Question: biocLite() does not accept 'lib.loc' for updating
0
gravatar for Martin Maechler
7.6 years ago by
Switzerland
Martin Maechler330 wrote:
For updating bioconductor, we recommend biocLite(character(), ask=FALSE) However, when I (have several versions of R and bioconductor and) keep my bioconductor packages in a specific library not first in my .libPaths(), I want to specify ' lib.loc = <my-bioc-library> ' but that works {via "..."} only for else { ... } clause in biocLite(), not for the first one : > biocLite function (pkgs = c("Biobase", "IRanges", "AnnotationDbi"), suppressUpdates = FALSE, suppressAutoUpdate = FALSE, ask = TRUE, ...) { svnRev <- as.integer(R.Version()$`svn rev`) if (svnRev < 55733) .stop("R-2.14 r55733 or newer required.") if (!suppressAutoUpdate && !bioconductorPackageIsCurrent()) { on.exit(updateBioconductorPackage(pkgs, ask = ask, suppressUpdates = suppressUpdates, ...)) } else { biocLiteInstall(pkgs, ask = ask, suppressUpdates = suppressUpdates, ...) } } <environment: namespace:biocinstaller=""> > maintainer("BiocInstaller") [1] "Biocore Team c/o BioC user list\n<bioconductor at="" stat.math.ethz.ch="">" > -------- Thank you for fixing/workaround/.. Martin
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ADD COMMENTlink modified 7.6 years ago by Dan Tenenbaum8.2k • written 7.6 years ago by Martin Maechler330
Answer: biocLite() does not accept 'lib.loc' for updating
0
gravatar for Dan Tenenbaum
7.6 years ago by
Dan Tenenbaum8.2k
United States
Dan Tenenbaum8.2k wrote:
Hi Martin, On Mon, Mar 19, 2012 at 2:27 AM, Martin Maechler <maechler at="" stat.math.ethz.ch=""> wrote: > For updating bioconductor, > > we recommend > > ? biocLite(character(), ask=FALSE) > > However, when I (have several versions of R and bioconductor and) > keep my bioconductor packages in a specific library not first in > my .libPaths(), > I want to specify ? ' lib.loc = <my-bioc-library> ' > > but that works {via "..."} only for else { ... } clause in > biocLite(), > not for the first one : > >> biocLite > function (pkgs = c("Biobase", "IRanges", "AnnotationDbi"), suppressUpdates = FALSE, > ? ?suppressAutoUpdate = FALSE, ask = TRUE, ...) > { > ? ?svnRev <- as.integer(R.Version()$`svn rev`) > ? ?if (svnRev < 55733) > ? ? ? ?.stop("R-2.14 r55733 or newer required.") > ? ?if (!suppressAutoUpdate && !bioconductorPackageIsCurrent()) { > ? ? ? ?on.exit(updateBioconductorPackage(pkgs, ask = ask, suppressUpdates = suppressUpdates, > ? ? ? ? ? ?...)) > ? ?} > ? ?else { > ? ? ? ?biocLiteInstall(pkgs, ask = ask, suppressUpdates = suppressUpdates, > ? ? ? ? ? ?...) > ? ?} > } > <environment: namespace:biocinstaller=""> > >> maintainer("BiocInstaller") > [1] "Biocore Team c/o BioC user list\n<bioconductor at="" stat.math.ethz.ch="">" >> > > -------- > > Thank you for fixing/workaround/.. This is fixed in BiocInstaller 1.3.8, which will be available tomorrow. Dan > > Martin > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD COMMENTlink written 7.6 years ago by Dan Tenenbaum8.2k
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