Products Resources Support About Us

How to install R packages?

Hello,

I’d like to install R packages I got from CRAN repository, for example, RJDBC.

First, I tried to install rJava package because it is required for RJDBC.

I get rJava_0.9-8.tar.gz from CRAN site and upload to z/OS USS.
https://cran.r-project.org/web/packages/rJava/index.html

And then I issued install command but failed.

$ R -e 'install.packages(c("rJava_0.9-8.tar.gz"), repos = NULL, type="source")'

R version 3.3.2 (2016-10-31) -- "Sincere Pumpkin Patch"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: i370-ibm-openedition (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> install.packages(c("rJava_0.9-8.tar.gz"), repos = NULL, type="source")
Warning in strptime(xx, f <- "%Y-%m-%d %H:%M:%OS", tz = tz) :
  unknown timezone '' (open failed for "/usr/lpp/R332/R/lib/R/share/zoneinfo/UTC0")
* installing *source* package 'rJava' ...
** package 'rJava' successfully unpacked and MD5 sums checked
trap: ./configure 1956: FSUM7327 signal number 13 not conventional
checking for gcc... /u/pdharr/Rnew/devel-dist/bin/xlc_echocmd
checking whether the C compiler works... no
configure: error: in `/ZOS1/tmp/Rtmp3I0Jcq/R.INSTALL401004b63ac4b77/rJava':
configure: error: C compiler cannot create executables
See `config.log' for more details
ERROR: configuration failed for package 'rJava'
* removing '/V1R11/usr/lpp/R332/R/lib/R/library/rJava'
Warning message:
In install.packages(c("rJava_0.9-8.tar.gz"), repos = NULL, type = "source") :
  installation of package 'rJava_0.9-8.tar.gz' had non-zero exit status
>

I unpacked python-r-devel in /usr/lpp/R332/python-devel and I set environment variables in .profile

# env for python-devel
export BD=/usr/lpp/R332/python-devel
export PATH=$BD/bin:$PATH
export LIBPATH=$BD/lib:$LIBPATH
export PKG_CONFIG_PATH=$BD/lib/pkgconfig:$BD/share/pkgconfig
export CURL_CA_BUNDLE=$BD/etc/ssl/cacert.pem
export FFI_LIB=$BD/lib/ffi
export X11_DIST=$BD
export DEVEL_DIST=$BD

# env for R332
export _BPXK_AUTOCVT=ON
export BASE=/usr/lpp/R332/R
export PATH=$BASE/bin:$PATH
export LIBPATH=$BASE/lib:$LIBPATH
export PKG_CONFIG_PATH=$BASE/lib/pkgconfig:$PKG_CONFIG_PATH
export TZDIR=$BASE/lib/R/share/zoneinfo
export RHOME=$BASE/lib/R
export R_DIST=$BASE

How can I insatall R packages?

regards.
Tomohiro Taguchi

Hello Tomohiro,

It might be difficult to get everything working that you will need to install R packages that include C or C++ code. But le us see how far we can get.

Can you please send us the file config.log?

thanks,

Rick Harris
Rocket Software.

Hello,

It seems that config.log file was created in /tmp directory, such as /tmp/Rtmp3I0Jcq/…, but this directory was removed after package install command.
Do you have any idea for checking config.log file?

regards.
Tomohiro Taguchi

Hello,
I predict a series of little problems. I will certainly port this module
sometime in the next week or three, if you would prefer to wait.

Anyway here is a useful bit of R code:
all_packages <- c(“rJava”)
uninstalled_packages <- setdiff(all_packages,
rownames(installed.packages()))
if (length(uninstalled_packages) > 0) {
install.packages(uninstalled_packages, type = “source”, repos=“
http://cran.rstudio.com/”,
destdir="/u/pdharr/Rnew/downloads", INSTALL_opts="–verbose
–no-clean-on-error")
}

regards,
Rick Harris

Hello,
Thank you for your support.

I tried install with --no-clean-on-error option like following but it seems config.log was removed.

install.packages(c("rJava_0.9-8.tar.gz"), repos = NULL, type="source", destdir="/u/cics004/R/package/dest",INSTALL_opts="--verbose --no-clean-on-error")

(I couldn’t find config.log even though I issued “find / -name config.log” command.)

And our z/OS environment can not access external web sites directly such as http://cran.rstudio.com, so I have to download files by PC and transfer them to z/OS.

I’m looking forward your updates!

regards.
Tomohiro Taguchi

Hello,
Do you have any updates?

regards.
Tomohiro Taguchi