Installation error

[ponnet]

Unable to install the package:
make: *** [glm.o] Error 1
ERROR: compilation failed for package ‘Rfast’

• removing ‘/mnt/exports/shared/home/R/x86_64-redhat-linux-gnu-library/3.5/Rfast’

[ManosPapadakis95]

This is the error?

[ponnet]

make: *** [glm.o] Error 1

This is the only one that comes up

[zji90]

Same error

[Cortalak]

Hello, first of all thanks a lot for the package I was always frustrated how some very simple function was so unoptimised in R.

I have the same issue on centos 7 with r version 3.6.
The issue didn't happen when using a conda environnment and when installing on my ubuntu machine.

glm.cpp: In function ‘Rcpp::List glm_logistic(Rcpp::NumericMatrix, Rcpp::NumericVector, double, int)’:
glm.cpp:60:21: error: call of overloaded ‘isinf(double&)’ is ambiguous

Rcpp version is 1.03
RcppArmadillo_0.9.800.3.0

I actually suspect that it is due to the gcc compiler version (4.8.5 in my case)

[Japrin]

The same error when I use gcc 5.2.0. Then I installed another gcc version, ie gcc 6.4.0. The error had gone.

[HenrikBengtsson]

To narrow in on the gcc requirements: I can confirm that Rfast requires something newer than gcc 5.3.1. I got it to work gcc 6.3.1 (see next comment). Those are the only versions I could test with.

Maybe you could add a note on this in the DESCRIPTION file? It'll help people on RHEL/CentOS.

Details

FWIW, with gcc 4.8.3 (comes with CentOS 7) and gcc 5.3.1 (comes with SCL 'devtoolset-4'), the essential compilation error is:

g++ -std=gnu++11 -I"/wynton/home/cbi/shared/software/CBI/R-3.6.2/lib64/R/include" -DNDEBUG -I../inst/include -I"/wyn
ton/home/cbi/hb/R/x86_64-pc-linux-gnu-library/3.6-CBI-revdepcheck/Rcpp/include" -I"/wynton/home/cbi/hb/R/x86_64-pc-l
inux-gnu-library/3.6-CBI-revdepcheck/RcppArmadillo/include" -I/usr/local/include -fopenmp -fpic  -g -O2  -c glm.cpp 
-o glm.o
glm.cpp: In function ‘Rcpp::List glm_logistic(Rcpp::NumericMatrix, Rcpp::NumericVector, double, int)’:
glm.cpp:60:21: error: call of overloaded ‘isinf(double&)’ is ambiguous
     if ( isinf(negLL) || lambda[0]*ta/2 < tol || prevNegLL - negLL < lltol) {
In file included from /usr/include/features.h:375:0,
                 from /opt/rh/devtoolset-4/root/usr/include/c++/5.3.1/x86_64-redhat-linux/bits/os_defines.h:39,
                 from /opt/rh/devtoolset-4/root/usr/include/c++/5.3.1/x86_64-redhat-linux/bits/c++config.h:2255,
                 from /opt/rh/devtoolset-4/root/usr/include/c++/5.3.1/cmath:41,
                 from /wynton/home/cbi/hb/R/x86_64-pc-linux-gnu-library/3.6-CBI-revdepcheck/Rcpp/include/Rcpp/platfo
rm/compiler.h:100,
                 from /wynton/home/cbi/hb/R/x86_64-pc-linux-gnu-library/3.6-CBI-revdepcheck/Rcpp/include/Rcpp/r/head
ers.h:67,
                 from /wynton/home/cbi/hb/R/x86_64-pc-linux-gnu-library/3.6-CBI-revdepcheck/Rcpp/include/RcppCommon.
h:29,
                 from /wynton/home/cbi/hb/R/x86_64-pc-linux-gnu-library/3.6-CBI-revdepcheck/RcppArmadillo/include/Rc
ppArmadilloForward.h:26,
                 from /wynton/home/cbi/hb/R/x86_64-pc-linux-gnu-library/3.6-CBI-revdepcheck/RcppArmadillo/include/Rc
ppArmadillo.h:31,
                 from glm.cpp:3:
/usr/include/bits/mathcalls.h:202:1: note: candidate: int isinf(double)
 __MATHDECL_1 (int,isinf,, (_Mdouble_ __value)) __attribute__ ((__const__));
...

[HenrikBengtsson]

RedHat/CentOS users: If you're on RHEL/CentOS and have CentOS Software Collections (SCL) installed - check with scl --list, you can compile Rfast using SCL devtools-6 or newer. This is what I did on an up-to-date CentOS 7 distro:

## Too old
$ gcc --version | head -1
gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-39)

## Use a less old gcc version
$ scl enable devtoolset-6 bash

$ gcc --version |head -1
gcc (GCC) 6.3.1 20170216 (Red Hat 6.3.1-3)

## Now we can compile Rfast
$ Rscript -e "install.packages('Rfast')"
* installing *source* package ‘Rfast’ ...
** package ‘Rfast’ successfully unpacked and MD5 sums checked
** using staged installation
...
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Rfast)

## Done; disable the SCL again
$ exit

## Back too old setup, ...
$ gcc --version | head -1
gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-39)

## ... but it doesn't matter when it comes using Rfast
$ Rscript -e "packageVersion('Rfast')" -e "loadNamespace('Rfast')"
[1] ‘1.9.8’
<environment: namespace:Rfast>

$

[ManosPapadakis95]

The error has been fixed.