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Question: Cannot install CummeRbund on R version 3.0.2 (2013-09-25)
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gravatar for gupta
2.4 years ago by
gupta0
gupta0 wrote:

Hi,

I have been trying to install cummerbund on R version 3.0.2 (2013-09-25), but I receive the following error:

* installing *source* package ‘RCurl’ ...
** Paket ‘RCurl’ erfolgreich entpackt und MD5 Summen überprüft
checking for curl-config... no
Cannot find curl-config
ERROR: configuration failed for package ‘RCurl’
* removing ‘/nfs/numerik/bzfgupta/R/x86_64-pc-linux-gnu-library/3.0/RCurl’
* installing *source* package ‘reshape2’ ...
** Paket ‘reshape2’ erfolgreich entpackt und MD5 Summen überprüft
** libs
g++ -I/usr/share/R/include -DNDEBUG   -I"/usr/lib/R/site-library/Rcpp/include"   -fpic  -O3 -pipe  -g  -c RcppExports.cpp -o RcppExports.o
g++ -I/usr/share/R/include -DNDEBUG   -I"/usr/lib/R/site-library/Rcpp/include"   -fpic  -O3 -pipe  -g  -c melt.cpp -o melt.o
g++ -shared -o reshape2.so RcppExports.o melt.o -L/usr/lib/R/lib -lR
installing to /nfs/numerik/bzfgupta/R/x86_64-pc-linux-gnu-library/3.0/reshape2/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) :
  namespace ‘plyr’ 1.8 is being loaded, but >= 1.8.1 is required
ERROR: lazy loading failed for package ‘reshape2’
* removing ‘/nfs/numerik/bzfgupta/R/x86_64-pc-linux-gnu-library/3.0/reshape2’
ERROR: dependency ‘RCurl’ is not available for package ‘biomaRt’
* removing ‘/nfs/numerik/bzfgupta/R/x86_64-pc-linux-gnu-library/3.0/biomaRt’
ERROR: dependency ‘RCurl’ is not available for package ‘rtracklayer’
* removing ‘/nfs/numerik/bzfgupta/R/x86_64-pc-linux-gnu-library/3.0/rtracklayer’
ERROR: dependencies ‘rtracklayer’, ‘biomaRt’, ‘RCurl’ are not available for package ‘GenomicFeatures’
* removing ‘/nfs/numerik/bzfgupta/R/x86_64-pc-linux-gnu-library/3.0/GenomicFeatures’
ERROR: dependency ‘GenomicFeatures’ is not available for package ‘biovizBase’
* removing ‘/nfs/numerik/bzfgupta/R/x86_64-pc-linux-gnu-library/3.0/biovizBase’
ERROR: dependencies ‘rtracklayer’, ‘biomaRt’, ‘GenomicFeatures’, ‘biovizBase’ are not available for package ‘Gviz’
* removing ‘/nfs/numerik/bzfgupta/R/x86_64-pc-linux-gnu-library/3.0/Gviz’
ERROR: dependencies ‘ggplot2’, ‘reshape2’, ‘rtracklayer’, ‘Gviz’ are not available for package ‘cummeRbund’
* removing ‘/nfs/numerik/bzfgupta/R/x86_64-pc-linux-gnu-library/3.0/cummeRbund’

The downloaded source packages are in
        ‘/tmp/RtmpiQlamh/downloaded_packages’
Warnmeldungen:
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 ‘reshape2’ 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 ‘rtracklayer’ had non-zero exit status
5: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
  installation of package ‘GenomicFeatures’ had non-zero exit status
6: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
  installation of package ‘biovizBase’ had non-zero exit status
7: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
  installation of package ‘Gviz’ had non-zero exit status
8: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
  installation of package ‘cummeRbund’ had non-zero exit status
9: installed directory not writable, cannot update packages 'abind', 'AMORE',
  'caTools', 'chron', 'coda', 'colorspace', 'DBI', 'deldir', 'DEoptimR',
  'doMC', 'doSNOW', 'eco', 'Epi', 'epiR', 'fAssets', 'fBasics', 'fCopulae',
  'fMultivar', 'fOptions', 'foreach', 'Formula', 'fPortfolio', 'fRegression',
  'gdata', 'g.data', 'genetics', 'gmodels', 'gplots', 'gtools', 'haplo.stats',
  'Hmisc', 'iterators', 'latticeExtra', 'lme4', 'lmtest', 'lpSolve', 'mapdata',
  'mapproj', 'maps', 'maptools', 'MatchIt', 'MCMCpack', 'minqa', 'mnormt',
  'MNP', 'msm', 'multcomp', 'mvtnorm', 'numDeriv', 'plotrix', 'polspline',
  'polyclip', 'polyCub', 'qtl', 'qvalue', 'randomForest', 'RColorBrewer',
  'Rcpp', 'RcppEigen', 'relimp', 'rggobi', 'rgl', 'Rglpk', 'RGtk2', 'rJava',
  'Rmpi', 'RMySQL', 'robustbase', 'ROCR', 'RODBC', 'RQuantLib', 'Rsymphony',
  'RUnit', 'sandwich', 'slam', 'sn', 'snow', 'sp', 'spc', 'statmod',
  'strucchange', 'tcltk2', 'TeachingDemos', 'TH.data', 'timeDate',
  'timeSeries', 'tseries' [... truncated]
  1. Can some please help me identify the problem?
  2. Do I need a newer version of R?
  3. Is there a version of cummerbund that is compatible with R version 3.0.2?

Thank you in advance.

Best, PG

ADD COMMENTlink modified 2.4 years ago by Martin Morgan ♦♦ 22k • written 2.4 years ago by gupta0
1
gravatar for Martin Morgan
2.4 years ago by
Martin Morgan ♦♦ 22k
United States
Martin Morgan ♦♦ 22k wrote:

There are hints in the Bioconductor FAQ particularly to look at the first error

** Paket ‘RCurl’ erfolgreich entpackt und MD5 Summen überprüft
checking for curl-config... no
Cannot find curl-config
ERROR: configuration failed for package ‘RCurl’

and then to install the appropriate system dependency, on ubuntu for instance sudo apt-get install libcurl4-openssl-dev. Likely you will also require libxml2-dev (or equivalent).

Your R is quite old and many packages are out of date; if you are starting a new project consider using the newest R version 3.3.0 and corresponding Bioconductor version 3.3.

The complaint about 'installed directory not writable' indicates that these packages were installed as 'root' or some user other than you. It is better practice for a single-user system to install only R and base / recommended packages as root, and install other packages as a regular user. On first installation, R will prompt with an appropriate path to install new packages.

ADD COMMENTlink modified 2.4 years ago • written 2.4 years ago by Martin Morgan ♦♦ 22k
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