Question: problem installing affycoretools in R in linux environment
0
gravatar for Manisha Brahmachary
11.1 years ago by
Manisha Brahmachary80 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]]
go affycoretools • 996 views
ADD COMMENTlink modified 11.1 years ago by James W. MacDonald51k • written 11.1 years ago by Manisha Brahmachary80
Answer: problem installing affycoretools in R in linux environment
0
gravatar for James W. MacDonald
11.1 years ago by
United States
James W. MacDonald51k wrote:
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 -- James W. MacDonald, M.S. Biostatistician Hildebrandt Lab 8220D MSRB III 1150 W. Medical Center Drive Ann Arbor MI 48109-0646 734-936-8662
ADD COMMENTlink written 11.1 years ago by James W. MacDonald51k
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@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 -- James W. MacDonald, M.S. Biostatistician Hildebrandt Lab 8220D MSRB III 1150 W. Medical Center Drive Ann Arbor MI 48109-0646 734-936-8662
ADD REPLYlink written 11.1 years ago by Manisha Brahmachary80
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 344 users visited in the last hour