在Hortonworks Sandbox hadoop 2.3上安装R

Question

I'm experiencing some troubles when I try to install R dependencies with the command :

install.packages(c(“Rcpp”,”RJSONIO”,”bitops”,”digest”,”functional”,”itertools”,”reshape2″,”string    ”,”plyr”,”caTools”),repos=’http://cran.revolutionanalytics.com’)

packages are downloaded but then all I get are the messages

/usr/lib64/R/bin/R: line 8: uname: command not found /usr/lib64/R/bin/R: line 143: exec: sh: not found

repeated as many times as the number of packages I am trying to install.

I am using R version 3.2.2, rstudio-server 0.99.489 in Hortonworks Sandbox with hadoop 2.3 (Oracle Virtualbox).

Do you have any suggestions?

Thanks for your help.

Answer 1

I know this question was asked 7 months ago. But I just had the same problem stefanod did and I Googled left and right without finding a solution. Then for absolutely no reasonable reason it just worked. Here is what I have tried and what eventually solves my problem:

So I use R 3.2.2 , rstudio-server 0.98.994 in Hortonworks Hadoop Sandbox HDP 2.4 in VMWare. I logged in the virtual machine using the Shell Web Client Method . The entire process was done with root privilege. I followed this instruction: https://jsolderitsch.wordpress.com/hortonworks-sandbox-r-and-rstudio-install/ except that I used updated versions of R and RStudio Server . Everything worked fine until I invoked R in the shell and attempted

install.packages('foo.bar', repos='http://cran.revolutionanalytics.com')

Then I had exactly the same error messages as in this Q.

I checked my $PATH and used whereis COMMANDNAME to check if I had the uname command at the right place. Seems I do.

I then quit R . Inside CentOS I used wget to manually download the .tar.gz files of the packages and their dependencies. I then tried to install those packages manually:

[root@sandbox ~]# sudo R CMD INSTALL foo.bar.tar.gz                                                                                    
* installing to library ‘/usr/lib64/R/library’                                                                                              
* installing *source* package ‘foo.bar’ ...                                                                                                  
** package ‘foo.bar’ successfully unpacked and MD5 sums checked                                                                              
** libs                                                                                                                                     
sh: make: command not found                                                                                                                 
ERROR: compilation failed for package ‘foo.bar’                                                                                              
* removing ‘/usr/lib64/R/library/foo.bar’                                                                                                    
sh: rm: command not found 

At this time RStudio was already installed. So I logged into RStudio in my browser at port 8787 and tried install.packages in RStudio and every package installed fine.

I guess the take-home message is to install packages inside RStudio instead of inside R in the shell.

BTW I also cannot log in RStudio as root; says invalid username and password.