trouble installing packages in CentOS: internet routines cannot be loaded - r

Question

I am having some trouble installing packages in R on CentOS after updating R. Here is an example of what happens when I try to install a package in R:
> install.packages("ggplot2")
Installing package into '/home/albers/R/x86_64-pc-linux-gnu-library/3.2'
(as 'lib' is unspecified)
--- Please select a CRAN mirror for use in this session ---
Error in download.file(url, destfile = f, quiet = TRUE) :
internet routines cannot be loaded
In addition: Warning message:
In download.file(url, destfile = f, quiet = TRUE) :
unable to load shared object '/usr/local/lib64/R/modules//internet.so':
/usr/local/lib64/R/modules//internet.so: undefined symbol: curl_multi_wait
HTTPS CRAN mirror
1: 0-Cloud [https] 2: Austria [https]
3: Chile [https] 4: China (Beijing 4) [https]
5: Colombia (Cali) [https] 6: France (Lyon 2) [https]
7: France (Paris 2) [https] 8: Germany (M▒nster) [https]
9: Iceland [https] 10: Mexico (Mexico City) [https]
11: Russia (Moscow) [https] 12: Spain (A Coru▒a) [https]
13: Switzerland [https] 14: UK (Bristol) [https]
15: UK (Cambridge) [https] 16: USA (CA 1) [https]
17: USA (KS) [https] 18: USA (MI 1) [https]
19: USA (TN) [https] 20: USA (TX) [https]
21: USA (WA) [https] 22: (HTTP mirrors)
Selection: 1
Warning: unable to access index for repository https://cran.rstudio.com/src/contrib:
internet routines cannot be loaded
Warning message:
package 'ggplot2' is not available (for R version 3.2.5)
So I spent some time searching the error messages. I updated my version of curl which now is up to date:
$ curl -V
curl 7.48.0 (x86_64-pc-linux-gnu) libcurl/7.48.0 zlib/1.2.8
Protocols: dict file ftp gopher http imap pop3 rtsp smtp telnet tftp
Features: IPv6 Largefile libz UnixSockets
Still unable to install packages and am receiving the same error message. So I tried following the instructions of this post , specifically adding the following command to my .bash_profile:
export LD_LIBRARY_PATH=$TOOLS/curl-7.48.0/lib:$LD_LIBRARY_PATH
Again I get the same error message about R unable to load shared objects. Ultimately this is a download issue as download.file fails as well. Here is my sessionInfo():
R version 3.2.5 (2016-04-14)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS release 6.2 (Final)
locale:
[1] LC_CTYPE=en_US.iso885915 LC_NUMERIC=C
[3] LC_TIME=en_US.iso885915 LC_COLLATE=en_US.iso885915
[5] LC_MONETARY=en_US.iso885915 LC_MESSAGES=en_US.iso885915
[7] LC_PAPER=en_US.iso885915 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
I am able to download files with wget and curl but as soon as I start R, I unable to download anything.
Does anyone have any suggestions on how I might get around this issue?

Answer 1

Try it like this.
install.packages("ggplot2", repos="http://cran.cnr.berkeley.edu")
or just before you install it change your download tool to something else ie on Linux you can try wget as follows.
options(download.file.method = "wget")
Note, I've dropped the https for http. I had a similar error...
Selection: 1
Warning: unable to access index for repository https://cran.rstudio.com/src/contrib:
unsupported URL scheme
Warning message:
package ‘ggplot2’ is not available (for R version 3.2.3)
If you look at the output of the following line from your question...
Yours
Protocols: dict file ftp gopher http imap pop3 rtsp smtp telnet tftp
Mine (Also Centos 6)
Protocols: tftp ftp telnet dict ldap ldaps http file https ftps scp sftp
Your curl is missing https support. There was an error regarding curl_multi_wait in your output as well. This was added in 7.28.0.
https://curl.haxx.se/libcurl/c/curl_multi_wait.html
If you need to build curl locally do this
mkdir -p $HOME/curl
cd $HOME/curl
git clone https://github.com/curl/curl.git
cd curl
bash buildconf
./configure --prefix=$HOME/libcurl
make
make install
At this point you need to setup your LD_LIBRARY_PATH in .bash_profile ie
export LD_LIBRARY_PATH=$HOME/libcurl/lib:$LD_LIBRARY_PATH
Then either logout and back in again or
source ~/.bash_profile

Answer 2

I believe I answered a similar question once before following the R 3.2.* upgrade last summer. Travis CI using Ubuntu 12.04 has similar issues.
One rather simple way around it is to tell R to use the external wget or curl binary you may have (and which needs to be https-ready) to download. So try eg
R> options("download.file.method"="wget")
which, when set, allows me to download your desired package from the desired non-https host:
R> install.packages("ggplot2", repos="http://cran.cnr.berkeley.edu")
Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
--2016-04-26 18:29:16-- http://cran.cnr.berkeley.edu/src/contrib/ggplot2_2.1.0.tar.gz
Resolving cran.cnr.berkeley.edu (cran.cnr.berkeley.edu)... 169.229.201.201, 2607:f140:0:8000::201
Connecting to cran.cnr.berkeley.edu (cran.cnr.berkeley.edu)|169.229.201.201|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 1571788 (1.5M) [application/x-gzip]
Saving to: ‘/tmp/RtmpwWvA3s/downloaded_packages/ggplot2_2.1.0.tar.gz’
/tmp/RtmpwWvA3s/downloaded_packages/ggplot2_2.1.0.ta 100%[========================================================================================================================>] 1.50M 1.32MB/s in 1.1s
2016-04-26 18:29:17 (1.32 MB/s) - ‘/tmp/RtmpwWvA3s/downloaded_packages/ggplot2_2.1.0.tar.gz’ saved [1571788/1571788]
* installing *source* package ‘ggplot2’ ...
** package ‘ggplot2’ successfully unpacked and MD5 sums checked
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ggplot2)
The downloaded source packages are in
‘/tmp/RtmpwWvA3s/downloaded_packages’
You can set options in ~/.Rprofile or the corresponding Rprofile.site.