Dear Bioconductors, since my R installation was upgraded to 2.14.1 I have a problem with loading and installing GenomicFeatures. here is what I try to do: library(Biostrings) Loading required package: IRanges Loading required package: BiocGenerics Attaching package: ?BiocGenerics? The following object(s) are masked from ?package:stats?: xtabs The following object(s) are masked from ?package:base?: anyDuplicated, cbind, colnames, duplicated, eval, Filter, Find, intersect, lapply, Map, mapply, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rbind, Reduce, rep.int, rownames, sapply, setdiff, table, tapply, union, unique > library(GenomicRanges) > library(GenomicFeatures) Error : classes "file", "connection" are not exported by 'namespace:Biostrings' In addition: Warning message: multiple methods tables found for ?getSeq? Error: package/namespace load failed for ?GenomicFeatures? > sessionInfo() R version 2.14.1 (2011-12-22) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] GenomicRanges_1.6.7 Biostrings_2.22.0 IRanges_1.13.26 [4] BiocGenerics_0.1.7 loaded via a namespace (and not attached): [1] biomaRt_2.8.1 BSgenome_1.20.0 DBI_0.2-5 RCurl_1.91-1 [5] RSQLite_0.11.1 XML_3.9-4 I think the relevant packages are up to date. Installing GenomicFeatures using BiocLight did not help: > source('http://bioconductor.org/biocLite.R') BiocInstaller version 1.2.1, ?biocLite for help Attaching package: ?BiocInstaller? The following object(s) are masked _by_ ?.GlobalEnv?: biocinstallRepos > install.packages("GenomicFeatures", lib="/home/gwo/rlib") --- Please select a CRAN mirror for use in this session --- Loading Tcl/Tk interface ... done Warning message: In getDependencies(pkgs, dependencies, available, lib) : package ?GenomicFeatures? is not available (for R version 2.14.1) So i tried installation by hand: $ R CMD INSTALL -l ~/rlib GenomicFeatures_1.6.8.tar.gz * installing *source* package ?GenomicFeatures? ... ** R ** inst ** preparing package for lazy loading Warning: multiple methods tables found for ?getSeq? Error : classes "file", "connection" are not exported by 'namespace:Biostrings' ERROR: lazy loading failed for package ?GenomicFeatures? Has anyone an idea what is going on? Best wishes, Georg

On 03/08/2012 08:42 AM, Georg Otto wrote: > Dear Bioconductors, > > since my R installation was upgraded to 2.14.1 I have a problem with > loading and installing GenomicFeatures. here is what I try to do: > > > library(Biostrings) > Loading required package: IRanges > Loading required package: BiocGenerics > > Attaching package: ?BiocGenerics? > > The following object(s) are masked from ?package:stats?: > > xtabs > > The following object(s) are masked from ?package:base?: > > anyDuplicated, cbind, colnames, duplicated, eval, Filter, Find, > intersect, lapply, Map, mapply, order, paste, pmax, pmax.int, pmin, > pmin.int, Position, rbind, Reduce, rep.int, rownames, sapply, > setdiff, table, tapply, union, unique > >> library(GenomicRanges) >> library(GenomicFeatures) > Error : classes "file", "connection" are not exported by 'namespace:Biostrings' > In addition: Warning message: > multiple methods tables found for ?getSeq? > Error: package/namespace load failed for ?GenomicFeatures? >> sessionInfo() > R version 2.14.1 (2011-12-22) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 > [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] GenomicRanges_1.6.7 Biostrings_2.22.0 IRanges_1.13.26 > [4] BiocGenerics_0.1.7 > > loaded via a namespace (and not attached): > [1] biomaRt_2.8.1 BSgenome_1.20.0 DBI_0.2-5 RCurl_1.91-1 > [5] RSQLite_0.11.1 XML_3.9-4 > > > > I think the relevant packages are up to date. Installing GenomicFeatures > using BiocLight did not help: > > >> source('http://bioconductor.org/biocLite.R') > BiocInstaller version 1.2.1, ?biocLite for help > > Attaching package: ?BiocInstaller? > > The following object(s) are masked _by_ ?.GlobalEnv?: > > biocinstallRepos > >> install.packages("GenomicFeatures", lib="/home/gwo/rlib") > --- Please select a CRAN mirror for use in this session --- > Loading Tcl/Tk interface ... done > Warning message: > In getDependencies(pkgs, dependencies, available, lib) : > package ?GenomicFeatures? is not available (for R version 2.14.1) Maybe you haven't chosen an appropriate Bioconductor repository... > > > So i tried installation by hand: > > > $ R CMD INSTALL -l ~/rlib GenomicFeatures_1.6.8.tar.gz > * installing *source* package ?GenomicFeatures? ... > ** R > ** inst > ** preparing package for lazy loading > Warning: multiple methods tables found for ?getSeq? > Error : classes "file", "connection" are not exported by 'namespace:Biostrings' > ERROR: lazy loading failed for package ?GenomicFeatures? > > > Has anyone an idea what is going on? It's likely a package version issue, and source('http://bioconductor.org/biocLite.R') biocLite(character()) will likely point to the out-of-date packages with an option to update... Martin > > Best wishes, > > Georg > > _______________________________________________ > 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 -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793

Martin Morgan <mtmorgan at="" fhcrc.org=""> writes: > On 03/08/2012 08:42 AM, Georg Otto wrote: >>> install.packages("GenomicFeatures", lib="/home/gwo/rlib") >> --- Please select a CRAN mirror for use in this session --- >> Loading Tcl/Tk interface ... done >> Warning message: >> In getDependencies(pkgs, dependencies, available, lib) : >> package ?GenomicFeatures? is not available (for R version 2.14.1) > > Maybe you haven't chosen an appropriate Bioconductor repository... > i tried several, but to no avail >> >> >> So i tried installation by hand: >> >> >> $ R CMD INSTALL -l ~/rlib GenomicFeatures_1.6.8.tar.gz >> * installing *source* package ?GenomicFeatures? ... >> ** R >> ** inst >> ** preparing package for lazy loading >> Warning: multiple methods tables found for ?getSeq? >> Error : classes "file", "connection" are not exported by 'namespace:Biostrings' >> ERROR: lazy loading failed for package ?GenomicFeatures? >> >> >> Has anyone an idea what is going on? > > It's likely a package version issue, and > > source('http://bioconductor.org/biocLite.R') > biocLite(character()) > > will likely point to the out-of-date packages with an option to update... in fact, it did update quite a lot of packages, but the instalation of GenomicFeatures failed: > biocLite(character()) BioC_mirror: 'http://www.bioconductor.org' Using R version 2.14, BiocInstaller version 1.2.1. Old packages: 'GenomicFeatures', 'leeBamViews', 'rtracklayer' Update all/some/none? [a/s/n]: a . . . . * installing *source* package ?GenomicFeatures? ... ** R ** inst ** preparing package for lazy loading Error : classes "file", "connection" are not exported by 'namespace:Biostrings' ERROR: lazy loading failed for package ?GenomicFeatures? Georg

Martin Morgan <mtmorgan at="" fhcrc.org=""> writes: > On 03/08/2012 10:01 AM, Georg Otto wrote: >> Martin Morgan<mtmorgan at="" fhcrc.org=""> writes: >> >>> On 03/08/2012 08:42 AM, Georg Otto wrote: >> Error : classes "file", "connection" are not exported by 'namespace:Biostrings' >> ERROR: lazy loading failed for package ?GenomicFeatures? > > I'm guess, but believe it continues to be a stale package version -- > IRanges, Biostrings, GenomicRanges. From your earlier message > >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] GenomicRanges_1.6.7 Biostrings_2.22.0 IRanges_1.13.26 >> [4] BiocGenerics_0.1.7 >> >> loaded via a namespace (and not attached): >> [1] biomaRt_2.8.1 BSgenome_1.20.0 DBI_0.2-5 RCurl_1.91-1 >> [5] RSQLite_0.11.1 XML_3.9-4 > > Bioconductor packages should have even version numbers when in > release, so your IRanges (and BiocGenerics) seems to be funky (the > version for R-2-14 is 1.12.6) so I'd try biocLite("IRanges"). Martin I updated IRanges and BiocGenerics, but that did not help either. Finally, I completely removed my Bioconductor installation and reinstalled everything. Now it works again and I was able to install GenomicFeatures. Thanks a lot for your help. Georg