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Bioconductor Changlog.
Tue, 13 Oct 2009
affyio
(1.7.8) Minor changes to the pgf/clf parsing code. In particular functionality for assessing whether the required fields in the headers are present.
affyio
(1.9.1) Fix parsing problem for calvin command console format CEL files on big endian machines.
affyio
(1.7.4) Fix issue related to parsing CDF file probeset units which do not have MM probes when using the binary xda format. This refers to an issue described/illustrated in this mailing list message: https://stat.ethz.ch/pipermail/bioc-devel/2007-October/001403.html
fix for decode_UINT8_t which was incorrectly returning an uint16. This should not have any effect for users using AGCC/Generic Binary Format CEL files, but improves the general robustness of the core parsing code.
affyio
(1.7.6) Add C code level pgf file parser. Note that no method of accessing the data stored in a PGF file at the R level has been provided (and may not ever be provided).
affyio
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
affyio
(1.7.17) Minor fixes for CLF/PGF parsers
affyio
(1.7.9) add functions to CLF parsing code for converting from/to probe_id and (x,y) pairs
affyio
(1.9.1) Fix parsing problem for calvin command console format CEL files on big endian machines.
affyio
(1.7.13) read.celfile() now includes a additional argument allowing the user to specify reading only the intensity values from the specified CEL file (ie exclude STDEV and NPIXEL)
affyio
(1.7.12) Fixes for C level command console format CEL file parsing. In particular the functions generic_get_detailed_header_info() and gzgeneric_get_detailed_header_info() had problems in some situations where various algorithm parameters were not stored as character strings.
affyio
(1.7.16) Fix bpmap problems on big endian machines (eg ppc, sparc). This is the same problem that affected and was fixed for little endian machines a number of months ago. To the user it manifested itself with the error message "Error: SET_VECTOR_ELT() can only be applied to a 'list', not a 'NULL'", but in fact caused by incorrect parsing of the bpmap file version number.
affyio
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
affyio
(1.7.16) Fix bpmap problems on big endian machines (eg ppc, sparc). This is the same problem that affected and was fixed for little endian machines a number of months ago. To the user it manifested itself with the error message "Error: SET_VECTOR_ELT() can only be applied to a 'list', not a 'NULL'", but in fact caused by incorrect parsing of the bpmap file version number.
affyio
(1.11.1) Fix issue with stack exhaustion in pthreads builds with read.probematrix()
affyio
fix for decode_UINT8_t which was incorrectly returning an uint16. This should not have any effect for users using AGCC/Generic Binary Format CEL files, but improves the general robustness of the core parsing code.
affyio
(1.11.1) Fix issue with stack exhaustion in pthreads builds with read.probematrix()
affyio
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
affyio
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
affyio
(1.7.9) add functions to CLF parsing code for converting from/to probe_id and (x,y) pairs
affyio
(1.7.5) Experimental pthreads based multi-threaded read_probematrix based on code contributed by Paul Gordon (U Calgary). A configure script detects if pthreads is installed on the system. If it is not the standard code is used. The environment variable R_THREADS is used to vary the number of threads. At the user level access to this function is via read.probematrix() in the affy package.
affyio
(1.7.13) read.celfile() now includes a additional argument allowing the user to specify reading only the intensity values from the specified CEL file (ie exclude STDEV and NPIXEL)
affyio
Prints more relevant error message when read.celfile.header() fails to read
the full header information.
Since r40196, affy::read.affybatch() tries to get the full header information
in order to extract the ScanDate info. This change to read.celfile.header()
will make it easier to understand why read.affybatch() fails on some CEL
files that don't have it (like extdata/118T1.cel in the matchprobes package).
Bumpmed version to 1.13.4
affyio
fix stack memory exhaustion problem in multi-threaded situations.
affyio
(1.11.2) Fix issue with binary CDF file parsing
affyio
(1.7.7) Add C code level clf file parser. Note that no method of accessing the data stored in a CLF file at the R level has been provided (and may not ever be provided).
affyio
(1.11.2) Fix issue with binary CDF file parsing
affyio
(1.7.10) Minor changes to generic format C parsing code. Several minor corrections of missing logical NOT (!) symbols and change several bitwise or (|) to (||). Should have no effect on user except in situations with truncated files.
affyio
(1.13.3) small fix to read.celfile.header() to deal with ScanDate
(1.13.2) Fix issues with CEL corruption not detected in read.probematrix
affyio
(1.13.1) read.celfile.header(FILENAME,"full") returns an additional field "ScanDate"
affyio
(1.7.11) When stdint.h is not found try to use inttypes.h (should help portability to Sun Solaris 9)
affyio
Standardizing affyio R files during code review to understand new date information.
affyio
removed \itemize from Rd files sections containing \value
affyio
(1.7.17) Minor fixes for CLF/PGF parsers
affyio
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
affyio
(1.7.14) Better checking of potential CEL file corruption. Specifically some vales are now checked to see if they are sensible (ie intensity values should not be negative and x,y locations should not be negative or outside the chip dimensions)
affyio
Put back the -lz reference for referencing zlib for non-Windows (as opposed to -lRzlib) builds.
Updated reference to the zlib library to reflect recent changes in R-devel. In particular, -lz has become -lRzlib.
affyio
(1.11.3) Fix a few minor VECTOR_ELT/STRING_ELT usages