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Bioconductor Changlog.
Tue, 13 Oct 2009
EBImage
fixed R CMD check memory leak (caused by a ReadImage() call after a drawtext() one); this was due to the MagickWandTerminus() destructor which also destroy MagickCore services (! see on ImageMagick wand/magick-wand.c for details)
metahdep
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
Rintact
updated the list2matrix function and man page
chipseq
Deprecate most of the context functions (moved to
GenomicFeatures). The context distribution stuff is ported, but untested.
bgx
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
yaqcaffy
yaqc.summary manual update
added summary(YAQCStatsObject) function
AnnotationDbi
adding to the TODO list
[/AnnotationDbi] permanent link
AnnotationDbi
Adds parameter for the inpIDMapper function.
This just adds another parameter so that you can choose to have the
final results limited to only one answer per initial ID even if you
map to something like a uniprot which may have many IDs for each
entrez gene ID. Default will still give you all of whatever you asked
for.
Added convenience function inpIDMapper
This function allows for easy mapping (using the appropriate
inparanoid packages) for IDs between species.
[/AnnotationDbi] permanent link
SemSim
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
chipseq
some cleanup
changed interpretation of nsteps
LMGene
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
chipseq
Another simulateReads rev.
Further speedup to simulateReads.
Further improvements to simulateReads function.
Improved performance of simulateReads.
Changed simulateReads function to use ShortReadQ class output
AnnotationDbi
This consolidates the INPARANOID_DB schemas into one.
By consolodating the INPARANOID schemas into one INPARANOID_DB schema,
I can now add more inparanoid packages without bloating up
AnnotationDbi any more than is strictly necessary...
[/AnnotationDbi] permanent link
chipseq
added alpha.hat to list of things computed
pdInfoBuilder
Prep'ing to add 2nd version of db-based annotation
[/pdInfoBuilder] permanent link
AnnotationDbi
end of testing.
testing
[/AnnotationDbi] permanent link
SPIA
small bug fix and vignette update
chipseq
Adjusted the number of bins in the density calculations.
AnnotationDbi
Fixes a small bug in SQLForge and expands inpIDMapper.
This fixes a small bug where SQLForge fails when organsisms don't have
unigene IDs, and also expands the number of species that inpIDMapper
should work for.
[/AnnotationDbi] permanent link
pdInfoBuilder
Fixed merging of POS and NDF files
[/pdInfoBuilder] permanent link
chipseq
one more mod
typo
one more set of tweaks
last piece
more updates to get the simulation code working
SPIA
updated pathway data by including interactions between genes and KEGG groups that contain at least one gene
AnnotationDbi
This adds support for worm, pig and chicken.
Adds code for planned support (October release) of these additional
organisms. These organisms are not supported at this moment.
[/AnnotationDbi] permanent link
RLMM
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
EBImage
New EBImage.dll compiled with R2.7.0, GTK 2.12.9 and ImageMagick 6.4.1
AnnotationDbi
Adds convenience function for listing .db0 packages.
[/AnnotationDbi] permanent link
AnnotationDbi
Major overhaul for chip packages.
This checkin includes changes to allow chip packages to be lightweight
and instead depend on organism packages for their data. It also adds
organism support for rhesus monkeys, chimpanzees, Anopheles mosquito,
Arabidopsis and Xenopus laevis.
[/AnnotationDbi] permanent link
codetoolsBioC
Made error message more informative.
Stopped using ":::" operator since it doesn't support extraction from packages without namespaces.
Used Luke's suggestion to pass a modified collectUsageLeaf function into makeUsageCollector so the findGlobals search enters closures.
Recreate functions from scratch before passing to findGlobals function.
[/codetoolsBioC] permanent link
EBImage
Tried to provide a slightly more instructive warning when GTK+ cannot
be initialised at run-time.
GraphAT
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
maanova
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
CGHbase
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
SPIA
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
Rintact
Fixed Rintact dependencies so package will pass check.
macat
fixes for enabling HTML output with .db data packages
macat
Replaced usage of soon to be defunct class exprSet with ExpressionSet.
BicARE
This add BicARE, arrayMvout and affyContam to bioconductor.
cosmo
Fixed small bug in reverse complement calculation pointed out by Heejung
macat
fix to handle .db annotation packages
pdInfoBuilder
Cleaning up package, exporting only used classes
Added TilingFeatureSet2 class to handle 2-colors applications of tiling arrays. Redefined the FeatureSet class and sampleNames method. Removed unused class.
[/pdInfoBuilder] permanent link