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Question: problem installing affycoretools in R in linux environment
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gravatar for rgentleman
10.0 years ago by
rgentleman5.5k
United States
rgentleman5.5k wrote:
same problem, only this time with RCurl. It looks like you did not properly update your packages at some point in time, and now you will need to do that one piece at a time. But really your R is out of date - you should update to 2.7.2, install all packages using biocLite and use somewhat more modern versions of the packages best wishes Robert Manisha Brahmachary wrote: > I also tried installing biomaRt separately but I was not able to do that. How > do I get around this problem? > > Please see the session below: > > biocLite("biomaRt") > Running biocinstall version 2.1.11 with R version 2.6.1 > Your version of R requires version 2.1 of BioConductor. > Warning in install.packages(pkgs = pkgs, repos = repos, dependencies = > dependencies, : > argument 'lib' is missing: using > '/nfs/apollo/2/c2b2/users/mb3058/R/x86_64-unknown-linux-gnu- library/2.6' > trying URL > 'http://bioconductor.org/packages/2.1/bioc/src/contrib/biomaRt_1.12. 2.tar.gz' > Content type 'application/x-gzip' length 276683 bytes (270 Kb) > opened URL > ================================================== > downloaded 270 Kb > > /nfs/apollo/2/c2b2/users/mb3058/R/x86_64-unknown-linux-gnu- library/2.6 > * Installing *source* package 'biomaRt' ... > ** R > ** inst > ** preparing package for lazy loading > Loading required package: RCurl > Error in library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = > lib.loc) : > 'RCurl' is not a valid package -- installed < 2.0.0? > Calls: .getRequiredPackages -> .getRequiredPackages2 -> library > Execution halted > ERROR: lazy loading failed for package 'biomaRt' > ** Removing > '/nfs/apollo/2/c2b2/users/mb3058/R/x86_64-unknown-linux-gnu- library/2.6/bioma > Rt' > ** Restoring previous > '/nfs/apollo/2/c2b2/users/mb3058/R/x86_64-unknown-linux-gnu- library/2.6/bioma > Rt' > > The downloaded packages are in > /tmp/RtmpdB1uCC/downloaded_packages > Warning message: > In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, > : > installation of package 'biomaRt' had non-zero exit status > > thanks > manisha > > > -----Original Message----- > From: James W. MacDonald [mailto:jmacdon at med.umich.edu] > Sent: Tuesday, September 30, 2008 4:10 PM > To: Manisha Brahmachary > Cc: bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] problem installing affycoretools in R in linux > environment > > Hi Manisha, > > That error indicates that biomaRt was installed incorrectly. Try > biocLite("biomaRt") and then see if you can install affycoretools. > > Best, > > Jim > > > > Manisha Brahmachary wrote: >> I am having problems installing affycoretools in R (2.6) on my linux >> environment. When I do the same thing with my R (2.6) in windows I donot > have >> any such problem and it gets properly installed. I will appreciate any >> suggestion on how to install it in linux environment >> >> >> >> I am trying to install affycoretools ver 1.10.2. >> >> >> >> Following is the session for installation: >> >> >> >>> biocLite("affycoretools") >> Running biocinstall version 2.1.11 with R version 2.6.1 >> >> Your version of R requires version 2.1 of BioConductor. >> >> Warning in install.packages(pkgs = pkgs, repos = repos, dependencies = >> dependencies, : >> >> argument 'lib' is missing: using >> '/nfs/apollo/2/c2b2/users/mb3058/R/x86_64-unknown-linux-gnu- library/2.6' >> >> trying URL >> > 'http://bioconductor.org/packages/2.1/bioc/src/contrib/affycoretools _1.10.2.t >> ar.gz' >> >> Content type 'application/x-gzip' length 6776315 bytes (6.5 Mb) >> >> opened URL >> >> ================================================== >> >> downloaded 6.5 Mb >> >> >> >> /nfs/apollo/2/c2b2/users/mb3058/R/x86_64-unknown-linux-gnu- library/2.6 >> >> * Installing *source* package 'affycoretools' ... >> >> ** R >> >> ** inst >> >> ** preparing package for lazy loading >> >> Loading required package: affy >> >> Loading required package: Biobase >> >> Loading required package: tools >> >> >> >> Welcome to Bioconductor >> >> >> >> Vignettes contain introductory material. To view, type >> >> 'openVignette()'. To cite Bioconductor, see >> >> 'citation("Biobase")' and for packages 'citation(pkgname)'. >> >> >> >> Loading required package: affyio >> >> Loading required package: preprocessCore >> >> Loading required package: limma >> >> Loading required package: GOstats >> >> Loading required package: graph >> >> Loading required package: GO.db >> >> Loading required package: AnnotationDbi >> >> Loading required package: DBI >> >> Loading required package: RSQLite >> >> Loading required package: annotate >> >> Loading required package: xtable >> >> Loading required package: RBGL >> >> Loading required package: Category >> >> Loading required package: genefilter >> >> Loading required package: survival >> >> Loading required package: splines >> >> Loading required package: biomaRt >> >> >> >> Error in library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc > = >> lib.loc) : >> >> 'biomaRt' is not a valid package -- installed < 2.0.0? >> >> Calls: .getRequiredPackages -> .getRequiredPackages2 -> library >> >> Execution halted >> >> ERROR: lazy loading failed for package 'affycoretools' >> >> ** Removing >> > '/nfs/apollo/2/c2b2/users/mb3058/R/x86_64-unknown-linux-gnu- library/2.6/affyc >> oretools' >> >> ** Restoring previous >> > '/nfs/apollo/2/c2b2/users/mb3058/R/x86_64-unknown-linux-gnu- library/2.6/affyc >> oretools' >> >> >> >> The downloaded packages are in >> >> /tmp/RtmpdB1uCC/downloaded_packages >> >> Warning message: >> >> In install.packages(pkgs = pkgs, repos = repos, dependencies = > dependencies, >> : >> >> installation of package 'affycoretools' had non-zero exit status >> >> >> >> thanks >> >> manisha >> >> >> >> >> >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 rgentlem at fhcrc.org
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