Hi Paul, GenomicFeatures is now fixed (in devel) and the new version should become available thru biocLite() in 7 to 8 hours. Cheers, H. On 03/07/2011 04:21 PM, Paul Leo wrote: > HI Martin > Many Thanks, especially for the instructions and the web sites so I can > check for myself in the future. > Cheers > Paul > > > > > > > -----Original Message----- > From: Martin Morgan<mtmorgan at="" fhcrc.org=""> > To: Paul Leo<p.leo at="" uq.edu.au=""> > Cc: bioconductor<bioconductor at="" r-project.org=""> > Subject: Re: [BioC] GenomicFeatures install error on developement > version > Date: Tue, 8 Mar 2011 09:55:30 +1000 > > > On 03/07/2011 03:16 PM, Paul Leo wrote: >> Failure to install on a fresh development/R version everything appears >> up to date: >> >> ###Check >> >>> source("http://bioconductor.org/biocLite.R") >> BioC_mirror = http://www.bioconductor.org >> Change using chooseBioCmirror(). >>> >> update.packages(lib.loc="/home/pleo/R_latest/library",repos=biocins tallRepos(), ask=FALSE) >>> >> >> #### The Error: "Error : object ???????extractTranscripts???????? is not exported by >> 'namespace:Biostrings'" in below >> >>> biocLite(c("GenomicFeatures")) >> Using R version 2.13.0 (R-devel), biocinstall version 2.8.2. >> Installing Bioconductor version 2.8 packages: >> [1] "GenomicFeatures" >> Please wait... >> >> trying URL >> 'http://www.bioconductor.org/packages/2.8/bioc/src/contrib/GenomicF eatures_1.3.13.tar.gz' >> Content type 'application/x-gzip' length 412765 bytes (403 Kb) >> opened URL >> ================================================== >> downloaded 403 Kb >> >> * installing *source* package ???????GenomicFeatures???????? ... >> ** R >> ** inst >> ** preparing package for lazy loading >> >> Attaching package: 'IRanges' >> >> The following object(s) are masked from 'package:base': >> >> Map, cbind, eval, intersect, mapply, order, paste, pmax, pmax.int, >> pmin, pmin.int, rbind, rep.int, setdiff, table, union >> >> Error : object ???????extractTranscripts???????? is not exported by >> 'namespace:Biostrings' >> ERROR: lazy loading failed for package ???????GenomicFeatures???????? > > There was a change in Biostrings. GenomicFeatures was updated, but from > > http://bioconductor.org/checkResults/devel/bioc-LATEST/ > > GenomicFeatures failed to pass check and so the updated version is not > available via biocLite. You could wait for GenomicFeatures to be fixed > (my guess: network issue with biomaRt, but not sure) or download and > INSTALL (no check) GenomicFeatures from svn > > http://bioconductor.org/developers/source-control/ > > Martin > >> * removing ???????/home/pleo/R_latest/library/GenomicFeatures???????? >> >> The downloaded packages are in >> ???????/tmp/RtmpulmTn5/downloaded_packages???????? >> Updating HTML index of packages in '.Library' >> Making packages.html ... done >> Warning message: >> In install.packages(pkgs = pkgs, repos = repos, ...) : >> installation of package 'GenomicFeatures' had non-zero exit status >>> sessionInfo() >> R version 2.13.0 Under development (unstable) (2011-03-06 r54683) >> Platform: x86_64-unknown-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C >> [3] LC_TIME=en_AU.UTF-8 LC_COLLATE=en_AU.UTF-8 >> [5] LC_MONETARY=C LC_MESSAGES=en_AU.UTF-8 >> [7] LC_PAPER=en_AU.UTF-8 LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods >> base >> >> loaded via a namespace (and not attached): >> [1] tools_2.13.0 >>> >> >> >> >> >> >> >> ########## try loading the namespace >> >>> library(Biostrings) >> Loading required package: IRanges >> >> Attaching package: 'IRanges' >> >> The following object(s) are masked from 'package:base': >> >> cbind, eval, intersect, Map, mapply, order, paste, pmax, pmax.int, >> pmin, pmin.int, rbind, rep.int, setdiff, table, union >> >>> biocLite(c("GenomicFeatures")) >> Using R version 2.13.0 (R-devel), biocinstall version 2.8.2. >> Installing Bioconductor version 2.8 packages: >> [1] "GenomicFeatures" >> Please wait... >> >> trying URL >> 'http://www.bioconductor.org/packages/2.8/bioc/src/contrib/GenomicF eatures_1.3.13.tar.gz' >> Content type 'application/x-gzip' length 412765 bytes (403 Kb) >> opened URL >> ================================================== >> downloaded 403 Kb >> >> * installing *source* package ???????GenomicFeatures???????? ... >> ** R >> ** inst >> ** preparing package for lazy loading >> >> Attaching package: 'IRanges' >> >> The following object(s) are masked from 'package:base': >> >> Map, cbind, eval, intersect, mapply, order, paste, pmax, pmax.int, >> pmin, pmin.int, rbind, rep.int, setdiff, table, union >> >> Error : object ???????extractTranscripts???????? is not exported by >> 'namespace:Biostrings' >> ERROR: lazy loading failed for package ???????GenomicFeatures???????? >> * removing ???????/home/pleo/R_latest/library/GenomicFeatures???????? >> >> The downloaded packages are in >> ???????/tmp/RtmpulmTn5/downloaded_packages???????? >> Updating HTML index of packages in '.Library' >> Making packages.html ... done >> Warning message: >> In install.packages(pkgs = pkgs, repos = repos, ...) : >> installation of package 'GenomicFeatures' had non-zero exit status >> >>> sessionInfo() >> R version 2.13.0 Under development (unstable) (2011-03-06 r54683) >> Platform: x86_64-unknown-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C >> [3] LC_TIME=en_AU.UTF-8 LC_COLLATE=en_AU.UTF-8 >> [5] LC_MONETARY=C LC_MESSAGES=en_AU.UTF-8 >> [7] LC_PAPER=en_AU.UTF-8 LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods >> base >> >> other attached packages: >> [1] Biostrings_2.19.15 IRanges_1.9.25 >> >> loaded via a namespace (and not attached): >> [1] Biobase_2.11.9 tools_2.13.0 >>> >> >> >> ######### Note sure if I have missed something obvious? >> >> Thanks >> Paul >> >> [[alternative HTML version deleted]] >> >> >> >> >> _______________________________________________ >> 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 > > > > [[alternative HTML version deleted]] > > > > > _______________________________________________ > 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 -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319