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Question: DESeq2 dependency hell
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4.3 years ago by
Guest User12k
Guest User12k wrote:
Hi all, I have entered dependency hell when trying to install DESEq2. I am using Rstudio that is running on linux Mint, with R version 3.0.1. When I run biocLite(c("DESeq2"), dependencies = TRUE), I get the following warnings at the end of what almost seems like a successful install (See below). I don't think this problem is specific to DESeq2, but does anybody have an idea as to what is going on here. Warning messages: 1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ... : installation of package ???RCurl??? had non-zero exit status 2: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ... : installation of package ???XML??? had non-zero exit status 3: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ... : installation of package ???biomaRt??? had non-zero exit status 4: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ... : installation of package ???annotate??? had non-zero exit status 5: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ... : installation of package ???geneplotter??? had non-zero exit status 6: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ... : installation of package ???DEXSeq??? had non-zero exit status 7: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ... : installation of package ???genefilter??? had non-zero exit status 8: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ... : installation of package ???DESeq??? had non-zero exit status 9: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ... : installation of package ???DESeq2??? had non-zero exit status 10: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ... : installation of package ???pasilla??? had non-zero exit status 11: installed directory not writable, cannot update packages 'MASS', 'spatial' Many Thanks! Mark Christie -- output of sessionInfo(): R version 3.0.1 (2013-05-16) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] BiocInstaller_1.10.3 loaded via a namespace (and not attached): [1] tools_3.0.1 -- Sent via the guest posting facility at bioconductor.org.
ADD COMMENTlink modified 4.3 years ago by James W. MacDonald45k • written 4.3 years ago by Guest User12k
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4.3 years ago by
United States
James W. MacDonald45k wrote:
Hi Mark, On 8/14/2013 11:57 AM, Mark Christie [guest] wrote: > Hi all, > > I have entered dependency hell when trying to install DESEq2. I am using Rstudio that is running on linux Mint, with R version 3.0.1. > > When I run biocLite(c("DESeq2"), dependencies = TRUE), I get the following warnings at the end of what almost seems like a successful install (See below). I don't think this problem is specific to DESeq2, but does anybody have an idea as to what is going on here. > > Warning messages: > 1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ... : > installation of package ???RCurl??? had non-zero exit status > 2: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ... : > installation of package ???XML??? had non-zero exit status > 3: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ... : > installation of package ???biomaRt??? had non-zero exit status > 4: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ... : > installation of package ???annotate??? had non-zero exit status > 5: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ... : > installation of package ???geneplotter??? had non-zero exit status > 6: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ... : > installation of package ???DEXSeq??? had non-zero exit status > 7: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ... : > installation of package ???genefilter??? had non-zero exit status > 8: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ... : > installation of package ???DESeq??? had non-zero exit status > 9: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ... : > installation of package ???DESeq2??? had non-zero exit status > 10: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ... : > installation of package ???pasilla??? had non-zero exit status > 11: installed directory not writable, cannot update packages 'MASS', 'spatial' You don't show the part of the install output that is of interest, but it is likely that you don't have the xml headers installed. A quick look indicates that Mint is a Debian offshoot, so something like sudo apt-get install libxml2-dev should do the trick. Best, Jim > > Many Thanks! > > Mark Christie > > -- output of sessionInfo(): > > R version 3.0.1 (2013-05-16) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] BiocInstaller_1.10.3 > > loaded via a namespace (and not attached): > [1] tools_3.0.1 > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
ADD COMMENTlink written 4.3 years ago by James W. MacDonald45k
Thanks for sharing your expertise Jim - that solution worked perfectly! On Wed, Aug 14, 2013 at 12:02 PM, James W. MacDonald <jmacdon@uw.edu> wrote: > Hi Mark, > > > On 8/14/2013 11:57 AM, Mark Christie [guest] wrote: > >> Hi all, >> >> I have entered dependency hell when trying to install DESEq2. I am using >> Rstudio that is running on linux Mint, with R version 3.0.1. >> >> When I run biocLite(c("DESeq2"), dependencies = TRUE), I get the >> following warnings at the end of what almost seems like a successful >> install (See below). I don't think this problem is specific to DESeq2, but >> does anybody have an idea as to what is going on here. >> >> Warning messages: >> 1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ... : >> installation of package ‘RCurl’ had non-zero exit status >> >> 2: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ... : >> installation of package ‘XML’ had non-zero exit status >> >> 3: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ... : >> installation of package ‘biomaRt’ had non-zero exit status >> >> 4: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ... : >> installation of package ‘annotate’ had non-zero exit status >> >> 5: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ... : >> installation of package ‘geneplotter’ had non-zero exit status >> >> 6: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ... : >> installation of package ‘DEXSeq’ had non-zero exit status >> >> 7: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ... : >> installation of package ‘genefilter’ had non-zero exit status >> >> 8: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ... : >> installation of package ‘DESeq’ had non-zero exit status >> >> 9: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ... : >> installation of package ‘DESeq2’ had non-zero exit status >> >> 10: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ... : >> installation of package ‘pasilla’ had non-zero exit status >> >> 11: installed directory not writable, cannot update packages 'MASS', >> 'spatial' >> > > You don't show the part of the install output that is of interest, but it > is likely that you don't have the xml headers installed. A quick look > indicates that Mint is a Debian offshoot, so something like > > sudo apt-get install libxml2-dev > > should do the trick. > > Best, > > Jim > > > >> Many Thanks! >> >> Mark Christie >> >> -- output of sessionInfo(): >> >> R version 3.0.1 (2013-05-16) >> Platform: x86_64-pc-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >> LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >> LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 >> [7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C >> LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 >> LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] BiocInstaller_1.10.3 >> >> loaded via a namespace (and not attached): >> [1] tools_3.0.1 >> >> -- >> Sent via the guest posting facility at bioconductor.org. >> >> ______________________________**_________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.e="" thz.ch="" mailman="" listinfo="" bioconductor=""> >> Search the archives: http://news.gmane.org/gmane.** >> science.biology.informatics.**conductor<http: news.gmane.org="" gmane="" .science.biology.informatics.conductor=""> >> > > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 > > -- Mark R. Christie, PhD Department of Zoology, Oregon State University http://www.science.oregonstate.edu/~christim/ [[alternative HTML version deleted]]
ADD REPLYlink written 4.3 years ago by Mark Christie30
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