biology/ssaha/files/patch-SequenceReaderFasta.cpp (new) > 1.1 +11 -0 ports/biology/ssaha/files/patch-SequenceReaderFasta.h (new) > 1.1 +20 -0 ports/biology/ssaha/files/patch-SequenceReaderFilter.h (new) > 1.1 +28 -0 ports/biology/ssaha/files/patch-SequenceReaderLocal.cpp (new) > 1.1 +30 -0 ports/biology/ssaha/files/patch-SequenceReaderMulti.cpp (new) > 1.1 +13 -0 ports/biology/ssaha/files/patch-SequenceReaderMulti.h (new) > 1.1 +26 -0 ports/biology/ssaha/files/patch-SequenceReaderString.h (new) > 1.1 +15 -0 ports/biology/ssaha/files/patch-makefile (new) > 1.1 +178 -0 ports/biology/ssaha/files/patch-testHashTableNoOverlap.cpp (new) > 1.1 +20 -0 ports/biology/ssaha/files/patch-testQueryManager.cpp (new) > 1.1 +171 -0 ports/biology/ssaha/files/patch-testSequenceReaderFasta.cpp (new) > 1.1 +11 -0 ports/biology/ssaha/pkg-descr (new) > 1.1 +9 -0 ports/biology/ssaha/pkg-plist (new) > Hi, You receive this email if you are either the maintainer of the port or if you recently committed to it. If the error is already fixed please ignore this email; if you submit a PR to fix it CC me and I'll commit it ASAP. The builds are done under tinderbox-2.4.3, on 7-STABLE on amd64, with tinderd_flags="-nullfs -plistcheck -onceonly" and ccache support, with the official up-to-date Ports Tree (for commit-triggered builds the files are fetched via CVSWeb), with the following vars set: NOPORTDOCS=yes, NOPORTEXAMPLES=yes, NOPORTDATA=yes, FORCE_PACKAGE=yes. The error which triggered this email is bellow followed by the link to the full log and explanations about the testing process. building ssaha-3.1c in directory /var/tinderbox/7-STABLE-FTP maintained by: fernan@iib.unsam.edu.ar building for: 7.0-STABLE amd64 port directory: /usr/ports/biology/ssaha Makefile ident: $FreeBSD: ports/biology/ssaha/Makefile,v 1.1 2008/06/21 00:01:56 lippe Exp $ prefixes: LOCALBASE=usr/local X11BASE=usr/local NO* env vars: NOPORTDOCS=yes NOPORTEXAMPLES=yes NOPORTDATA=yes build started at Sat Jun 21 01:43:34 UTC 2008 ...... ====================<phase 5: make test>==================== make: don't know how to make regression-test(continuing) ================================================================ ====================<phase 6: make install>==================== add_pkg ===> Installing for ssaha-3.1c ===> Generating temporary packing list ===> Checking if biology/ssaha already installed install -s -o root -g wheel -m 555 /work/a/ports/biology/ssaha/work/Binary/ssaha /usr/local/bin install -o root -g wheel -m 555 /work/a/ports/biology/ssaha/work/Binary/testSSAHA.csh /usr/local/share/ssaha/ install -o root -g wheel -m 444 /work/a/ports/biology/ssaha/work/test.fasta /work/a/ports/biology/ssaha/work/test_extract.fasta /work/a/ports/biology/ssaha/work/test_filter.fail /work/a/ports/biology/ssaha/work/test_filter.fastq /work/a/ports/biology/ssaha/work/test_protein.fasta /work/a/ports/biology/ssaha/work/README /usr/local/share/ssaha/ install: /work/a/ports/biology/ssaha/work/test.fasta: No such file or directory *** Error code 71 Stop in /a/ports/biology/ssaha. ================================================================ build of /usr/ports/biology/ssaha ended at Sat Jun 21 01:44:24 UTC 2008 http://t64.tecnik93.com/errors/7-STABLE-FTP/ssaha-3.1c.log These emails are generated in one of the following cases: - an automated build was scheduled because the port was touched in CVS - the periodic QA build has reached it. - the port was scheduled because it is a dependency of a port from the cases above. There is no fixed interval for this; if other ports depend on it you will receive this emails more often since testing those other ports is made impossible by this port being broken. Efforts are made to restrict the number of outgoing emails to one/port/week for QA or dependency builds (but not for commit-triggered builds; if you commit 3 times in 5 minutes to the same port and the first 2 versions fail you'll receive 2 emails). When you fix install/plist errors please bear in mind that each of the 3 NO* vars controls the installation of different type of files, so constructs like: .ifndef NOPORTDOCS @${MKDIR} ${DATADIR} ... .endif or %%PORTDOCS%%%%EXAMPLESDIR%%/some_example_file are WRONG. Please use the right pairs like: %%PORTDOCS%%%%DOCSDIR%% %%PORTEXAMPLES%%%%EXAMPLESDIR%% %%PORTDATA%%%%DATADIR%% Thanks for your work on making FreeBSD better, -- IOnut - Un^d^dregistered ;) FreeBSD "user" "Intellectual Property" is nowhere near as valuable as "Intellect" FreeBSD committer -> itetcu@FreeBSD.org, PGP Key ID 057E9F8B493A297B
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