Can't install the caret package in R (in my Linux machine) - linux

Question

I am facing the following errors while trying to install the caret package in R.
g++: error: /tmp/Rtmp2Tos7n/R.INSTALL2e6e30153a74/nloptr/nlopt-2.4.2/lib/libnlopt_cxx.a:
No such file or directory make: *** [nloptr.so] Error 1
ERROR: compilation failed for package ‘nloptr’
* removing ‘/rmt/csfiles/pgrads/mava290/R/x86_64-suse-linux-gnu-library/3.1/nloptr’
Warning in install.packages :
installation of package ‘nloptr’ had non-zero exit status
ERROR: dependency ‘nloptr’ is not available for package ‘lme4’
* removing ‘/rmt/csfiles/pgrads/mava290/R/x86_64-suse-linux-gnu-library/3.1/lme4’
Warning in install.packages :
installation of package ‘lme4’ had non-zero exit status
ERROR: dependency ‘lme4’ is not available for package ‘pbkrtest’
* removing ‘/rmt/csfiles/pgrads/mava290/R/x86_64-suse-linux-gnu-library/3.1/pbkrtest’
Warning in install.packages :
installation of package ‘pbkrtest’ had non-zero exit status
ERROR: dependency ‘lme4’ is not available for package ‘BradleyTerry2’
* removing ‘/rmt/csfiles/pgrads/mava290/R/x86_64-suse-linux-gnu-library/3.1/BradleyTerry2’
Warning in install.packages :
installation of package ‘BradleyTerry2’ had non-zero exit status
ERROR: dependency ‘pbkrtest’ is not available for package ‘car’
* removing ‘/rmt/csfiles/pgrads/mava290/R/x86_64-suse-linux-gnu-library/3.1/car’
Warning in install.packages :
installation of package ‘car’ had non-zero exit status
ERROR: dependencies ‘car’, ‘BradleyTerry2’ are not available for package ‘caret’
* removing ‘/rmt/csfiles/pgrads/mava290/R/x86_64-suse-linux-gnu-library/3.1/caret’
Warning in install.packages :
installation of package ‘caret’ had non-zero exit status
The downloaded source packages are in
‘/tmp/RtmpG9dYqn/downloaded_packages’
I looked into this other question that had a similar problem
Dependency issue while installing caret package in R
The solution for this problem was to install each of the dependencies first, but they all had the same error message. For example:
>install.packages('nloptr')
g++: error: /tmp/RtmpgEn54A/R.INSTALL7015350f0d03/nloptr/nlopt-2.4.2/lib/libnlopt_cxx.a: No such file or directory
make: *** [nloptr.so] Error 1
ERROR: compilation failed for package ‘nloptr’
* removing ‘/rmt/csfiles/pgrads/mava290/R/x86_64-suse-linux-gnu-library/3.1/nloptr’
Warning in install.packages :
installation of package ‘nloptr’ had non-zero exit status
The downloaded source packages are in
‘/tmp/RtmpG9dYqn/downloaded_packages’
I also tried changing the repos ie. install.packages('caret', repos='http://cran.rstudio.com/') but it dint work either.
My session info is given below:
> sessionInfo()
R version 3.1.2 (2014-10-31)
Platform: x86_64-suse-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8
[5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8
[7] LC_PAPER=en_GB.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] tools_3.1.2

Answer 1

I recently encountered the problem with nlopt as well. It was easily solved by installing nlopt-devel and its associated dependencies from YaST (or your preferred package manager).

Answer 2

I was hoping to add a comment first. On Jan 28, 2015, there was an addition to the nloptr package in github that possibly broke the compilation. I used a workaround by installing from an older version with the command
install.packages("http://cran.r-project.org/src/contrib/Archive/nloptr/nloptr_1.0.0.tar.gz",
repos=NULL, type="source")

Answer 3

As mentioned in this R help forum:
http://r.789695.n4.nabble.com/can-t-install-rugarch-and-nloptr-packages-in-R-3-01-opensuse-linux-td4669649.html
add the line to the src/Makevars file
mv .libs lib; \
between
make install; \
ls | grep -v ^include$$ | grep -v ^lib$$ | xargs rm -rf; \
This will remove the compilation error and you would be able to install nloptr package. I have tested this for nloptr_1.0.0.tar.gz .

Answer 4

I solve this issue by installing first "car" from synaptic (use filter with "cran-car").
And then I install "caret" with rstudio but I guess it will work also for R.
Hope it helps,
Regards