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Bioconductor Changlog.
Tue, 16 Jun 2009
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Bug fix for PWAmat()
This just makes the PWAmat() a little smarter so that it will not
explode when it runs into an NA.
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Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
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deprecated and defuncted some old functions.
These functions don't appear to be used anywhere else (I checked).
Also, they are long overdue for this.
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Fixed uncommented underscores in htmlpage documentation.
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Modifications to allow end users to add arbitrary repositories for use with the htmlpage() function.
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Revised import of AnnotationDbi to include only a subset of the package.
Replaced tab with spaces.
Bumped the version number.
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Updated NAMESPACE and DESCRIPTION.
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updating a bit, removing empty parts in man pages, moving xtable to be
an import, not a depends
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Version bump.
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Added allValidKeys function.
The allValidKeys function returns all the valid primary IDs for an
annoation package.
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Long overdue update to the useDataPkgs vignette.
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Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
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Minor adjustments.
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Replaces a couple of lost Entrez Gene www functions.
This just replaces a couple of functions that had been removed due to
many changes in the annotation packages (locusLinkByID() and
locusLinkQuery()) with new functions entrezGeneByID() and
entrezGeneQuery() which are as true to the original spirit of these
functions as I could make them (they each make URLs that will take you
to the relevant data at NCBI).
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Removed usage (or reference) to pstricks tex style in BioC vignettes.
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some extras
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some extras
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minor addition to list
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some stuff for pubmed-based literature page generation
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Updates the useHomology vignette.
This replaces the useHomology vignette with a small vignette that
describes how to use the newer inparanoid homology packages.
Backed hsahomology and xlahomology out of Depends field in DESCRIPTION file.
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Partial update to the useHomology Vignette.
This partially updates this vignette so that it contains more current
information. This vignette is still not ready for prime time though,
so it is temporarily remaining a .bak file.
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Changed useHomology vignette so it won't interfere with build. Will replace with a new version soon.
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Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
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wrapped the p2LL example in dontrun as the function is now deprecated
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Updating a slightly outdated chromLocation object.
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Minor change in vignette text to reflect changes that were made to example code introduced in Revisions 16330, 23990, and 27757.
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Swapped usage of old style deprecated annotation paradigm with new AnnotationDbi paradigm.
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more bug fixing and version number bump
dropped some functions that have not worked for more than a year (no
deprecation/defunct cycle needed since they cannot have been used)
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Small changes to the htmlpage() help page to hopefully make things less opaque.
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Changes to htmlpage(). The repository argument must now be a list. Deprecated the 'LL' functions in lieu of the 'EN' functions, intended for querying Entrez Gene. Also ceased exporting internal function used by htmlpage such as getCells(), the getQuery4XX functions, etc.
minor bug fixes for htmlpage, also seem to be issues with the way
that character data are being stuck into data.frames - they come out AsIs
and that breaks lots of things
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Swapped usage of old style deprecated annotation paradigm with new AnnotationDbi paradigm.
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dropped one more place the hgu95av2 was being called
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Version bump for the fix in previous checkin.
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Modifications to make PWAmat() work with new pkgs
Changes were to PWAmat() and enable it to get an incidence matrix for
the newer organism based annotations as well as the older chip based
packages. Changes primarily are to allow PWAmat() to know when it has
an organism based package or chip based package so it can return the
correct result.
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Added a function getQuery4TR() that allows people to create links to the TAIR website using TAIR accession numbers.
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Changed default repository in htmlpage() from 'll' to
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Fix to htmlpage(). The repository is supposed to be a list, and this is what is claimed in the help page, but the default was a character vector. The default is now list(ll).