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Bioconductor Changlog.
Fri, 18 Apr 2008
AnnotationDbi
Fixed slowdown bugs
These bugs only impacts the speed at which SQLForge does it's job.
The results will be the same. But if you are building ~ 700 packages,
you might appreciate this change.
Bug fix for increased AnnBuilder file format compatibility
This fix makes things more compatible for people who are using classic
AnnBuilder style files.
[/AnnotationDbi] permanent link
flowViz
making sure the truncated sample names are still unique
rsbml
Remove stray debugging command (which somehow broke linking too).
GSEABase
API and other changes necessary to pass R CMD check without error
- GeneSet construction from GOCollection requires a geneIdType arugment
- GOCollection provided with optional arugment err=FALSE controlling
consequences of missing identifiers
flowCore
more on the outline
more cleaning up of name space
Biostrings
Added "isEmpty", "max" and "min" methods for IRanges/NormalIRanges objects. Disabled subsetting and narrowing of NormalIRanges objects (these operations do NOT preserve normality in general). Small improvement to the "gaps" semantic and implementation.
Performance optimization of the pairwiseAlignment function.
Added more information into the XStringAlign class to provide users with better information on the alignment.
Renamed the C file containing pairwise alignment code to get it to conform to package conventions and minor cleanup edits.
Added the ability to handle affine gaps in pairwiseAlignment.
Ringo
fixed an inconsistency in function 'findChersOnSmoothed' that can occur with certain values supplied for its argument 'cellType'
ArrayExpress
Delete the files copied from the website when an error occurs and kills
the program.
[/ArrayExpress] permanent link
GEOquery
Fixed getDirListing to close a temporary textConnection
plw
Fixed problem with bg.correct.rma2
xcms
fixed: peak parameters lmin,lmax were accidentally removed
docu fix
stam
now uses *.db annotation packages
fixed "no visible binding" warning
M R/06_predict.R
M R/01_stam.R
M R/08_util.R
M R/02_node.R
M R/05_fit.R
M R/03_net.R
M R/04_cv.R
M R/07_eval.R
M R/09_server.R
M R/TAGS
M DESCRIPTION
M data/golubTrain.cv.rda
M data/golubTrain.fit.rda
M NAMESPACE
M inst/doc/tr_2004_03.Rnw
M inst/doc/tr_2004_03.pdf
Biobase
added ... to the generic definition for description in order to be able to use it in the flowCore package