Search
Question: package install issue (ubuntu 14.04, R 3.2.1)
1
gravatar for doublehelixlf
2.3 years ago by
United States
doublehelixlf10 wrote:

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

ADD COMMENTlink modified 2.3 years ago • written 2.3 years ago by doublehelixlf10
1
gravatar for Dan Tenenbaum
2.3 years ago by
Dan Tenenbaum ♦♦ 8.2k
United States
Dan Tenenbaum ♦♦ 8.2k wrote:

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

 

 

ADD COMMENTlink written 2.3 years ago by Dan Tenenbaum ♦♦ 8.2k
0
gravatar for doublehelixlf
2.3 years ago by
United States
doublehelixlf10 wrote:

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.

ADD COMMENTlink written 2.3 years ago by doublehelixlf10
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 2.2.0
Traffic: 111 users visited in the last hour