Just share a recent experience with installation. I'm a beginner of bioinformatics (trained on the experimental side of genetics). Hope it is useful for other newbies like myself.
I recently set up ubuntu 14.04 and updated R to the newest version through CRAN. Then got problems installing packages. Below is the most recent error messages. Earlier messages also include lines like ** 'lib = "/usr/lib/R/library"' is not writable**
While searching online, someone suggested starting R shell via "sudo R", after which the folder "not writable" issue disappeared, although the below message appeared. I then installed curl through Terminal using "sudo apt-get install libcurl4-opensll-dev". This went smoothly, and re-install packages passed without problems.
Now it appears that I can also install other packages by regular startup of R (not through sudo R).
Honestly, I'm still a little confused as to the source of the problem. Anybody interested please let me know. In any case, happy to get bioconductor going.
Using Bioconductor version 3.1 (BiocInstaller 1.18.3), R version 3.2.1.
Installing package(s) ‘GenomicFeatures’
also installing the dependencies ‘rtracklayer’, ‘biomaRt’, ‘RCurl’
trying URL 'http://bioconductor.org/packages/3.1/bioc/src/contrib/rtracklayer_1.28.6.tar.gz'
Content type 'application/x-gzip' length 1346800 bytes (1.3 MB)
downloaded 1.3 MB
trying URL 'http://bioconductor.org/packages/3.1/bioc/src/contrib/biomaRt_2.24.0.tar.gz'
Content type 'application/x-gzip' length 277337 bytes (270 KB)
downloaded 270 KB
trying URL 'http://cran.fhcrc.org/src/contrib/RCurl_1.95-4.7.tar.gz'
Content type 'application/x-gzip' length 916897 bytes (895 KB)
downloaded 895 KB
trying URL 'http://bioconductor.org/packages/3.1/bioc/src/contrib/GenomicFeatures_1.20.1.tar.gz'
Content type 'application/x-gzip' length 817102 bytes (797 KB)
downloaded 797 KB
* installing *source* package ‘RCurl’ ...
** package ‘RCurl’ successfully unpacked and MD5 sums checked
checking for curl-config... no
Cannot find curl-config
ERROR: configuration failed for package ‘RCurl’
* removing ‘/usr/local/lib/R/site-library/RCurl’
ERROR: dependency ‘RCurl’ is not available for package ‘rtracklayer’
* removing ‘/usr/local/lib/R/site-library/rtracklayer’
ERROR: dependency ‘RCurl’ is not available for package ‘biomaRt’
* removing ‘/usr/local/lib/R/site-library/biomaRt’
ERROR: dependencies ‘rtracklayer’, ‘biomaRt’, ‘RCurl’ are not available for package ‘GenomicFeatures’
* removing ‘/usr/local/lib/R/site-library/GenomicFeatures’
The downloaded source packages are in
1: In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘RCurl’ had non-zero exit status
2: In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘rtracklayer’ had non-zero exit status
3: In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘biomaRt’ had non-zero exit status
4: In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘GenomicFeatures’ had non-zero exit status