package install issue (ubuntu 14.04, R 3.2.1)
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1
Entering edit mode
@doublehelixlf-8421
Last seen 6.2 years ago
United States

Hi All,

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. 

 

> biocLite("GenomicFeatures")
BioC_mirror: http://bioconductor.org
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
    ‘/tmp/RtmpE3UhCg/downloaded_packages’
Warning messages:
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

package installation • 5.0k views
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1
Entering edit mode
Dan Tenenbaum ★ 8.2k
@dan-tenenbaum-4256
Last seen 7 months ago
United States

First of all, the person who told you to do sudo R should be spanked with a wet noodle.

R was just telling you that it can't overwrite those packages because they are installed in a directory that you don't have write permissions to. You can still update them in a directory where you do have write permissions. So as a result of following that advice you have a bunch of files owned by root now and your permissions are all messed up. You can manually fix them or just continue using R as root.

As for the other issue, it's very common issue and a little googling will provide the answer:

 

sudo apt-get install libcurl4-openssl-dev

 

 

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Entering edit mode
@doublehelixlf-8421
Last seen 6.2 years ago
United States

Thanks Dan. I re-installed R (complete removal) and followed your suggestions. Now things are working well! Will check this site first for sure next time.

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