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 ...

QA Tindy (Ion-Mihai Tetcu) itetcu at FreeBSD.org
Sat Jun 21 01:47:48 UTC 2008


On Sat, 21 Jun 2008 00:01:57 +0000 (UTC)
Felippe de Meirelles Motta <lippe at 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 at 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 at 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 at FreeBSD.org, PGP Key ID 057E9F8B493A297B


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