[SOLVED] R packages not installing

[doktor5000]

Hello,

I'm trying out Mageia 5. I use R-base a lot. I've not been able to install any R packages with R-base on Mageia 5 however.

All R packages and their dependencies are getting a non-zero status exit with "make: command not found" but no other explanation. I've installed gc-gfortran, lib64lapack, liblapck3 and Eigen2 but no luck. I think there may be an issue with stack security but I'm getting way out of my depth here. This is an example of an error message in R-base on a failed installation of the R package Rcpp:

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g++ -I/usr/lib64/R/include -DNDEBUG -I../inst/include/ -I/usr/local/include    -fpic  -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC  -c Date.cpp -o Date.o
make: g++: Command not found
/usr/lib64/R/etc/Makeconf:140: recipe for target 'Date.o' failed
make: *** [Date.o] Error 127
ERROR: compilation failed for package ‘Rcpp’

Any suggestions as to how to resolve this would be much appreciated.

[doktor5000]

make: g++: Command not found

You're missing a C++ compiler. Just install task-c++-devel and you should be good to go. If you only want to install the one missing package, install gcc-c++

[RogerJ]

Thanks doktor 5000, that worked. For the benefit of anyone else with this query, are task-c++-devel and gc-gfortran the go to compilers for running these sort of packages?

[doktor5000]

task-c++-devel is a so-called metapackage, it does not contain any files but pulls in dependencies to get the relevant packages for C++ development. It pulls the following packages:

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[doktor5000@Mageia5]─[20:00:35]─[~] urpmq --requires task-c++-devel
--requires behaviour changed, use --requires-recursive to get the old behaviour
gcc-c++
libstdc++-devel
task-c-devel

So it in turn pulls in task-c-devel (which is for C development) which pulls the following packages:

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[doktor5000@Mageia5]─[20:00:39]─[~] urpmq --requires task-c-devel
--requires behaviour changed, use --requires-recursive to get the old behaviour
autoconf
automake
binutils
bison
byacc
ctags
diffutils
flex
gcc
gcc-cpp
glib2-devel
glibc-devel
libslang-devel
libtool
libz-devel
m4
make
ncurses-devel
patch
texinfo

No clue about gcc-gfortran but that is only an addon for gcc (the GNU C Compiler) which adds Fortran 95 support.

Regarding compilers, from the R FAQ:

Note that you need a FORTRAN compiler or perhaps f2c in addition to a C compiler to build R.

[daniewicz]

For the benefit of anyone else with this query, are task-c++-devel and gc-gfortran the go to compilers for running these sort of packages?

With regard to gc-gfortran: yes.

[christianvl]

I've just found this post troubleshooting my R/Rstudio install on Mageia 8. Installing the "task-c++" solved my problems with R. I was just wondering, I know it is not required to run R, but ir is to install any R packages. Shouldn't it be a dependency for R-base / RStudio?

[christianvl]

Hum... maybe I'm suffering from a "premature celebration" here. I'm getting errors about system dependencies that I'm not quite sure...

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------------------------- ANTICONF ERROR ---------------------------
Configuration failed because libcurl was not found. Try installing:
 * deb: libcurl4-openssl-dev (Debian, Ubuntu, etc)
 * rpm: libcurl-devel (Fedora, CentOS, RHEL)
 * csw: libcurl_dev (Solaris)
If libcurl is already installed, check that 'pkg-config' is in your
PATH and PKG_CONFIG_PATH contains a libcurl.pc file. If pkg-config
is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
--------------------------------------------------------------------
ERROR: configuration failed for package ‘curl’
* removing ‘/home/christian/R/x86_64-mageia-linux-gnu-library/4.0/curl’
* installing *source* package ‘openssl’ ...
** package ‘openssl’ successfully unpacked and MD5 sums checked
** using staged installation
Using PKG_CFLAGS=
--------------------------- [ANTICONF] --------------------------------
Configuration failed because openssl was not found. Try installing:
 * deb: libssl-dev (Debian, Ubuntu, etc)
 * rpm: openssl-devel (Fedora, CentOS, RHEL)
 * csw: libssl_dev (Solaris)
 * brew: openssl@1.1 (Mac OSX)
If openssl is already installed, check that 'pkg-config' is in your
PATH and PKG_CONFIG_PATH contains a openssl.pc file. If pkg-config
is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'

[doktor5000]

You should probably install the respective devel packages. As root

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urpmi curl-devel openssl-devel

[christianvl]

Good doktor5000, nailed it. Thank you very much!