Hi, Perhaps a more user-friendly way to run w/ both versions is to simply install the R-devel *.pkg available from http://r.research.att.com specifically: http://r.research.att.com/snowleopard/R-devel/R-devel-snowleopard- signed.pkg Make sure you pay close attention to the installer and follow the instructions provided in the splash window so that the installation doesn't blow out your current (release) install (this will involve running some command from the terminal that has to do w/ the install receipts, or something). Then, to switch between R and R-devel, you "simply" use the RSwitch app available from the same site: http://r.research.att.com/RSwitch-1.2.dmg Which is an app front end w/ simply does some swapping of symlinks so that the right links point to the right version of R that you want to run. Note that I believe this approach isn't amenable to running both versions of R *at the same time.* -steve On Fri, Jan 17, 2014 at 1:47 PM, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> wrote: > > > ----- Original Message ----- >> From: "Kristina M Fontanez" <fontanez at="" mit.edu=""> >> To: bioconductor at r-project.org >> Sent: Friday, January 17, 2014 1:36:48 PM >> Subject: [BioC] Error installing development version of DESeq2 >> >> Mike- >> >> I tried downloading the development version of DESeq2 following your >> directions but it didn?t work. It seems I have 2 problems, 1) I am >> not using the development version of R (3.1) and therefore this >> prevents me from using the development version of Bioconductor >> (2.14). Is that right? I don?t particularly want to use an unstable >> version of R. Can I get the development version of Bioconductor >> without having to use the development version of R? > > > No. If you want to run the devel version of a package, you need to install the version of R that Bioc-devel is meant to run on, in this case R-devel a/k/a 3.1. You can have multiple versions of R on your machine, if you want. > For example, you could rename your current version so it's no longer used: > cd /Library/Frameworks > mv R.framework R.framework.release > > Then download R-devel. Then when you are done using R-devel: > > cd /Library/Frameworks > mv R.framework R.framework.devel > mv R.framework.release R.framework > > Others have other preferred ways. I have bash aliases to help make this easier. > > Dan > > >> My R session is >> pasted below. >> >> Kristina >> >> R version 3.0.2 (2013-09-25) -- "Frisbee Sailing" >> Copyright (C) 2013 The R Foundation for Statistical Computing >> Platform: x86_64-apple-darwin10.8.0 (64-bit) >> >> R is free software and comes with ABSOLUTELY NO WARRANTY. >> You are welcome to redistribute it under certain conditions. >> Type 'license()' or 'licence()' for distribution details. >> >> Natural language support but running in an English locale >> >> R is a collaborative project with many contributors. >> Type 'contributors()' for more information and >> 'citation()' on how to cite R or R packages in publications. >> >> Type 'demo()' for some demos, 'help()' for on-line help, or >> 'help.start()' for an HTML browser interface to help. >> Type 'q()' to quit R. >> >> [R.app GUI 1.62 (6558) x86_64-apple-darwin10.8.0] >> >> [History restored from /Users/fontanez/.Rapp.history] >> >> > source("http://bioconductor.org/biocLite.R") >> Bioconductor version 2.13 (BiocInstaller 1.12.0), ?biocLite for help >> > biocLite() >> BioC_mirror: http://bioconductor.org >> Using Bioconductor version 2.13 (BiocInstaller 1.12.0), R version >> 3.0.2. >> > useDevel() >> Error: 'devel' version requires a more recent R >> > install.packages("DESeq2_1.3.28.tgz",repos=NULL) >> > library(DESeq2) >> Loading required package: GenomicRanges >> Loading required package: BiocGenerics >> Loading required package: parallel >> >> Attaching package: ?BiocGenerics? >> >> The following objects are masked from ?package:parallel?: >> >> clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, >> clusterExport, clusterMap, parApply, parCapply, parLapply, >> parLapplyLB, parRapply, parSapply, parSapplyLB >> >> The following object is masked from ?package:stats?: >> >> xtabs >> >> The following objects are masked from ?package:base?: >> >> anyDuplicated, append, as.data.frame, as.vector, cbind, colnames, >> duplicated, eval, evalq, Filter, Find, get, intersect, >> is.unsorted, >> lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, >> pmin, pmin.int, Position, rank, rbind, Reduce, rep.int, rownames, >> sapply, setdiff, sort, table, tapply, union, unique, unlist >> >> Loading required package: IRanges >> Loading required package: XVector >> Loading required package: Rcpp >> Loading required package: RcppArmadillo >> Error in dyn.load(file, DLLpath = DLLpath, ...) : >> unable to load shared object >> '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/D ESeq2/libs/DESeq2.so': >> dlopen(/Library/Frameworks/R.framework/Versions/3.0/Resources/lib rary/DESeq2/libs/DESeq2.so, >> 6): Library not loaded: >> /Library/Frameworks/R.framework/Versions/3.1/Resources/lib/libRla pack.dylib >> Referenced from: >> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/DE Seq2/libs/DESeq2.so >> Reason: image not found >> In addition: Warning message: >> package ?DESeq2? was built under R version 3.1.0 >> Error: package or namespace load failed for ?DESeq2? >> > traceback() >> 2: stop(gettextf("package or namespace load failed for %s", >> sQuote(package)), >> call. = FALSE, domain = NA) >> 1: library(DESeq2) >> > sessionInfo() >> R version 3.0.2 (2013-09-25) >> Platform: x86_64-apple-darwin10.8.0 (64-bit) >> >> locale: >> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >> >> attached base packages: >> [1] parallel stats graphics grDevices utils datasets >> methods >> [8] base >> >> other attached packages: >> [1] RcppArmadillo_0.4.000 Rcpp_0.10.6 GenomicRanges_1.14.4 >> [4] XVector_0.2.0 IRanges_1.20.6 BiocGenerics_0.8.0 >> [7] BiocInstaller_1.12.0 >> >> loaded via a namespace (and not attached): >> [1] annotate_1.40.0 AnnotationDbi_1.24.0 Biobase_2.22.0 >> [4] DBI_0.2-7 genefilter_1.44.0 geneplotter_1.40.0 >> [7] grid_3.0.2 lattice_0.20-24 locfit_1.5-9.1 >> [10] RColorBrewer_1.0-5 RSQLite_0.11.4 splines_3.0.2 >> [13] stats4_3.0.2 survival_2.37-4 tools_3.0.2 >> [16] XML_3.95-0.2 xtable_1.7-1 >> >> ------------------------------------------------------------------ >> Kristina Fontanez, Postdoctoral Fellow >> fontanez at mit.edu<mailto:fontanez at="" mit.edu=""> >> Massachusetts Institute of Technology >> Department of Civil and Environmental Engineering >> 48-120E >> 15 Vassar Street >> Cambridge, MA 02139 >> >> >> >> >> [[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 > > _______________________________________________ > 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 -- Steve Lianoglou Computational Biologist Genentech

Dan- Thank you for that insight. I downloaded the development version and kept around my stable 3.0 version as well. I was then able to successfully download the development version of DESeq. Although, I am nervous about encountering the “Unsuffered Consequences” promised in the title. Thanks! Kristina R Under development (unstable) (2014-01-16 r64804) -- "Unsuffered Consequences" Copyright (C) 2014 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin10.8.0 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. [R.app GUI 1.62 (6623) x86_64-apple-darwin10.8.0] [History restored from /Users/fontanez/.Rapp.history] > source("http://bioconductor.org/biocLite.R") trying URL 'http://www.bioconductor.org/packages/2.14/bioc/bin/macosx/ contrib/3.1/BiocInstaller_1.13.3.tgz' Content type 'application/x-gzip' length 49888 bytes (48 Kb) opened URL ================================================== downloaded 48 Kb The downloaded binary packages are in /var/folders/90/zq2q8_fs0355_g769gsx46bc0000gn/T//Rtmp56LETx/downloade d_packages Bioconductor version 2.14 (BiocInstaller 1.13.3), ?biocLite for help > biocLite("DESeq2") BioC_mirror: http://bioconductor.org Using Bioconductor version 2.14 (BiocInstaller 1.13.3), R version 3.1.0. Installing package(s) 'DESeq2' also installing the dependencies ‘DBI’, ‘RSQLite’, ‘xtable’, ‘XML’, ‘XVector’, ‘AnnotationDbi’, ‘annotate’, ‘Biobase’, ‘GenomicRanges’, ‘IRanges’, ‘Rcpp’, ‘RcppArmadillo’, ‘BiocGenerics’, ‘locfit’, ‘genefilter’, ‘geneplotter’, ‘RColorBrewer’ .. > library(DESeq2) Loading required package: GenomicRanges Loading required package: BiocGenerics Loading required package: parallel Attaching package: ‘BiocGenerics’ The following objects are masked from ‘package:parallel’: clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following object is masked from ‘package:stats’: xtabs The following objects are masked from ‘package:base’: anyDuplicated, append, as.data.frame, as.vector, cbind, colnames, do.call, duplicated, eval, evalq, Filter, Find, get, intersect, is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rep.int, rownames, sapply, setdiff, sort, table, tapply, union, unique, unlist Loading required package: IRanges Loading required package: XVector Loading required package: Rcpp Loading required package: RcppArmadillo On Jan 17, 2014, at 4:47 PM, Dan Tenenbaum <dtenenba@fhcrc.org<mailto:dtenenba@fhcrc.org>> wrote: No. If you want to run the devel version of a package, you need to install the version of R that Bioc-devel is meant to run on, in this case R-devel a/k/a 3.1. You can have multiple versions of R on your machine, if you want. For example, you could rename your current version so it's no longer used: cd /Library/Frameworks mv R.framework R.framework.release Then download R-devel. Then when you are done using R-devel: cd /Library/Frameworks mv R.framework R.framework.devel mv R.framework.release R.framework Others have other preferred ways. I have bash aliases to help make this easier. Dan ------------------------------------------------------------------ Kristina Fontanez, Postdoctoral Fellow fontanez@mit.edu<mailto:fontanez@mit.edu> Massachusetts Institute of Technology Department of Civil and Environmental Engineering 48-120E 15 Vassar Street Cambridge, MA 02139 [[alternative HTML version deleted]]