From ajb at ebi.ac.uk Tue Sep 6 04:50:18 2011 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Tue, 6 Sep 2011 09:50:18 +0100 (BST) Subject: [emboss-announce] EMBOSS and mEMBOSS bug-fix set 1-21 released Message-ID: <35557.82.26.12.214.1315299018.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 include those recently fixed (12-21), listed below, and all those fixed by previous patches (1-11). 1) UNIX As usual, the most convenient way of applying the bug-fixes is to apply the patch file: ftp://emboss.open-bio.org/pub/EMBOSS/fixes/patches/patch-1-21.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 new and previous bug-fixes. Uninstall your previous mEMBOSS installation and download and install the new setup file from: ftp://emboss.open-bio.org/pub/EMBOSS/windows/mEMBOSS-6.4.0.3-setup.exe Alan ----------------------------------------------------------------------- Fix 12. EMBOSS-6.4.0/nucleus/embgroup.c 18-Aug-2011: An internal string variable should be initialised as NULL. Fix 13. EMBOSS-6.4.0/ajax/core/ajseqread.c 18-Aug-2011: Reading protein GFF3 files ignored the EMBOSS type comment. This appears to be the only way to detect a protein GFF3 file. Fix 14. EMBOSS-6.4.0/emboss/data/Efeatures.gff3protein 18-Aug-2011: In writing GFF3 protein file, uses the current term name from the Sequence Ontology to clear errors from the GFF3 online validator. Fix 15. EMBOSS-6.4.0/ajax/core/ajfeatwrite.c 18-Aug-2011: When writing GFF3 format, tags names are explicitly converted to lower case as required by the GFF3 standard. This includes EC_number and /PCR_conditions in EMBL/GenBank/DDBJ and several RefseqP tags. The score is written using g format to represent very low values. Fix 16. EMBOSS-6.4.0/ajax/core/ajnexus.c EMBOSS-6.4.0/ajax/core/ajseqread.c 22-Aug-2011: When reading nexus data format with no taxlabels block the attempt to read the taxa (sequence names) from the matrix block failed. Fix 17. EMBOSS-6.4.0/ajax/ajaxdb/ajtextdb.c 22-Aug-2011: The SRS access method added a stray '+' character to the getz command line. Fix 18. EMBOSS-6.4.0/ajax/core/ajquery.c 25-Aug-2011: In some cases a query using a simple identifier could try to test an undefined "sv" field. Fix 19. EMBOSS-6.4.0/ajax/core/ajseqread.c 02-Sep-2011: Reading "raw" sequence format failed when piped from standard input. In release 6.4.0 "raw" format was redefined as a binary format to catch binary files that start with one or more sequence characters followed by a NULL character. This fix continues to check binary files, but has to drop the check for data piped through standard input which is read as text and cannot be reread as binary. Fix 20. EMBOSS-6.4.0/ajax/core/ajnam.c 02-Sep-2011: Complex database definitions with more than one type or format are allowed in 6.4.0 but caused an error message from showdb when the type and format were tested. Fix 21. EMBOSS-6.4.0/emboss/drfinddata.c EMBOSS-6.4.0/emboss/drfindformat.c EMBOSS-6.4.0/emboss/drfindid.c EMBOSS-6.4.0/emboss/drfindresource.c 02-Sep-2011: Running with -debug fails. Debug calls used obsolete datatype for data resource internals. Without -debug there was no problem. From ajb at ebi.ac.uk Tue Sep 6 08:50:18 2011 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Tue, 6 Sep 2011 09:50:18 +0100 (BST) Subject: [emboss-announce] EMBOSS and mEMBOSS bug-fix set 1-21 released Message-ID: <35557.82.26.12.214.1315299018.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 include those recently fixed (12-21), listed below, and all those fixed by previous patches (1-11). 1) UNIX As usual, the most convenient way of applying the bug-fixes is to apply the patch file: ftp://emboss.open-bio.org/pub/EMBOSS/fixes/patches/patch-1-21.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 new and previous bug-fixes. Uninstall your previous mEMBOSS installation and download and install the new setup file from: ftp://emboss.open-bio.org/pub/EMBOSS/windows/mEMBOSS-6.4.0.3-setup.exe Alan ----------------------------------------------------------------------- Fix 12. EMBOSS-6.4.0/nucleus/embgroup.c 18-Aug-2011: An internal string variable should be initialised as NULL. Fix 13. EMBOSS-6.4.0/ajax/core/ajseqread.c 18-Aug-2011: Reading protein GFF3 files ignored the EMBOSS type comment. This appears to be the only way to detect a protein GFF3 file. Fix 14. EMBOSS-6.4.0/emboss/data/Efeatures.gff3protein 18-Aug-2011: In writing GFF3 protein file, uses the current term name from the Sequence Ontology to clear errors from the GFF3 online validator. Fix 15. EMBOSS-6.4.0/ajax/core/ajfeatwrite.c 18-Aug-2011: When writing GFF3 format, tags names are explicitly converted to lower case as required by the GFF3 standard. This includes EC_number and /PCR_conditions in EMBL/GenBank/DDBJ and several RefseqP tags. The score is written using g format to represent very low values. Fix 16. EMBOSS-6.4.0/ajax/core/ajnexus.c EMBOSS-6.4.0/ajax/core/ajseqread.c 22-Aug-2011: When reading nexus data format with no taxlabels block the attempt to read the taxa (sequence names) from the matrix block failed. Fix 17. EMBOSS-6.4.0/ajax/ajaxdb/ajtextdb.c 22-Aug-2011: The SRS access method added a stray '+' character to the getz command line. Fix 18. EMBOSS-6.4.0/ajax/core/ajquery.c 25-Aug-2011: In some cases a query using a simple identifier could try to test an undefined "sv" field. Fix 19. EMBOSS-6.4.0/ajax/core/ajseqread.c 02-Sep-2011: Reading "raw" sequence format failed when piped from standard input. In release 6.4.0 "raw" format was redefined as a binary format to catch binary files that start with one or more sequence characters followed by a NULL character. This fix continues to check binary files, but has to drop the check for data piped through standard input which is read as text and cannot be reread as binary. Fix 20. EMBOSS-6.4.0/ajax/core/ajnam.c 02-Sep-2011: Complex database definitions with more than one type or format are allowed in 6.4.0 but caused an error message from showdb when the type and format were tested. Fix 21. EMBOSS-6.4.0/emboss/drfinddata.c EMBOSS-6.4.0/emboss/drfindformat.c EMBOSS-6.4.0/emboss/drfindid.c EMBOSS-6.4.0/emboss/drfindresource.c 02-Sep-2011: Running with -debug fails. Debug calls used obsolete datatype for data resource internals. Without -debug there was no problem.