From haruosuz at yahoo.co.jp Sun Jun 4 20:23:30 2006 From: haruosuz at yahoo.co.jp (haruosuz at yahoo.co.jp) Date: Sun, 4 Jun 2006 17:23:30 -0700 Subject: [EMBOSS] install EMBOSS-3.0.0 on Intel Mac Message-ID: Dear Sir, [1] http://lists.open-bio.org/pipermail/emboss/2006-May/002531.html Although I read README and applied all the fixes from: ftp://emboss.open-bio.org/pub/EMBOSS/fixes/ I failed to install. % make *snip* ajindex.c: In function 'ajBtreeCacheNewC': ajindex.c:200: error: storage size of 'buf' isn't known ajindex.c: In function 'ajBtreeSecCacheNewC': ajindex.c:8234: error: storage size of 'buf' isn't known make[1]: *** [ajindex.lo] Error 1 make: *** [all-recursive] Error 1 [2] http://lists.open-bio.org/pipermail/emboss/2006-May/002532.html I also used fink to install EMBOSS on my Mac, but I failed to install. % fink install emboss *snip* dpkg: error processing /sw/fink/dists/unstable/main/binary-darwin- i386/graphics/libjpeg_6b-16_darwin-i386.deb (--install): package architecture (darwin-i386) does not match system (darwin- powerpc) dpkg: error processing /sw/fink/dists/unstable/main/binary-darwin- i386/graphics/libjpeg-bin_6b-16_darwin-i386.deb (--install): package architecture (darwin-i386) does not match system (darwin- powerpc) Errors were encountered while processing: /sw/fink/dists/unstable/main/binary-darwin-i386/graphics/ libjpeg_6b-16_darwin-i386.deb /sw/fink/dists/unstable/main/binary-darwin-i386/graphics/libjpeg- bin_6b-16_darwin-i386.deb ### execution of dpkg failed, exit code 1 Failed: can't batch-install packages: /sw/fink/dists/unstable/main/ binary-darwin-i386/graphics/libjpeg_6b-16_darwin-i386.deb /sw/fink/ dists/unstable/main/binary-darwin-i386/graphics/libjpeg- bin_6b-16_darwin-i386.deb [About my Mac] Mac OS X 10.4.6 Darwin 8.6.1 MacBookPro1,1 Intel Core Duo I am looking forward to hearing from you. Sincerely yours, Haruo Suzuki -------------------------------------- Let's start Yahoo! Auction - Free Campaign Now! http://pr.mail.yahoo.co.jp/auction/ From kvddrift at earthlink.net Sun Jun 4 20:58:44 2006 From: kvddrift at earthlink.net (Koen van der Drift) Date: Sun, 4 Jun 2006 20:58:44 -0400 Subject: [EMBOSS] install EMBOSS-3.0.0 on Intel Mac In-Reply-To: References: Message-ID: On Jun 4, 2006, at 8:23 PM, haruosuz at yahoo.co.jp wrote: > dpkg: error processing /sw/fink/dists/unstable/main/binary-darwin- > i386/graphics/libjpeg_6b-16_darwin-i386.deb (--install): > package architecture (darwin-i386) does not match system (darwin- > powerpc) > dpkg: error processing /sw/fink/dists/unstable/main/binary-darwin- > i386/graphics/libjpeg-bin_6b-16_darwin-i386.deb (--install): > package architecture (darwin-i386) does not match system (darwin- > powerpc) > Errors were encountered while processing: > /sw/fink/dists/unstable/main/binary-darwin-i386/graphics/ > libjpeg_6b-16_darwin-i386.deb > /sw/fink/dists/unstable/main/binary-darwin-i386/graphics/libjpeg- > bin_6b-16_darwin-i386.deb > ### execution of dpkg failed, exit code 1 > Failed: can't batch-install packages: /sw/fink/dists/unstable/main/ > binary-darwin-i386/graphics/libjpeg_6b-16_darwin-i386.deb /sw/fink/ > dists/unstable/main/binary-darwin-i386/graphics/libjpeg- > bin_6b-16_darwin-i386.deb Haruo, That's an error for the libjpeg package in fink. I suggest you contact the libjpeg package maintainer (%fink info libjpeg). good luck, - Koen. From ajb at ebi.ac.uk Mon Jun 5 03:12:50 2006 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Mon, 5 Jun 2006 08:12:50 +0100 (BST) Subject: [EMBOSS] install EMBOSS-3.0.0 on Intel Mac In-Reply-To: References: Message-ID: <33758.81.98.244.247.1149491570.squirrel@webmail.ebi.ac.uk> Dear Haruo, > ajindex.c: In function 'ajBtreeCacheNewC': > ajindex.c:200: error: storage size of 'buf' isn't known > ajindex.c: In function 'ajBtreeSecCacheNewC': > ajindex.c:8234: error: storage size of 'buf' isn't known > make[1]: *** [ajindex.lo] Error 1 > make: *** [all-recursive] Error 1 That error shows that something went wrong when you tried to apply the fixes from the ftp server. You are trying to compile the original ajindex.c file. I'd suggest that you compare the file sizes on your local system with those in the fixes directory and reapply any fixes as appropriate. HTH Alan From haruosuz at yahoo.co.jp Mon Jun 5 14:58:23 2006 From: haruosuz at yahoo.co.jp (haruosuz at yahoo.co.jp) Date: Mon, 5 Jun 2006 11:58:23 -0700 Subject: [EMBOSS] install EMBOSS-3.0.0 on Intel Mac In-Reply-To: <33758.81.98.244.247.1149491570.squirrel@webmail.ebi.ac.uk> References: <33758.81.98.244.247.1149491570.squirrel@webmail.ebi.ac.uk> Message-ID: <0DAC5E74-E414-4CD4-9C59-6FBEE9C5F992@yahoo.co.jp> Thank you very much for your advice. On 2006/06/05, at 0:12, ajb at ebi.ac.uk wrote: > Dear Haruo, > >> ajindex.c: In function 'ajBtreeCacheNewC': >> ajindex.c:200: error: storage size of 'buf' isn't known >> ajindex.c: In function 'ajBtreeSecCacheNewC': >> ajindex.c:8234: error: storage size of 'buf' isn't known >> make[1]: *** [ajindex.lo] Error 1 >> make: *** [all-recursive] Error 1 > > That error shows that something went wrong when you tried to apply > the fixes from the ftp server. You are trying to compile the > original ajindex.c file. I'd suggest that you compare the file sizes > on your local system with those in the fixes directory and reapply > any fixes as appropriate. > > HTH > > Alan Although I made sure if I replaced the old files with new files in the fixes directory and redo the 'make', I failed. % make *snip* /bin/sh ../libtool --tag=CC --mode=link gcc -O1 -o aaindexextract aaindexextract.o ../nucleus/libnucleus.la ../ajax/libajaxg.la ../ajax/ libajax.la ../plplot/libplplot.la -L/usr/X11R6/lib -lX11 -lm -lgd - lpng -lz -lm mkdir .libs libtool: link: warning: library `/usr/local/lib/libgd.la' was moved. libtool: link: warning: library `/usr/local/lib/libgd.la' was moved. libtool: link: cannot find the library `/opt/local/lib/libjpeg.la' make[2]: *** [aaindexextract] Error 1 make[1]: *** [all-recursive] Error 1 make: *** [all-recursive] Error 1 On 2006/06/04, at 17:58, Koen van der Drift wrote: > > On Jun 4, 2006, at 8:23 PM, haruosuz at yahoo.co.jp wrote: > >> dpkg: error processing /sw/fink/dists/unstable/main/binary-darwin- >> i386/graphics/libjpeg_6b-16_darwin-i386.deb (--install): >> package architecture (darwin-i386) does not match system (darwin- >> powerpc) >> dpkg: error processing /sw/fink/dists/unstable/main/binary-darwin- >> i386/graphics/libjpeg-bin_6b-16_darwin-i386.deb (--install): >> package architecture (darwin-i386) does not match system (darwin- >> powerpc) >> Errors were encountered while processing: >> /sw/fink/dists/unstable/main/binary-darwin-i386/graphics/ >> libjpeg_6b-16_darwin-i386.deb >> /sw/fink/dists/unstable/main/binary-darwin-i386/graphics/libjpeg- >> bin_6b-16_darwin-i386.deb >> ### execution of dpkg failed, exit code 1 >> Failed: can't batch-install packages: /sw/fink/dists/unstable/main/ >> binary-darwin-i386/graphics/libjpeg_6b-16_darwin-i386.deb /sw/fink/ >> dists/unstable/main/binary-darwin-i386/graphics/libjpeg- >> bin_6b-16_darwin-i386.deb > > > Haruo, > > That's an error for the libjpeg package in fink. I suggest you > contact the libjpeg package maintainer (%fink info libjpeg). > > good luck, > > - Koen. Begin forwarded message: > Actually, the problem is not with the libjpeg package in fink. The > problem is that you are somehow mixing the intel and powerpc > versions of fink. My guess is that you installed fink by using the > Fink-0.8.0-Installer? Unfortunately, that only works correctly on > powerpc. To install fink on intel, you must bootstrap it from > scratch, as mentioned on the fink homepage. If you have trouble > with this, please consult the mailing list fink- > users at lists.sourceforge.net -------------------------------------- Let's start Yahoo! Auction - Free Campaign Now! http://pr.mail.yahoo.co.jp/auction/ From ajb at ebi.ac.uk Mon Jun 5 17:45:52 2006 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Mon, 5 Jun 2006 22:45:52 +0100 (BST) Subject: [EMBOSS] install EMBOSS-3.0.0 on Intel Mac In-Reply-To: <0DAC5E74-E414-4CD4-9C59-6FBEE9C5F992@yahoo.co.jp> References: <33758.81.98.244.247.1149491570.squirrel@webmail.ebi.ac.uk> <0DAC5E74-E414-4CD4-9C59-6FBEE9C5F992@yahoo.co.jp> Message-ID: <37136.81.98.244.247.1149543952.squirrel@webmail.ebi.ac.uk> > Thank you very much for your advice. > > On 2006/06/05, at 0:12, ajb at ebi.ac.uk wrote: >> Dear Haruo, >> >>> ajindex.c: In function 'ajBtreeCacheNewC': >>> ajindex.c:200: error: storage size of 'buf' isn't known >>> ajindex.c: In function 'ajBtreeSecCacheNewC': >>> ajindex.c:8234: error: storage size of 'buf' isn't known >>> make[1]: *** [ajindex.lo] Error 1 >>> make: *** [all-recursive] Error 1 >> >> That error shows that something went wrong when you tried to apply >> the fixes from the ftp server. You are trying to compile the >> original ajindex.c file. I'd suggest that you compare the file sizes >> on your local system with those in the fixes directory and reapply >> any fixes as appropriate. >> >> HTH >> >> Alan > > Although I made sure if I replaced the old files with new files > in the fixes directory and redo the 'make', I failed. > > % make > > *snip* > > /bin/sh ../libtool --tag=CC --mode=link gcc -O1 -o aaindexextract > aaindexextract.o ../nucleus/libnucleus.la ../ajax/libajaxg.la ../ajax/ > libajax.la ../plplot/libplplot.la -L/usr/X11R6/lib -lX11 -lm -lgd - > lpng -lz -lm > mkdir .libs > libtool: link: warning: library `/usr/local/lib/libgd.la' was moved. > libtool: link: warning: library `/usr/local/lib/libgd.la' was moved. > libtool: link: cannot find the library `/opt/local/lib/libjpeg.la' > make[2]: *** [aaindexextract] Error 1 > make[1]: *** [all-recursive] Error 1 > make: *** [all-recursive] Error 1 > > On 2006/06/04, at 17:58, Koen van der Drift wrote: >> >> On Jun 4, 2006, at 8:23 PM, haruosuz at yahoo.co.jp wrote: >> >>> dpkg: error processing /sw/fink/dists/unstable/main/binary-darwin- >>> i386/graphics/libjpeg_6b-16_darwin-i386.deb (--install): >>> package architecture (darwin-i386) does not match system (darwin- >>> powerpc) >>> dpkg: error processing /sw/fink/dists/unstable/main/binary-darwin- >>> i386/graphics/libjpeg-bin_6b-16_darwin-i386.deb (--install): >>> package architecture (darwin-i386) does not match system (darwin- >>> powerpc) >>> Errors were encountered while processing: >>> /sw/fink/dists/unstable/main/binary-darwin-i386/graphics/ >>> libjpeg_6b-16_darwin-i386.deb >>> /sw/fink/dists/unstable/main/binary-darwin-i386/graphics/libjpeg- >>> bin_6b-16_darwin-i386.deb >>> ### execution of dpkg failed, exit code 1 >>> Failed: can't batch-install packages: /sw/fink/dists/unstable/main/ >>> binary-darwin-i386/graphics/libjpeg_6b-16_darwin-i386.deb /sw/fink/ >>> dists/unstable/main/binary-darwin-i386/graphics/libjpeg- >>> bin_6b-16_darwin-i386.deb >> >> >> Haruo, >> >> That's an error for the libjpeg package in fink. I suggest you >> contact the libjpeg package maintainer (%fink info libjpeg). >> >> good luck, >> >> - Koen. > > > Begin forwarded message: > >> Actually, the problem is not with the libjpeg package in fink. The >> problem is that you are somehow mixing the intel and powerpc >> versions of fink. My guess is that you installed fink by using the >> Fink-0.8.0-Installer? Unfortunately, that only works correctly on >> powerpc. To install fink on intel, you must bootstrap it from >> scratch, as mentioned on the fink homepage. If you have trouble >> with this, please consult the mailing list fink- >> users at lists.sourceforge.net > > > -------------------------------------- > Let's start Yahoo! Auction - Free Campaign Now! > http://pr.mail.yahoo.co.jp/auction/ > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > From ajb at ebi.ac.uk Mon Jun 5 18:00:06 2006 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Mon, 5 Jun 2006 23:00:06 +0100 (BST) Subject: [EMBOSS] install EMBOSS-3.0.0 on Intel Mac In-Reply-To: <0DAC5E74-E414-4CD4-9C59-6FBEE9C5F992@yahoo.co.jp> References: <33758.81.98.244.247.1149491570.squirrel@webmail.ebi.ac.uk> <0DAC5E74-E414-4CD4-9C59-6FBEE9C5F992@yahoo.co.jp> Message-ID: <54667.81.98.244.247.1149544806.squirrel@webmail.ebi.ac.uk> Apologies for the last message. Wrong button clicked on my mailer. You may be able to get past your current error by specifying --without-pngdriver on the configure line. However, as Koen has said, it is probably caused by something wrong in your FINK installation and is best fixed. Koen and the FINK team are the best people to ask about that. It isn't an EMBOSS problem as such. We make sure that EMBOSS works on relatively virgin OS installations; other projects such as FINK can then add bells and whistles. HTH Alan > Thank you very much for your advice. > > On 2006/06/05, at 0:12, ajb at ebi.ac.uk wrote: >> Dear Haruo, >> >>> ajindex.c: In function 'ajBtreeCacheNewC': >>> ajindex.c:200: error: storage size of 'buf' isn't known >>> ajindex.c: In function 'ajBtreeSecCacheNewC': >>> ajindex.c:8234: error: storage size of 'buf' isn't known >>> make[1]: *** [ajindex.lo] Error 1 >>> make: *** [all-recursive] Error 1 >> >> That error shows that something went wrong when you tried to apply >> the fixes from the ftp server. You are trying to compile the >> original ajindex.c file. I'd suggest that you compare the file sizes >> on your local system with those in the fixes directory and reapply >> any fixes as appropriate. >> >> HTH >> >> Alan > > Although I made sure if I replaced the old files with new files > in the fixes directory and redo the 'make', I failed. > > % make > > *snip* > > /bin/sh ../libtool --tag=CC --mode=link gcc -O1 -o aaindexextract > aaindexextract.o ../nucleus/libnucleus.la ../ajax/libajaxg.la ../ajax/ > libajax.la ../plplot/libplplot.la -L/usr/X11R6/lib -lX11 -lm -lgd - > lpng -lz -lm > mkdir .libs > libtool: link: warning: library `/usr/local/lib/libgd.la' was moved. > libtool: link: warning: library `/usr/local/lib/libgd.la' was moved. > libtool: link: cannot find the library `/opt/local/lib/libjpeg.la' > make[2]: *** [aaindexextract] Error 1 > make[1]: *** [all-recursive] Error 1 > make: *** [all-recursive] Error 1 > > On 2006/06/04, at 17:58, Koen van der Drift wrote: >> >> On Jun 4, 2006, at 8:23 PM, haruosuz at yahoo.co.jp wrote: >> >>> dpkg: error processing /sw/fink/dists/unstable/main/binary-darwin- >>> i386/graphics/libjpeg_6b-16_darwin-i386.deb (--install): >>> package architecture (darwin-i386) does not match system (darwin- >>> powerpc) >>> dpkg: error processing /sw/fink/dists/unstable/main/binary-darwin- >>> i386/graphics/libjpeg-bin_6b-16_darwin-i386.deb (--install): >>> package architecture (darwin-i386) does not match system (darwin- >>> powerpc) >>> Errors were encountered while processing: >>> /sw/fink/dists/unstable/main/binary-darwin-i386/graphics/ >>> libjpeg_6b-16_darwin-i386.deb >>> /sw/fink/dists/unstable/main/binary-darwin-i386/graphics/libjpeg- >>> bin_6b-16_darwin-i386.deb >>> ### execution of dpkg failed, exit code 1 >>> Failed: can't batch-install packages: /sw/fink/dists/unstable/main/ >>> binary-darwin-i386/graphics/libjpeg_6b-16_darwin-i386.deb /sw/fink/ >>> dists/unstable/main/binary-darwin-i386/graphics/libjpeg- >>> bin_6b-16_darwin-i386.deb >> >> >> Haruo, >> >> That's an error for the libjpeg package in fink. I suggest you >> contact the libjpeg package maintainer (%fink info libjpeg). >> >> good luck, >> >> - Koen. > > > Begin forwarded message: > >> Actually, the problem is not with the libjpeg package in fink. The >> problem is that you are somehow mixing the intel and powerpc >> versions of fink. My guess is that you installed fink by using the >> Fink-0.8.0-Installer? Unfortunately, that only works correctly on >> powerpc. To install fink on intel, you must bootstrap it from >> scratch, as mentioned on the fink homepage. If you have trouble >> with this, please consult the mailing list fink- >> users at lists.sourceforge.net > > > -------------------------------------- > Let's start Yahoo! Auction - Free Campaign Now! > http://pr.mail.yahoo.co.jp/auction/ > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > From haruosuz at yahoo.co.jp Wed Jun 7 22:11:06 2006 From: haruosuz at yahoo.co.jp (haruosuz at yahoo.co.jp) Date: Wed, 7 Jun 2006 19:11:06 -0700 Subject: [EMBOSS] install EMBOSS-3.0.0 on Intel Mac In-Reply-To: <54667.81.98.244.247.1149544806.squirrel@webmail.ebi.ac.uk> References: <33758.81.98.244.247.1149491570.squirrel@webmail.ebi.ac.uk> <0DAC5E74-E414-4CD4-9C59-6FBEE9C5F992@yahoo.co.jp> <54667.81.98.244.247.1149544806.squirrel@webmail.ebi.ac.uk> Message-ID: <293361E9-766F-41AF-849E-41B57D8D692A@yahoo.co.jp> Finally, installing emboss on a intel-Mac has been successful. By the way, when running "prettyseq" and "cusp", the following massage was shown: Died: Unknown qualifier -cfile ---------------------------------------------------------------- [install memo] (1) remove following directory sudo rm -rf /usr/X11R6/ sudo rm -rf /etc/X11/ sudo rm -rf /sw sudo rm -rf /usr/local/bin/ (2) reinstall them. install fink ./bootstrap.sh add 'source /sw/bin/init.sh' to the script '.bashrc' add 'source .bashrc' to the init script '.bash_profile' fink selfupdate-cvs sudo emacs /sw/etc/fink.conf 'Trees: local/main stable/main stable/crypto unstable/main unstable/ crypto' install X11SDK (3) install EMBOSS fink install emboss ---------------------------------------------------------------- -------------------------------------- Let's start Yahoo! Auction - Free Campaign Now! http://pr.mail.yahoo.co.jp/auction/ From pmr at ebi.ac.uk Thu Jun 8 02:25:10 2006 From: pmr at ebi.ac.uk (pmr at ebi.ac.uk) Date: Thu, 8 Jun 2006 07:25:10 +0100 (BST) Subject: [EMBOSS] install EMBOSS-3.0.0 on Intel Mac In-Reply-To: <293361E9-766F-41AF-849E-41B57D8D692A@yahoo.co.jp> References: <33758.81.98.244.247.1149491570.squirrel@webmail.ebi.ac.uk> <0DAC5E74-E414-4CD4-9C59-6FBEE9C5F992@yahoo.co.jp> <54667.81.98.244.247.1149544806.squirrel@webmail.ebi.ac.uk> <293361E9-766F-41AF-849E-41B57D8D692A@yahoo.co.jp> Message-ID: <2201.86.141.181.123.1149747910.squirrel@webmail.ebi.ac.uk> Hi Haruosuz at yahoo.co.jp, > Finally, installing emboss on a intel-Mac has been successful. > > By the way, when running "prettyseq" and "cusp", > the following massage was shown: > Died: Unknown qualifier -cfile Do you have an old version installed somewhere? Running "prettyseq -debug" or "cusp -debug" will produce a prettyseq.dbg (or cusp.dbg) file that will tell you which ACD file they are reading. This does not match the program that you are running. Running "embossversion" will show which version of the programs you are actually running. regards, Peter Rice From aengus.stewart at cancer.org.uk Wed Jun 14 14:59:09 2006 From: aengus.stewart at cancer.org.uk (Aengus Stewart) Date: Wed, 14 Jun 2006 19:59:09 +0100 Subject: [EMBOSS] Error with dbiflat and Refseq Message-ID: <44905C7D.4060101@cancer.org.uk> Hi Sorry for asking this but dbiflat is dying on me with the refseq nucleotides I am using dbiflat -dbname RefSeqN -idformat refseq -directory . -filenames "*.gbff" -release 17.0 -date 14/06/06 -fields "acnum,seqvn,des,keyword,taxon" and I get Warning: Duplicate ID skipped: 'XM_757618' All hits will point to first ID found Warning: Duplicate ID skipped: 'XM_757619' All hits will point to first ID found Warning: Duplicate ID skipped: 'XM_757620' All hits will point to first ID found EMBOSS An error in embdbi.c at line 1238: Error in embDbiSortWriteFields, expected entry NM_001004399 not found I know its probably something simple, but for the life of me I cant see it............. Any suggestions? Regards Aengus -- ----------------------------------------------------------------------- Aengus Stewart Group Leader Bioinformatics and BioStatistics Tel: +44 (0)20 7269 3679 Cancer Research UK, Lincoln's Inn Fields, Holborn, London, WC2A 3PX, UK ----------------------------------------------------------------------- This electronic message contains information which may be privileged and confidential. The information is intended to be for the use of the individual(s) or entity named above. Be aware that any third party disclosure, distribution, copying or use of this communication, without prior permission, is strictly prohibited. From pmr at ebi.ac.uk Wed Jun 14 18:05:17 2006 From: pmr at ebi.ac.uk (pmr at ebi.ac.uk) Date: Wed, 14 Jun 2006 23:05:17 +0100 (BST) Subject: [EMBOSS] Error with dbiflat and Refseq In-Reply-To: <44905C7D.4060101@cancer.org.uk> References: <44905C7D.4060101@cancer.org.uk> Message-ID: <2229.192.130.162.193.1150322717.squirrel@webmail.ebi.ac.uk> Hi Aengus, > dbiflat is dying on me with the refseq nucleotides > > I am using > > dbiflat -dbname RefSeqN -idformat refseq -directory . -filenames "*.gbff" > -release 17.0 -date 14/06/06 -fields "acnum,seqvn,des,keyword,taxon" > > and I get > > Warning: Duplicate ID skipped: 'XM_757618' All hits will point to first ID > found > Warning: Duplicate ID skipped: 'XM_757619' All hits will point to first ID > found > Warning: Duplicate ID skipped: 'XM_757620' All hits will point to first ID > found > > EMBOSS An error in embdbi.c at line 1238: > Error in embDbiSortWriteFields, expected entry NM_001004399 not found Hmmm ... what refseq files are you using (I'm trying now with the ftp://ftp.ncbi.nih.gov/refseq/release/complete/*.gbff.gz files) Could you have a duplicate entry from an old file? Could your sort space have filled up? Running with -noclean will leave the temporary files around and make it easier to check for truncation - though simpoly rerunning would probably give a different result if that is the problem (note to self - must find a way to test the error messages without really filling up a disk) regards, Peter From isabelle.wells at roche.com Tue Jun 20 09:18:00 2006 From: isabelle.wells at roche.com (Wells, Isabelle) Date: Tue, 20 Jun 2006 15:18:00 +0200 Subject: [EMBOSS] New EMBL release Message-ID: Hi All, EMBL release 87 has just been made available and changes to the entry ID line were made. Did anyone install it and index the files with dbiflat? I am just wondering whether the change in ID line structure causes problems. Thanks, Isabelle From pmr at ebi.ac.uk Tue Jun 20 10:06:46 2006 From: pmr at ebi.ac.uk (Peter Rice) Date: Tue, 20 Jun 2006 15:06:46 +0100 Subject: [EMBOSS] New EMBL release In-Reply-To: References: Message-ID: <449800F6.3070604@ebi.ac.uk> Wells, Isabelle wrote: > Hi All, > > EMBL release 87 has just been made available and changes to the entry ID > line were made. Did anyone install it and index the files with dbiflat? > I am just wondering whether the change in ID line structure causes > problems. There are some small changes needed. We will produce patch files next week for 3.0.0 (the 4.0.0 code in CVS already works). We waited to see a full release before making the patches, in case there are any surprises. I will send an announcement to this list when the patches are tested and copied to emboss.open-bio.org regards, Peter From jison at ebi.ac.uk Tue Jun 20 10:35:49 2006 From: jison at ebi.ac.uk (Jon Ison) Date: Tue, 20 Jun 2006 15:35:49 +0100 (BST) Subject: [EMBOSS] New EMBL release In-Reply-To: References: Message-ID: <60298.172.31.100.168.1150814149.squirrel@webmail.ebi.ac.uk> Hi Isabelle EMBOSS 4 (out on July 15th) will support the new style lines. The developers (CVS version) should too (but I'm not 100% certain). You can expect problems with other versions. Cheers Jon > Hi All, > > EMBL release 87 has just been made available and changes to the entry ID > line were made. Did anyone install it and index the files with dbiflat? > I am just wondering whether the change in ID line structure causes > problems. > > Thanks, > Isabelle > > > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > From haruosuz at yahoo.co.jp Mon Jun 5 00:23:30 2006 From: haruosuz at yahoo.co.jp (haruosuz at yahoo.co.jp) Date: Sun, 4 Jun 2006 17:23:30 -0700 Subject: [EMBOSS] install EMBOSS-3.0.0 on Intel Mac Message-ID: Dear Sir, [1] http://lists.open-bio.org/pipermail/emboss/2006-May/002531.html Although I read README and applied all the fixes from: ftp://emboss.open-bio.org/pub/EMBOSS/fixes/ I failed to install. % make *snip* ajindex.c: In function 'ajBtreeCacheNewC': ajindex.c:200: error: storage size of 'buf' isn't known ajindex.c: In function 'ajBtreeSecCacheNewC': ajindex.c:8234: error: storage size of 'buf' isn't known make[1]: *** [ajindex.lo] Error 1 make: *** [all-recursive] Error 1 [2] http://lists.open-bio.org/pipermail/emboss/2006-May/002532.html I also used fink to install EMBOSS on my Mac, but I failed to install. % fink install emboss *snip* dpkg: error processing /sw/fink/dists/unstable/main/binary-darwin- i386/graphics/libjpeg_6b-16_darwin-i386.deb (--install): package architecture (darwin-i386) does not match system (darwin- powerpc) dpkg: error processing /sw/fink/dists/unstable/main/binary-darwin- i386/graphics/libjpeg-bin_6b-16_darwin-i386.deb (--install): package architecture (darwin-i386) does not match system (darwin- powerpc) Errors were encountered while processing: /sw/fink/dists/unstable/main/binary-darwin-i386/graphics/ libjpeg_6b-16_darwin-i386.deb /sw/fink/dists/unstable/main/binary-darwin-i386/graphics/libjpeg- bin_6b-16_darwin-i386.deb ### execution of dpkg failed, exit code 1 Failed: can't batch-install packages: /sw/fink/dists/unstable/main/ binary-darwin-i386/graphics/libjpeg_6b-16_darwin-i386.deb /sw/fink/ dists/unstable/main/binary-darwin-i386/graphics/libjpeg- bin_6b-16_darwin-i386.deb [About my Mac] Mac OS X 10.4.6 Darwin 8.6.1 MacBookPro1,1 Intel Core Duo I am looking forward to hearing from you. Sincerely yours, Haruo Suzuki -------------------------------------- Let's start Yahoo! Auction - Free Campaign Now! http://pr.mail.yahoo.co.jp/auction/ From kvddrift at earthlink.net Mon Jun 5 00:58:44 2006 From: kvddrift at earthlink.net (Koen van der Drift) Date: Sun, 4 Jun 2006 20:58:44 -0400 Subject: [EMBOSS] install EMBOSS-3.0.0 on Intel Mac In-Reply-To: References: Message-ID: On Jun 4, 2006, at 8:23 PM, haruosuz at yahoo.co.jp wrote: > dpkg: error processing /sw/fink/dists/unstable/main/binary-darwin- > i386/graphics/libjpeg_6b-16_darwin-i386.deb (--install): > package architecture (darwin-i386) does not match system (darwin- > powerpc) > dpkg: error processing /sw/fink/dists/unstable/main/binary-darwin- > i386/graphics/libjpeg-bin_6b-16_darwin-i386.deb (--install): > package architecture (darwin-i386) does not match system (darwin- > powerpc) > Errors were encountered while processing: > /sw/fink/dists/unstable/main/binary-darwin-i386/graphics/ > libjpeg_6b-16_darwin-i386.deb > /sw/fink/dists/unstable/main/binary-darwin-i386/graphics/libjpeg- > bin_6b-16_darwin-i386.deb > ### execution of dpkg failed, exit code 1 > Failed: can't batch-install packages: /sw/fink/dists/unstable/main/ > binary-darwin-i386/graphics/libjpeg_6b-16_darwin-i386.deb /sw/fink/ > dists/unstable/main/binary-darwin-i386/graphics/libjpeg- > bin_6b-16_darwin-i386.deb Haruo, That's an error for the libjpeg package in fink. I suggest you contact the libjpeg package maintainer (%fink info libjpeg). good luck, - Koen. From ajb at ebi.ac.uk Mon Jun 5 07:12:50 2006 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Mon, 5 Jun 2006 08:12:50 +0100 (BST) Subject: [EMBOSS] install EMBOSS-3.0.0 on Intel Mac In-Reply-To: References: Message-ID: <33758.81.98.244.247.1149491570.squirrel@webmail.ebi.ac.uk> Dear Haruo, > ajindex.c: In function 'ajBtreeCacheNewC': > ajindex.c:200: error: storage size of 'buf' isn't known > ajindex.c: In function 'ajBtreeSecCacheNewC': > ajindex.c:8234: error: storage size of 'buf' isn't known > make[1]: *** [ajindex.lo] Error 1 > make: *** [all-recursive] Error 1 That error shows that something went wrong when you tried to apply the fixes from the ftp server. You are trying to compile the original ajindex.c file. I'd suggest that you compare the file sizes on your local system with those in the fixes directory and reapply any fixes as appropriate. HTH Alan From haruosuz at yahoo.co.jp Mon Jun 5 18:58:23 2006 From: haruosuz at yahoo.co.jp (haruosuz at yahoo.co.jp) Date: Mon, 5 Jun 2006 11:58:23 -0700 Subject: [EMBOSS] install EMBOSS-3.0.0 on Intel Mac In-Reply-To: <33758.81.98.244.247.1149491570.squirrel@webmail.ebi.ac.uk> References: <33758.81.98.244.247.1149491570.squirrel@webmail.ebi.ac.uk> Message-ID: <0DAC5E74-E414-4CD4-9C59-6FBEE9C5F992@yahoo.co.jp> Thank you very much for your advice. On 2006/06/05, at 0:12, ajb at ebi.ac.uk wrote: > Dear Haruo, > >> ajindex.c: In function 'ajBtreeCacheNewC': >> ajindex.c:200: error: storage size of 'buf' isn't known >> ajindex.c: In function 'ajBtreeSecCacheNewC': >> ajindex.c:8234: error: storage size of 'buf' isn't known >> make[1]: *** [ajindex.lo] Error 1 >> make: *** [all-recursive] Error 1 > > That error shows that something went wrong when you tried to apply > the fixes from the ftp server. You are trying to compile the > original ajindex.c file. I'd suggest that you compare the file sizes > on your local system with those in the fixes directory and reapply > any fixes as appropriate. > > HTH > > Alan Although I made sure if I replaced the old files with new files in the fixes directory and redo the 'make', I failed. % make *snip* /bin/sh ../libtool --tag=CC --mode=link gcc -O1 -o aaindexextract aaindexextract.o ../nucleus/libnucleus.la ../ajax/libajaxg.la ../ajax/ libajax.la ../plplot/libplplot.la -L/usr/X11R6/lib -lX11 -lm -lgd - lpng -lz -lm mkdir .libs libtool: link: warning: library `/usr/local/lib/libgd.la' was moved. libtool: link: warning: library `/usr/local/lib/libgd.la' was moved. libtool: link: cannot find the library `/opt/local/lib/libjpeg.la' make[2]: *** [aaindexextract] Error 1 make[1]: *** [all-recursive] Error 1 make: *** [all-recursive] Error 1 On 2006/06/04, at 17:58, Koen van der Drift wrote: > > On Jun 4, 2006, at 8:23 PM, haruosuz at yahoo.co.jp wrote: > >> dpkg: error processing /sw/fink/dists/unstable/main/binary-darwin- >> i386/graphics/libjpeg_6b-16_darwin-i386.deb (--install): >> package architecture (darwin-i386) does not match system (darwin- >> powerpc) >> dpkg: error processing /sw/fink/dists/unstable/main/binary-darwin- >> i386/graphics/libjpeg-bin_6b-16_darwin-i386.deb (--install): >> package architecture (darwin-i386) does not match system (darwin- >> powerpc) >> Errors were encountered while processing: >> /sw/fink/dists/unstable/main/binary-darwin-i386/graphics/ >> libjpeg_6b-16_darwin-i386.deb >> /sw/fink/dists/unstable/main/binary-darwin-i386/graphics/libjpeg- >> bin_6b-16_darwin-i386.deb >> ### execution of dpkg failed, exit code 1 >> Failed: can't batch-install packages: /sw/fink/dists/unstable/main/ >> binary-darwin-i386/graphics/libjpeg_6b-16_darwin-i386.deb /sw/fink/ >> dists/unstable/main/binary-darwin-i386/graphics/libjpeg- >> bin_6b-16_darwin-i386.deb > > > Haruo, > > That's an error for the libjpeg package in fink. I suggest you > contact the libjpeg package maintainer (%fink info libjpeg). > > good luck, > > - Koen. Begin forwarded message: > Actually, the problem is not with the libjpeg package in fink. The > problem is that you are somehow mixing the intel and powerpc > versions of fink. My guess is that you installed fink by using the > Fink-0.8.0-Installer? Unfortunately, that only works correctly on > powerpc. To install fink on intel, you must bootstrap it from > scratch, as mentioned on the fink homepage. If you have trouble > with this, please consult the mailing list fink- > users at lists.sourceforge.net -------------------------------------- Let's start Yahoo! Auction - Free Campaign Now! http://pr.mail.yahoo.co.jp/auction/ From ajb at ebi.ac.uk Mon Jun 5 21:45:52 2006 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Mon, 5 Jun 2006 22:45:52 +0100 (BST) Subject: [EMBOSS] install EMBOSS-3.0.0 on Intel Mac In-Reply-To: <0DAC5E74-E414-4CD4-9C59-6FBEE9C5F992@yahoo.co.jp> References: <33758.81.98.244.247.1149491570.squirrel@webmail.ebi.ac.uk> <0DAC5E74-E414-4CD4-9C59-6FBEE9C5F992@yahoo.co.jp> Message-ID: <37136.81.98.244.247.1149543952.squirrel@webmail.ebi.ac.uk> > Thank you very much for your advice. > > On 2006/06/05, at 0:12, ajb at ebi.ac.uk wrote: >> Dear Haruo, >> >>> ajindex.c: In function 'ajBtreeCacheNewC': >>> ajindex.c:200: error: storage size of 'buf' isn't known >>> ajindex.c: In function 'ajBtreeSecCacheNewC': >>> ajindex.c:8234: error: storage size of 'buf' isn't known >>> make[1]: *** [ajindex.lo] Error 1 >>> make: *** [all-recursive] Error 1 >> >> That error shows that something went wrong when you tried to apply >> the fixes from the ftp server. You are trying to compile the >> original ajindex.c file. I'd suggest that you compare the file sizes >> on your local system with those in the fixes directory and reapply >> any fixes as appropriate. >> >> HTH >> >> Alan > > Although I made sure if I replaced the old files with new files > in the fixes directory and redo the 'make', I failed. > > % make > > *snip* > > /bin/sh ../libtool --tag=CC --mode=link gcc -O1 -o aaindexextract > aaindexextract.o ../nucleus/libnucleus.la ../ajax/libajaxg.la ../ajax/ > libajax.la ../plplot/libplplot.la -L/usr/X11R6/lib -lX11 -lm -lgd - > lpng -lz -lm > mkdir .libs > libtool: link: warning: library `/usr/local/lib/libgd.la' was moved. > libtool: link: warning: library `/usr/local/lib/libgd.la' was moved. > libtool: link: cannot find the library `/opt/local/lib/libjpeg.la' > make[2]: *** [aaindexextract] Error 1 > make[1]: *** [all-recursive] Error 1 > make: *** [all-recursive] Error 1 > > On 2006/06/04, at 17:58, Koen van der Drift wrote: >> >> On Jun 4, 2006, at 8:23 PM, haruosuz at yahoo.co.jp wrote: >> >>> dpkg: error processing /sw/fink/dists/unstable/main/binary-darwin- >>> i386/graphics/libjpeg_6b-16_darwin-i386.deb (--install): >>> package architecture (darwin-i386) does not match system (darwin- >>> powerpc) >>> dpkg: error processing /sw/fink/dists/unstable/main/binary-darwin- >>> i386/graphics/libjpeg-bin_6b-16_darwin-i386.deb (--install): >>> package architecture (darwin-i386) does not match system (darwin- >>> powerpc) >>> Errors were encountered while processing: >>> /sw/fink/dists/unstable/main/binary-darwin-i386/graphics/ >>> libjpeg_6b-16_darwin-i386.deb >>> /sw/fink/dists/unstable/main/binary-darwin-i386/graphics/libjpeg- >>> bin_6b-16_darwin-i386.deb >>> ### execution of dpkg failed, exit code 1 >>> Failed: can't batch-install packages: /sw/fink/dists/unstable/main/ >>> binary-darwin-i386/graphics/libjpeg_6b-16_darwin-i386.deb /sw/fink/ >>> dists/unstable/main/binary-darwin-i386/graphics/libjpeg- >>> bin_6b-16_darwin-i386.deb >> >> >> Haruo, >> >> That's an error for the libjpeg package in fink. I suggest you >> contact the libjpeg package maintainer (%fink info libjpeg). >> >> good luck, >> >> - Koen. > > > Begin forwarded message: > >> Actually, the problem is not with the libjpeg package in fink. The >> problem is that you are somehow mixing the intel and powerpc >> versions of fink. My guess is that you installed fink by using the >> Fink-0.8.0-Installer? Unfortunately, that only works correctly on >> powerpc. To install fink on intel, you must bootstrap it from >> scratch, as mentioned on the fink homepage. If you have trouble >> with this, please consult the mailing list fink- >> users at lists.sourceforge.net > > > -------------------------------------- > Let's start Yahoo! Auction - Free Campaign Now! > http://pr.mail.yahoo.co.jp/auction/ > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > From ajb at ebi.ac.uk Mon Jun 5 22:00:06 2006 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Mon, 5 Jun 2006 23:00:06 +0100 (BST) Subject: [EMBOSS] install EMBOSS-3.0.0 on Intel Mac In-Reply-To: <0DAC5E74-E414-4CD4-9C59-6FBEE9C5F992@yahoo.co.jp> References: <33758.81.98.244.247.1149491570.squirrel@webmail.ebi.ac.uk> <0DAC5E74-E414-4CD4-9C59-6FBEE9C5F992@yahoo.co.jp> Message-ID: <54667.81.98.244.247.1149544806.squirrel@webmail.ebi.ac.uk> Apologies for the last message. Wrong button clicked on my mailer. You may be able to get past your current error by specifying --without-pngdriver on the configure line. However, as Koen has said, it is probably caused by something wrong in your FINK installation and is best fixed. Koen and the FINK team are the best people to ask about that. It isn't an EMBOSS problem as such. We make sure that EMBOSS works on relatively virgin OS installations; other projects such as FINK can then add bells and whistles. HTH Alan > Thank you very much for your advice. > > On 2006/06/05, at 0:12, ajb at ebi.ac.uk wrote: >> Dear Haruo, >> >>> ajindex.c: In function 'ajBtreeCacheNewC': >>> ajindex.c:200: error: storage size of 'buf' isn't known >>> ajindex.c: In function 'ajBtreeSecCacheNewC': >>> ajindex.c:8234: error: storage size of 'buf' isn't known >>> make[1]: *** [ajindex.lo] Error 1 >>> make: *** [all-recursive] Error 1 >> >> That error shows that something went wrong when you tried to apply >> the fixes from the ftp server. You are trying to compile the >> original ajindex.c file. I'd suggest that you compare the file sizes >> on your local system with those in the fixes directory and reapply >> any fixes as appropriate. >> >> HTH >> >> Alan > > Although I made sure if I replaced the old files with new files > in the fixes directory and redo the 'make', I failed. > > % make > > *snip* > > /bin/sh ../libtool --tag=CC --mode=link gcc -O1 -o aaindexextract > aaindexextract.o ../nucleus/libnucleus.la ../ajax/libajaxg.la ../ajax/ > libajax.la ../plplot/libplplot.la -L/usr/X11R6/lib -lX11 -lm -lgd - > lpng -lz -lm > mkdir .libs > libtool: link: warning: library `/usr/local/lib/libgd.la' was moved. > libtool: link: warning: library `/usr/local/lib/libgd.la' was moved. > libtool: link: cannot find the library `/opt/local/lib/libjpeg.la' > make[2]: *** [aaindexextract] Error 1 > make[1]: *** [all-recursive] Error 1 > make: *** [all-recursive] Error 1 > > On 2006/06/04, at 17:58, Koen van der Drift wrote: >> >> On Jun 4, 2006, at 8:23 PM, haruosuz at yahoo.co.jp wrote: >> >>> dpkg: error processing /sw/fink/dists/unstable/main/binary-darwin- >>> i386/graphics/libjpeg_6b-16_darwin-i386.deb (--install): >>> package architecture (darwin-i386) does not match system (darwin- >>> powerpc) >>> dpkg: error processing /sw/fink/dists/unstable/main/binary-darwin- >>> i386/graphics/libjpeg-bin_6b-16_darwin-i386.deb (--install): >>> package architecture (darwin-i386) does not match system (darwin- >>> powerpc) >>> Errors were encountered while processing: >>> /sw/fink/dists/unstable/main/binary-darwin-i386/graphics/ >>> libjpeg_6b-16_darwin-i386.deb >>> /sw/fink/dists/unstable/main/binary-darwin-i386/graphics/libjpeg- >>> bin_6b-16_darwin-i386.deb >>> ### execution of dpkg failed, exit code 1 >>> Failed: can't batch-install packages: /sw/fink/dists/unstable/main/ >>> binary-darwin-i386/graphics/libjpeg_6b-16_darwin-i386.deb /sw/fink/ >>> dists/unstable/main/binary-darwin-i386/graphics/libjpeg- >>> bin_6b-16_darwin-i386.deb >> >> >> Haruo, >> >> That's an error for the libjpeg package in fink. I suggest you >> contact the libjpeg package maintainer (%fink info libjpeg). >> >> good luck, >> >> - Koen. > > > Begin forwarded message: > >> Actually, the problem is not with the libjpeg package in fink. The >> problem is that you are somehow mixing the intel and powerpc >> versions of fink. My guess is that you installed fink by using the >> Fink-0.8.0-Installer? Unfortunately, that only works correctly on >> powerpc. To install fink on intel, you must bootstrap it from >> scratch, as mentioned on the fink homepage. If you have trouble >> with this, please consult the mailing list fink- >> users at lists.sourceforge.net > > > -------------------------------------- > Let's start Yahoo! Auction - Free Campaign Now! > http://pr.mail.yahoo.co.jp/auction/ > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > From haruosuz at yahoo.co.jp Thu Jun 8 02:11:06 2006 From: haruosuz at yahoo.co.jp (haruosuz at yahoo.co.jp) Date: Wed, 7 Jun 2006 19:11:06 -0700 Subject: [EMBOSS] install EMBOSS-3.0.0 on Intel Mac In-Reply-To: <54667.81.98.244.247.1149544806.squirrel@webmail.ebi.ac.uk> References: <33758.81.98.244.247.1149491570.squirrel@webmail.ebi.ac.uk> <0DAC5E74-E414-4CD4-9C59-6FBEE9C5F992@yahoo.co.jp> <54667.81.98.244.247.1149544806.squirrel@webmail.ebi.ac.uk> Message-ID: <293361E9-766F-41AF-849E-41B57D8D692A@yahoo.co.jp> Finally, installing emboss on a intel-Mac has been successful. By the way, when running "prettyseq" and "cusp", the following massage was shown: Died: Unknown qualifier -cfile ---------------------------------------------------------------- [install memo] (1) remove following directory sudo rm -rf /usr/X11R6/ sudo rm -rf /etc/X11/ sudo rm -rf /sw sudo rm -rf /usr/local/bin/ (2) reinstall them. install fink ./bootstrap.sh add 'source /sw/bin/init.sh' to the script '.bashrc' add 'source .bashrc' to the init script '.bash_profile' fink selfupdate-cvs sudo emacs /sw/etc/fink.conf 'Trees: local/main stable/main stable/crypto unstable/main unstable/ crypto' install X11SDK (3) install EMBOSS fink install emboss ---------------------------------------------------------------- -------------------------------------- Let's start Yahoo! Auction - Free Campaign Now! http://pr.mail.yahoo.co.jp/auction/ From pmr at ebi.ac.uk Thu Jun 8 06:25:10 2006 From: pmr at ebi.ac.uk (pmr at ebi.ac.uk) Date: Thu, 8 Jun 2006 07:25:10 +0100 (BST) Subject: [EMBOSS] install EMBOSS-3.0.0 on Intel Mac In-Reply-To: <293361E9-766F-41AF-849E-41B57D8D692A@yahoo.co.jp> References: <33758.81.98.244.247.1149491570.squirrel@webmail.ebi.ac.uk> <0DAC5E74-E414-4CD4-9C59-6FBEE9C5F992@yahoo.co.jp> <54667.81.98.244.247.1149544806.squirrel@webmail.ebi.ac.uk> <293361E9-766F-41AF-849E-41B57D8D692A@yahoo.co.jp> Message-ID: <2201.86.141.181.123.1149747910.squirrel@webmail.ebi.ac.uk> Hi Haruosuz at yahoo.co.jp, > Finally, installing emboss on a intel-Mac has been successful. > > By the way, when running "prettyseq" and "cusp", > the following massage was shown: > Died: Unknown qualifier -cfile Do you have an old version installed somewhere? Running "prettyseq -debug" or "cusp -debug" will produce a prettyseq.dbg (or cusp.dbg) file that will tell you which ACD file they are reading. This does not match the program that you are running. Running "embossversion" will show which version of the programs you are actually running. regards, Peter Rice From aengus.stewart at cancer.org.uk Wed Jun 14 18:59:09 2006 From: aengus.stewart at cancer.org.uk (Aengus Stewart) Date: Wed, 14 Jun 2006 19:59:09 +0100 Subject: [EMBOSS] Error with dbiflat and Refseq Message-ID: <44905C7D.4060101@cancer.org.uk> Hi Sorry for asking this but dbiflat is dying on me with the refseq nucleotides I am using dbiflat -dbname RefSeqN -idformat refseq -directory . -filenames "*.gbff" -release 17.0 -date 14/06/06 -fields "acnum,seqvn,des,keyword,taxon" and I get Warning: Duplicate ID skipped: 'XM_757618' All hits will point to first ID found Warning: Duplicate ID skipped: 'XM_757619' All hits will point to first ID found Warning: Duplicate ID skipped: 'XM_757620' All hits will point to first ID found EMBOSS An error in embdbi.c at line 1238: Error in embDbiSortWriteFields, expected entry NM_001004399 not found I know its probably something simple, but for the life of me I cant see it............. Any suggestions? Regards Aengus -- ----------------------------------------------------------------------- Aengus Stewart Group Leader Bioinformatics and BioStatistics Tel: +44 (0)20 7269 3679 Cancer Research UK, Lincoln's Inn Fields, Holborn, London, WC2A 3PX, UK ----------------------------------------------------------------------- This electronic message contains information which may be privileged and confidential. The information is intended to be for the use of the individual(s) or entity named above. Be aware that any third party disclosure, distribution, copying or use of this communication, without prior permission, is strictly prohibited. From pmr at ebi.ac.uk Wed Jun 14 22:05:17 2006 From: pmr at ebi.ac.uk (pmr at ebi.ac.uk) Date: Wed, 14 Jun 2006 23:05:17 +0100 (BST) Subject: [EMBOSS] Error with dbiflat and Refseq In-Reply-To: <44905C7D.4060101@cancer.org.uk> References: <44905C7D.4060101@cancer.org.uk> Message-ID: <2229.192.130.162.193.1150322717.squirrel@webmail.ebi.ac.uk> Hi Aengus, > dbiflat is dying on me with the refseq nucleotides > > I am using > > dbiflat -dbname RefSeqN -idformat refseq -directory . -filenames "*.gbff" > -release 17.0 -date 14/06/06 -fields "acnum,seqvn,des,keyword,taxon" > > and I get > > Warning: Duplicate ID skipped: 'XM_757618' All hits will point to first ID > found > Warning: Duplicate ID skipped: 'XM_757619' All hits will point to first ID > found > Warning: Duplicate ID skipped: 'XM_757620' All hits will point to first ID > found > > EMBOSS An error in embdbi.c at line 1238: > Error in embDbiSortWriteFields, expected entry NM_001004399 not found Hmmm ... what refseq files are you using (I'm trying now with the ftp://ftp.ncbi.nih.gov/refseq/release/complete/*.gbff.gz files) Could you have a duplicate entry from an old file? Could your sort space have filled up? Running with -noclean will leave the temporary files around and make it easier to check for truncation - though simpoly rerunning would probably give a different result if that is the problem (note to self - must find a way to test the error messages without really filling up a disk) regards, Peter From isabelle.wells at roche.com Tue Jun 20 13:18:00 2006 From: isabelle.wells at roche.com (Wells, Isabelle) Date: Tue, 20 Jun 2006 15:18:00 +0200 Subject: [EMBOSS] New EMBL release Message-ID: Hi All, EMBL release 87 has just been made available and changes to the entry ID line were made. Did anyone install it and index the files with dbiflat? I am just wondering whether the change in ID line structure causes problems. Thanks, Isabelle From pmr at ebi.ac.uk Tue Jun 20 14:06:46 2006 From: pmr at ebi.ac.uk (Peter Rice) Date: Tue, 20 Jun 2006 15:06:46 +0100 Subject: [EMBOSS] New EMBL release In-Reply-To: References: Message-ID: <449800F6.3070604@ebi.ac.uk> Wells, Isabelle wrote: > Hi All, > > EMBL release 87 has just been made available and changes to the entry ID > line were made. Did anyone install it and index the files with dbiflat? > I am just wondering whether the change in ID line structure causes > problems. There are some small changes needed. We will produce patch files next week for 3.0.0 (the 4.0.0 code in CVS already works). We waited to see a full release before making the patches, in case there are any surprises. I will send an announcement to this list when the patches are tested and copied to emboss.open-bio.org regards, Peter From jison at ebi.ac.uk Tue Jun 20 14:35:49 2006 From: jison at ebi.ac.uk (Jon Ison) Date: Tue, 20 Jun 2006 15:35:49 +0100 (BST) Subject: [EMBOSS] New EMBL release In-Reply-To: References: Message-ID: <60298.172.31.100.168.1150814149.squirrel@webmail.ebi.ac.uk> Hi Isabelle EMBOSS 4 (out on July 15th) will support the new style lines. The developers (CVS version) should too (but I'm not 100% certain). You can expect problems with other versions. Cheers Jon > Hi All, > > EMBL release 87 has just been made available and changes to the entry ID > line were made. Did anyone install it and index the files with dbiflat? > I am just wondering whether the change in ID line structure causes > problems. > > Thanks, > Isabelle > > > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss >