[Bioc-devel] Matching "." in regular expressions

[Seth Falcon]

Hi all,

R-2.5 has the following entry in NEWS:

    o   There is a (currently experimental) warning if \ is used
        unnecessarily in a string when being parsed, e.g. "\." where
        probably "\\." was intended.  ("\." is valid, but the same as
        ".".)  Thanks to Bill Dunlap for the suggestion.

I did a search of the BioC packages and found many instances of "\."
in a pattern where almost certainly "\\." was intended.  I went ahead
and committed a patch to address this.  If your package is listed in
the commit message below, please have a look and make sure the change
is reasonable.

Best,

+ seth


r20628 | sethf | 2006-10-17 10:47:13 -0700 (Tue, 17 Oct 2006) | 8 lines
Changed paths:
   M /trunk/madman/Rpacks/AnnBuilder/DESCRIPTION
   M /trunk/madman/Rpacks/AnnBuilder/R/athPkgBuilder.R
   M /trunk/madman/Rpacks/AnnBuilder/inst/scripts/dataPkgLoad.R
   M /trunk/madman/Rpacks/BeadExplorer/DESCRIPTION
   M /trunk/madman/Rpacks/BeadExplorer/R/readBead.R
   M /trunk/madman/Rpacks/Biobase/DESCRIPTION
   M /trunk/madman/Rpacks/Biobase/inst/UnitTests/UpdateObject_test.R
   M /trunk/madman/Rpacks/Biobase/inst/UnitTests/runalltests.R
   M /trunk/madman/Rpacks/Biostrings/Biostrings1/R/test.R
   M /trunk/madman/Rpacks/Category/DESCRIPTION
   M /trunk/madman/Rpacks/Category/inst/UnitTests/runalltests.R
   M /trunk/madman/Rpacks/Category/inst/scripts/CLLex.R
   M /trunk/madman/Rpacks/GOstats/DESCRIPTION
   M /trunk/madman/Rpacks/GOstats/inst/UnitTests/runalltests.R
   M /trunk/madman/Rpacks/Rgdbm/DESCRIPTION
   M /trunk/madman/Rpacks/Rgdbm/R/serializers.R
   M /trunk/madman/Rpacks/affy/DESCRIPTION
   M /trunk/madman/Rpacks/affy/R/read.affybatch.R
   M /trunk/madman/Rpacks/affy/R/zzz.R
   M /trunk/madman/Rpacks/affyPLM/DESCRIPTION
   M /trunk/madman/Rpacks/affyPLM/R/init_fns.R
   M /trunk/madman/Rpacks/affyr/R/registerProcessMethods.R
   M /trunk/madman/Rpacks/affyr/R/zzz.R
   M /trunk/madman/Rpacks/annotate/DESCRIPTION
   M /trunk/madman/Rpacks/annotate/R/chromLocation.R
   M /trunk/madman/Rpacks/beadarray/R/readBeadSummaryData.R
   M /trunk/madman/Rpacks/beadarraySNP/DESCRIPTION
   M /trunk/madman/Rpacks/beadarraySNP/R/methods-SnpSetIllumina.R
   M /trunk/madman/Rpacks/biocViews/DESCRIPTION
   M /trunk/madman/Rpacks/biocViews/R/packageDetails.R
   M /trunk/madman/Rpacks/biocViews/R/repository.R
   M /trunk/madman/Rpacks/buildBioC/DESCRIPTION
   M /trunk/madman/Rpacks/buildBioC/R/updateRepos.R
   M /trunk/madman/Rpacks/buildBioC/R/webPage.R
   M /trunk/madman/Rpacks/ecolitk/DESCRIPTION
   M /trunk/madman/Rpacks/ecolitk/R/internalFuncs.R
   M /trunk/madman/Rpacks/graph/DESCRIPTION
   M /trunk/madman/Rpacks/graph/inst/unitTests/runalltests.R
   M /trunk/madman/Rpacks/graphPart/DESCRIPTION
   M /trunk/madman/Rpacks/graphPart/inst/unitTests/runalltests.R
   M /trunk/madman/Rpacks/hypergraph/DESCRIPTION
   M /trunk/madman/Rpacks/hypergraph/inst/unitTests/runalltests.R
   M /trunk/madman/Rpacks/makePMG/DESCRIPTION
   M /trunk/madman/Rpacks/makePMG/inst/scripts/dataPkgLoad.R
   M /trunk/madman/Rpacks/makecdfenv/DESCRIPTION
   M /trunk/madman/Rpacks/makecdfenv/R/make.cdf.env.R
   M /trunk/madman/Rpacks/oligo/DESCRIPTION
   M /trunk/madman/Rpacks/oligo/R/read.celfiles.R
   M /trunk/madman/Rpacks/oligo/R/readxys.R
   M /trunk/madman/Rpacks/oligochips/R/zzz.R
   M /trunk/madman/Rpacks/rdxml/DESCRIPTION
   M /trunk/madman/Rpacks/rdxml/R/render.R
   M /trunk/madman/Rpacks/sagenhaft/DESCRIPTION
   M /trunk/madman/Rpacks/sagenhaft/R/sagenhaft.R

Fix invalid regular expressions: "\." => "\\."

R-2.5 gives a warning when it encounters unknown escapes.  To
match "." in a regex and not have a warning, use "\\." in the
pattern.

Maintainers: please review for correct behavior.