From ajb at ebi.ac.uk Wed Oct 5 11:05:00 2011 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Wed, 5 Oct 2011 16:05:00 +0100 (BST) Subject: [emboss-announce] EMBOSS patch set 1-24 available. New mEMBOSS available. Message-ID: <39214.82.26.12.214.1317827100.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 (22-24), listed below, and all those fixed by previous patches (1-21). 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-1-24.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-6.4.0.4-setup.exe Alan ----------------------------------------------------------------------- Fix 22. EMBOSS-6.4.0/emboss/diffseq.c EMBOSS-6.4.0/ajax/core/ajreport.c 14-Sep-2011: Diffseq reports insertions in the second sequence with a length 2 reversed region in the first sequence instead of a length 0 empty sequence. This bug was introduced in release 6.0.0 when reversed sequence features were updated. Fix 23. EMBOSS-6.4.0/ajax/core/ajindex.c 04-Oct-2011: Dbx index files from earlier releases do not include a type parameter to indicate an Identifier or Secondary index. The code to test index field names failed to define id and acc fields as Identifiers. This fix allows old indexes to work with EMBOSS 6.4.0. Fix 24. EMBOSS-6.4.0/ajax/core/ajfileio.c 05-Oct-2011: Trimming carriage controls from the ends of lines in a buffer failed when MacOSX-style characters are used and the line buffer is a reference counted string. An example on non-MacOSX systems was processing the data returned by the NCBI Entrez server. From ajb at ebi.ac.uk Wed Oct 5 15:05:00 2011 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Wed, 5 Oct 2011 16:05:00 +0100 (BST) Subject: [emboss-announce] EMBOSS patch set 1-24 available. New mEMBOSS available. Message-ID: <39214.82.26.12.214.1317827100.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 (22-24), listed below, and all those fixed by previous patches (1-21). 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-1-24.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-6.4.0.4-setup.exe Alan ----------------------------------------------------------------------- Fix 22. EMBOSS-6.4.0/emboss/diffseq.c EMBOSS-6.4.0/ajax/core/ajreport.c 14-Sep-2011: Diffseq reports insertions in the second sequence with a length 2 reversed region in the first sequence instead of a length 0 empty sequence. This bug was introduced in release 6.0.0 when reversed sequence features were updated. Fix 23. EMBOSS-6.4.0/ajax/core/ajindex.c 04-Oct-2011: Dbx index files from earlier releases do not include a type parameter to indicate an Identifier or Secondary index. The code to test index field names failed to define id and acc fields as Identifiers. This fix allows old indexes to work with EMBOSS 6.4.0. Fix 24. EMBOSS-6.4.0/ajax/core/ajfileio.c 05-Oct-2011: Trimming carriage controls from the ends of lines in a buffer failed when MacOSX-style characters are used and the line buffer is a reference counted string. An example on non-MacOSX systems was processing the data returned by the NCBI Entrez server.