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Question: Error installing development version of DESeq2
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gravatar for Kristina M Fontanez
4.8 years ago by
Kristina M Fontanez220 wrote:
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? 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/Versio ns/3.0/Resources/library/DESeq2/libs/DESeq2.so': dlopen(/Library/Frameworks/R.framework/Versions/3.0/Resources/librar y/DESeq2/libs/DESeq2.so, 6): Library not loaded: /Library/Frameworks/R .framework/Versions/3.1/Resources/lib/libRlapack.dylib Referenced from: /Library/Frameworks/R.framework/Versions/3.0/Resour ces/library/DESeq2/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@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]]
ADD COMMENTlink modified 4.8 years ago by Dan Tenenbaum ♦♦ 8.2k • written 4.8 years ago by Kristina M Fontanez220
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gravatar for Dan Tenenbaum
4.8 years ago by
Dan Tenenbaum ♦♦ 8.2k
United States
Dan Tenenbaum ♦♦ 8.2k 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/DE Seq2/libs/DESeq2.so': > dlopen(/Library/Frameworks/R.framework/Versions/3.0/Resources/libr ary/DESeq2/libs/DESeq2.so, > 6): Library not loaded: > /Library/Frameworks/R.framework/Versions/3.1/Resources/lib/libRlap ack.dylib > Referenced from: > /Library/Frameworks/R.framework/Versions/3.0/Resources/library/DES eq2/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
ADD COMMENTlink written 4.8 years ago by Dan Tenenbaum ♦♦ 8.2k
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
ADD REPLYlink written 4.8 years ago by Steve Lianoglou12k
Hi Steve- Unfortunately, your e-mail came about 10 minutes too late for me. I did indeed destroy my old version (3.0) of R. I did use the R-devel*.pkg available at att.com<http: att.com=""> but I must have missed the installer prompt that prevented it from killing my current release install. Do you have any advice for how I can fix this? I tried to restore my release version of R from a Time Machine backup but I still get the message “R cannot be opened because of a problem”. thanks, Kristina ------------------------------------------------------------------ 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 On Jan 17, 2014, at 5:05 PM, Steve Lianoglou <lianoglou.steve@gene.com<mailto:lianoglou.steve@gene.com>> wrote: 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<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 [[alternative HTML version deleted]]
ADD REPLYlink written 4.8 years ago by Kristina M Fontanez220
Hi Kristina, On Fri, Jan 17, 2014 at 2:29 PM, Kristina M Fontanez <fontanez at="" mit.edu=""> wrote: > Hi Steve- > > Unfortunately, your e-mail came about 10 minutes too late for me. I did indeed destroy my old version (3.0) of R. I did use the R-devel*.pkg available at att.com<http: att.com=""> but I must have missed the installer prompt that prevented it from killing my current release install. > > Do you have any advice for how I can fix this? I tried to restore my release version of R from a Time Machine backup but I still get the message ?R cannot be opened because of a problem?. Ack -- so .. "[Un]suffered Consequences" ... sorry to hear that. It's actually been a long time since this has happened to me, so I forget the exact details of the collateral damage you've just suffered :-) The good news is that it's not too onerous to recover from scratch. Just download the latest R-release installer pkg from CRAN. The installer will (should) contain the same warning telling you what the command is to perform a "non-destructive" isntall. For what it's worth, you simply have to open up a terminal and type in the following command: sudo pkgutil --forget org.r-project.R.x86_64.fw.pkg Then continue with the installation and all will be Feng Shui. After doing so, launching "R" from the terminal should now open R-3.0.2 (no need to use RSwitch). Just do the usual biocinstall (ie. source the biocLite script then re-install the packages you need). Being at MIT, the bandwidth available to you should make this a quick process, especially since the packages for the mac do not need to be compiled for installation. The good news is that after you've done that, you'll have a "working" multi-R environment you can jump back and forth between by simply using RSwitch. HTH, -steve -- Steve Lianoglou Computational Biologist Genentech
ADD REPLYlink written 4.8 years ago by Steve Lianoglou12k
Hi Steve- Thanks for the help. I deleted the development and corrupted release versions of R from my computer. Then, I downloaded the release version. Next, I renamed the release version in my Applications folder to R_3.0. Then I downloaded the installer package from att.com<http: att.com=""> for the development version. I opened up a terminal and in my / directory I typed in sudo pkgutil —forget org.r-project.R.x86_64.fw.pkg. parsons-three-sixty:/ fontanez$ sudo pkgutil --forget org.r-project.R.x86_64.fw.pkg Forgot package 'org.r-project.R.x86_64.fw.pkg' on '/'. Then, I proceeded to install the development version from the R development installer package. It installed correctly and I was able to download the development version of DESeq and my other packages. However, this is where I ran into a problem. I shut down R and opened up the R_3.0 app from my Applications. It opened, which was good but it drops a ton of warnings. Anytime I try to type something (as I’m typing) that “anyNA” is not a builtin function error pops up. It looks like my R 3.0 is still corrupted. I didn’t change anything in /Library/Frameworks - should I have done that as well, like Dan suggested? Thanks, 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. Error : object 'anyNA' not found whilst loading namespace 'grDevices' In addition: Warning messages: 1: package ‘methods’ was built under R version 3.1.0 2: package "methods" in options("defaultPackages") was not found 3: package ‘datasets’ was built under R version 3.1.0 4: package ‘datasets’ in options("defaultPackages") was not found 5: package ‘utils’ was built under R version 3.1.0 6: package ‘utils’ in options("defaultPackages") was not found 7: package ‘grDevices’ was built under R version 3.1.0 Error : object 'anyNA' not found whilst loading namespace 'grDevices' In addition: Warning messages: 1: package ‘grDevices’ in options("defaultPackages") was not found 2: package ‘graphics’ was built under R version 3.1.0 Error : object 'anyNA' not found whilst loading namespace 'grDevices' In addition: Warning messages: 1: package ‘graphics’ in options("defaultPackages") was not found 2: package ‘stats’ was built under R version 3.1.0 During startup - Warning messages: 1: package ‘stats’ in options("defaultPackages") was not found 2: package ‘methods’ was built under R version 3.1.0 3: package ‘methods’ in options("defaultPackages") was not found Error in .deparseOpts(control) : "anyNA" is not a BUILTIN function [History restored from /Users/fontanez/.Rapp.history] Error in .deparseOpts(control) : "anyNA" is not a BUILTIN function > library(DESeq2) Loading required package: GenomicRanges Loading required package: methods Error in .deparseOpts(control) : "anyNA" is not a BUILTIN function In addition: Warning messages: 1: package ‘DESeq2’ was built under R version 3.1.0 2: package ‘GenomicRanges’ was built under R version 3.1.0 3: In get(".__S3MethodsTable__.", envir = env, inherits = FALSE) : internal error -3 in R_decompress1 Error in .deparseOpts(control) : "anyNA" is not a BUILTIN function > traceback() 11: .deparseOpts(control) 10: deparse(x[[1L]]) 9: mode(expr) 8: match(x, table, nomatch = 0L) 7: mode(expr) %in% c("call", "expression", "(", "function") 6: deparse(call) 5: value[[3L]](cond) 4: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 3: tryCatchList(expr, classes, parentenv, handlers) 2: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call)[1L] prefix <- paste("Error in", dcall, ": ") LONG <- 75L msg <- conditionMessage(e) sm <- strsplit(msg, "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && identical(getOption("show.error.messages"), TRUE)) { cat(msg, file = stderr()) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e)) }) 1: try(gsub("\\s+<smb: s+="">", " ", paste(capture.output(print(args(traceback))), collapse = "")), silent = TRUE) ------------------------------------------------------------------ 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 On Jan 17, 2014, at 5:37 PM, Steve Lianoglou <lianoglou.steve@gene.com<mailto:lianoglou.steve@gene.com>> wrote: The good news is that it's not too onerous to recover from scratch. Just download the latest R-release installer pkg from CRAN. The installer will (should) contain the same warning telling you what the command is to perform a "non-destructive" isntall. For what it's worth, you simply have to open up a terminal and type in the following command: sudo pkgutil --forget org.r-project.R.x86_64.fw.pkg Then continue with the installation and all will be Feng Shui. After doing so, launching "R" from the terminal should now open R-3.0.2 (no need to use RSwitch). Just do the usual biocinstall (ie. source the biocLite script then re-install the packages you need). Being at MIT, the bandwidth available to you should make this a quick process, especially since the packages for the mac do not need to be compiled for installation. [[alternative HTML version deleted]]
ADD REPLYlink written 4.8 years ago by Kristina M Fontanez220
Hi Katrina, Sounds like we're almost there ... comments inline: On Fri, Jan 17, 2014 at 3:12 PM, Kristina M Fontanez <fontanez at="" mit.edu=""> wrote: > Hi Steve- > > Thanks for the help. I deleted the development and corrupted release versions of R from my computer. Then, I downloaded the release version. Next, I renamed the release version in my Applications folder to R_3.0. Nice one! Good move on your part to have done that and sorry that I neglected to point that out earlier -- I don't use R.app, so it slipped my mind. > Then I downloaded the installer package from att.com<http: att.com=""> for the development version. I opened up a terminal and in my / directory I typed in sudo pkgutil ?forget org.r-project.R.x86_64.fw.pkg. > > parsons-three-sixty:/ fontanez$ sudo pkgutil --forget org.r-project.R.x86_64.fw.pkg > Forgot package 'org.r-project.R.x86_64.fw.pkg' on '/'. > > Then, I proceeded to install the development version from the R development installer package. It installed correctly and I was able to download the development version of DESeq and my other packages. However, this is where I ran into a problem. > > I shut down R and opened up the R_3.0 app from my Applications. It opened, which was good but it drops a ton of warnings. Anytime I try to type something (as I?m typing) that ?anyNA? is not a builtin function error pops up. It looks like my R 3.0 is still corrupted. I didn?t change anything in /Library/Frameworks - should I have done that as well, like Dan suggested? No, do not change anything in /Library/Frameworks/* manually -- RSwitch handles those "delicate" details for you. So, you now have to download RSwitch and use that to change the version of R that is currently "live". So, if you want to use R 3.0.x, you would: (i) first quit the current R process you are running (ii) open up RSwitch and select "R 3.0". This does some magic inside the /LibraryFrameworks/R.framwork/* for you. (iii) After selecting that, you can then launch your R_3.0.app If you want to run R-devel you would (i) Quit current version of R (ii) Open up RSwitch and select R 3.1 (iii) open up the R.app that the R-devel package installed for you. That should do the trick -- if not, please post back with an update as I'm *pretty* sure you don't have to do anything much more involved than that. -steve -- Steve Lianoglou Computational Biologist Genentech
ADD REPLYlink written 4.8 years ago by Steve Lianoglou12k
Steve- Thank you for your help with this issue. Your last post solved my problems with the errors and I now have R 3.0 and R 3.1 installed side by side on my system. I’m sorry for the late reply as I was away over the weekend. Thanks again, Kristina ------------------------------------------------------------------ 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 On Jan 17, 2014, at 6:58 PM, Steve Lianoglou <lianoglou.steve@gene.com<mailto:lianoglou.steve@gene.com>> wrote: Hi Katrina, Sounds like we're almost there ... comments inline: On Fri, Jan 17, 2014 at 3:12 PM, Kristina M Fontanez <fontanez@mit.edu<mailto:fontanez@mit.edu>> wrote: Hi Steve- Thanks for the help. I deleted the development and corrupted release versions of R from my computer. Then, I downloaded the release version. Next, I renamed the release version in my Applications folder to R_3.0. Nice one! Good move on your part to have done that and sorry that I neglected to point that out earlier -- I don't use R.app, so it slipped my mind. Then I downloaded the installer package from att.com<http: att.com=""><http: att.com=""> for the development version. I opened up a terminal and in my / directory I typed in sudo pkgutil —forget org.r-project.R.x86_64.fw.pkg. parsons-three-sixty:/ fontanez$ sudo pkgutil --forget org.r-project.R.x86_64.fw.pkg Forgot package 'org.r-project.R.x86_64.fw.pkg' on '/'. Then, I proceeded to install the development version from the R development installer package. It installed correctly and I was able to download the development version of DESeq and my other packages. However, this is where I ran into a problem. I shut down R and opened up the R_3.0 app from my Applications. It opened, which was good but it drops a ton of warnings. Anytime I try to type something (as I’m typing) that “anyNA” is not a builtin function error pops up. It looks like my R 3.0 is still corrupted. I didn’t change anything in /Library/Frameworks - should I have done that as well, like Dan suggested? No, do not change anything in /Library/Frameworks/* manually -- RSwitch handles those "delicate" details for you. So, you now have to download RSwitch and use that to change the version of R that is currently "live". So, if you want to use R 3.0.x, you would: (i) first quit the current R process you are running (ii) open up RSwitch and select "R 3.0". This does some magic inside the /LibraryFrameworks/R.framwork/* for you. (iii) After selecting that, you can then launch your R_3.0.app If you want to run R-devel you would (i) Quit current version of R (ii) Open up RSwitch and select R 3.1 (iii) open up the R.app that the R-devel package installed for you. That should do the trick -- if not, please post back with an update as I'm *pretty* sure you don't have to do anything much more involved than that. -steve -- Steve Lianoglou Computational Biologist Genentech [[alternative HTML version deleted]]
ADD REPLYlink written 4.7 years ago by Kristina M Fontanez220
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]]
ADD REPLYlink written 4.8 years ago by Kristina M Fontanez220
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