From ajb at ebi.ac.uk Thu Aug 11 09:21:22 2011 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Thu, 11 Aug 2011 14:21:22 +0100 (BST) Subject: [emboss-announce] EMBOSS and mEMBOSS bug-fixes for 6.4.0 released Message-ID: <53900.82.26.12.214.1313068882.squirrel@imap04.ebi.ac.uk> New bug-fix files are available for EMBOSS-6.4.0 and, for Windows users, a new version of mEMBOSS is available. The bugs fixed are appended for easy reference. 1) UNIX As usual, the most convenient way of applying the bug-fixes should be to apply the patch file: ftp://emboss.open-bio.org/pub/EMBOSS/fixes/patches/patch-1-11.gz to a freshly extracted copy of the EMBOSS-6.4.0.tar.gz source code and recompiling/installing. (see ftp://emboss.open-bio.org/pub/EMBOSS/fixes/patches/README.patch for instructions on using 'patch'). Alternatively, you can individually copy the patched files from the ftp://emboss.open-bio.org/pub/EMBOSS/fixes/ directory if your system does not support 'patch'. 2) mEMBOSS The new version incorporates all the bug-fixes listed below. Uninstall your previous mEMBOSS installation and download and install the new setup file from: ftp://emboss.open-bio.org/pub/EMBOSS/windows/mEMBOSS-6.4.0.2-setup.exe Alan ----------------------------------------------------------------------- Fix 1. EMBOSS-6.4.0/emboss/dbiflat.c EMBOSS-6.4.0/emboss/dbxflat.c 10 Aug 2011: The SwissProt description line format includes additional tags which interfere with the EMBL parser used in previous releases. The fix replaces this with a SwissProt parser that strips out the extra tags. After patching the release, any existing SwissProt description index files should be reindexed. Other indexes are unchanged. Fix 2. EMBOSS-6.4.0/ajax/core/ajquery.c 10 Aug 2011: For databases with more than one valid format (examples include the EBI dbfetch server) this fix allows the format to be specified with a qualifier on the command line. In the original release, only a format in the query string was used. Fix 3. EMBOSS-6.4.0/ajax/core/ajfeatread.c 10 Aug 2011: When parsing GFF3 format input, long feature tags (for example extremely long translations) exceeded limits in regular expression parsing. This fix decouples testing for escaped quotes from the main task of finding quoted strings. Fix 4. EMBOSS-6.4.0/emboss/data/Etcode.dat 10 Aug 2001: The local data file used by application tcode had a missing parameter line. Fix 5. EMBOSS-6.4.0/ajax/core/ajrange.c 10 Aug 2011: When sequence ranges (and possible highlighting for showalign) were in a list file, the parser overwrote string values. Fix 5. EMBOSS-6.4.0/ajax/core/ajseqabi.c 10 Aug 2011: Sample names in ABI format files were stored in incompletely defined strings. This fix corrects the string object. The sample name is also used as the sequence name. Fix 6. EMBOSS-6.4.0/emboss/dbxresource.c 10 Aug 2011: A future change to the format of Data Resource Catalogue entries in DRCAT.dat requires an update to the parsing of category lines. The current version is not affected. Fix 7. EMBOSS-6.4.0/emboss/server.ensemblgenomes EMBOSS-6.4.0/emboss/cacheensembl.c EMBOSS-6.4.0/ajax/ensembl/ensregistry.c EMBOSS-6.4.0/ajax/ensembl/ensregistry.c EMBOSS-6.4.0/ajax/ensembl/ensdatabaseadaptor.c EMBOSS-6.4.0/ajax/ensembl/ensdatabaseadaptor.h 10 Aug 2011: Microbial genomes use an enumerated species code which must be added to the query for data retrieval. This fix adds the species code to the comment field. In the next release a more complete solution will be implemented. Fix 8. EMBOSS-6.4.0/ajax/core/ajarch.h 10-Aug-2011: Corrects the size of long integers on Windows systems only. Fix 9. EMBOSS-6.4.0/emboss/cirdna.c 10-Aug-2011: Cirdna prints text inside solid blocks invisibly. When printed outside the text scaling was too small. The text scale is now adjusted for the radius and sequence length so that labels should be readable outside the box. Fix 10. EMBOSS-6.4.0/ajax/core/ajpat.c 10-Aug-2011: Fuzznuc, fuzzpro and fuzztran using a pattern file ignored the command line -mismatch qualifier for the first pattern. The default mismatch is now set to this value at the start of the pattern matching loop in the library. Fix 11. EMBOSS-6.4.0/ajax/core/ajfmt.c 11-Aug-2011: The function ajFmtScanF() handled va_list incorrectly. Only potentially affected code developers. From ajb at ebi.ac.uk Thu Aug 11 11:56:44 2011 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Thu, 11 Aug 2011 16:56:44 +0100 (BST) Subject: [emboss-announce] EMBOSS and mEMBOSS bug-fixes for 6.4.0 released Message-ID: <48997.82.26.12.214.1313078204.squirrel@imap04.ebi.ac.uk> UNIX users who downloaded the bug-fix patch file for EMBOSS earlier this afternoon may have found that there were compilation problems on a limited number of architectures. The patch has been amended slightly to hopefully fix this problem so please download it again if you were affected. If anyone continues to experience compilation problems then please let me know. Alan From ajb at ebi.ac.uk Thu Aug 11 13:21:22 2011 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Thu, 11 Aug 2011 14:21:22 +0100 (BST) Subject: [emboss-announce] EMBOSS and mEMBOSS bug-fixes for 6.4.0 released Message-ID: <53900.82.26.12.214.1313068882.squirrel@imap04.ebi.ac.uk> New bug-fix files are available for EMBOSS-6.4.0 and, for Windows users, a new version of mEMBOSS is available. The bugs fixed are appended for easy reference. 1) UNIX As usual, the most convenient way of applying the bug-fixes should be to apply the patch file: ftp://emboss.open-bio.org/pub/EMBOSS/fixes/patches/patch-1-11.gz to a freshly extracted copy of the EMBOSS-6.4.0.tar.gz source code and recompiling/installing. (see ftp://emboss.open-bio.org/pub/EMBOSS/fixes/patches/README.patch for instructions on using 'patch'). Alternatively, you can individually copy the patched files from the ftp://emboss.open-bio.org/pub/EMBOSS/fixes/ directory if your system does not support 'patch'. 2) mEMBOSS The new version incorporates all the bug-fixes listed below. Uninstall your previous mEMBOSS installation and download and install the new setup file from: ftp://emboss.open-bio.org/pub/EMBOSS/windows/mEMBOSS-6.4.0.2-setup.exe Alan ----------------------------------------------------------------------- Fix 1. EMBOSS-6.4.0/emboss/dbiflat.c EMBOSS-6.4.0/emboss/dbxflat.c 10 Aug 2011: The SwissProt description line format includes additional tags which interfere with the EMBL parser used in previous releases. The fix replaces this with a SwissProt parser that strips out the extra tags. After patching the release, any existing SwissProt description index files should be reindexed. Other indexes are unchanged. Fix 2. EMBOSS-6.4.0/ajax/core/ajquery.c 10 Aug 2011: For databases with more than one valid format (examples include the EBI dbfetch server) this fix allows the format to be specified with a qualifier on the command line. In the original release, only a format in the query string was used. Fix 3. EMBOSS-6.4.0/ajax/core/ajfeatread.c 10 Aug 2011: When parsing GFF3 format input, long feature tags (for example extremely long translations) exceeded limits in regular expression parsing. This fix decouples testing for escaped quotes from the main task of finding quoted strings. Fix 4. EMBOSS-6.4.0/emboss/data/Etcode.dat 10 Aug 2001: The local data file used by application tcode had a missing parameter line. Fix 5. EMBOSS-6.4.0/ajax/core/ajrange.c 10 Aug 2011: When sequence ranges (and possible highlighting for showalign) were in a list file, the parser overwrote string values. Fix 5. EMBOSS-6.4.0/ajax/core/ajseqabi.c 10 Aug 2011: Sample names in ABI format files were stored in incompletely defined strings. This fix corrects the string object. The sample name is also used as the sequence name. Fix 6. EMBOSS-6.4.0/emboss/dbxresource.c 10 Aug 2011: A future change to the format of Data Resource Catalogue entries in DRCAT.dat requires an update to the parsing of category lines. The current version is not affected. Fix 7. EMBOSS-6.4.0/emboss/server.ensemblgenomes EMBOSS-6.4.0/emboss/cacheensembl.c EMBOSS-6.4.0/ajax/ensembl/ensregistry.c EMBOSS-6.4.0/ajax/ensembl/ensregistry.c EMBOSS-6.4.0/ajax/ensembl/ensdatabaseadaptor.c EMBOSS-6.4.0/ajax/ensembl/ensdatabaseadaptor.h 10 Aug 2011: Microbial genomes use an enumerated species code which must be added to the query for data retrieval. This fix adds the species code to the comment field. In the next release a more complete solution will be implemented. Fix 8. EMBOSS-6.4.0/ajax/core/ajarch.h 10-Aug-2011: Corrects the size of long integers on Windows systems only. Fix 9. EMBOSS-6.4.0/emboss/cirdna.c 10-Aug-2011: Cirdna prints text inside solid blocks invisibly. When printed outside the text scaling was too small. The text scale is now adjusted for the radius and sequence length so that labels should be readable outside the box. Fix 10. EMBOSS-6.4.0/ajax/core/ajpat.c 10-Aug-2011: Fuzznuc, fuzzpro and fuzztran using a pattern file ignored the command line -mismatch qualifier for the first pattern. The default mismatch is now set to this value at the start of the pattern matching loop in the library. Fix 11. EMBOSS-6.4.0/ajax/core/ajfmt.c 11-Aug-2011: The function ajFmtScanF() handled va_list incorrectly. Only potentially affected code developers. From ajb at ebi.ac.uk Thu Aug 11 15:56:44 2011 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Thu, 11 Aug 2011 16:56:44 +0100 (BST) Subject: [emboss-announce] EMBOSS and mEMBOSS bug-fixes for 6.4.0 released Message-ID: <48997.82.26.12.214.1313078204.squirrel@imap04.ebi.ac.uk> UNIX users who downloaded the bug-fix patch file for EMBOSS earlier this afternoon may have found that there were compilation problems on a limited number of architectures. The patch has been amended slightly to hopefully fix this problem so please download it again if you were affected. If anyone continues to experience compilation problems then please let me know. Alan