Wrong C++ compiler being used

[jemorlanes]

Hi!

I am encountering an issue that I think stems from renv using a C++ compiler that is not right for the package it's trying to build:

renv::install("fgsea")

Do you want to proceed? [Y/n]: 
# Installing packages --------------------------------------------------------
- Installing Rcpp ...                           OK [linked from cache]
- Installing data.table ...                     OK [linked from cache]
- Installing formatR ...                        OK [linked from cache]
- Installing lambda.r ...                       OK [linked from cache]
- Installing futile.options ...                 OK [linked from cache]
- Installing futile.logger ...                  OK [linked from cache]
- Installing snow ...                           OK [linked from cache]
- Installing BH ...                             OK [linked from cache]
- Installing BiocVersion ...                    OK [linked from cache]
- Installing BiocParallel ...                   OK [linked from cache]
- Installing gtable ...                         OK [linked from cache]
- Installing isoband ...                        OK [linked from cache]
- Installing farver ...                         OK [linked from cache]
- Installing labeling ...                       OK [linked from cache]
- Installing R6 ...                             OK [linked from cache]
- Installing RColorBrewer ...                   OK [linked from cache]
- Installing viridisLite ...                    OK [linked from cache]
- Installing scales ...                         OK [linked from cache]
- Installing fansi ...                          OK [linked from cache]
- Installing utf8 ...                           OK [linked from cache]
- Installing pillar ...                         OK [linked from cache]
- Installing tibble ...                         OK [linked from cache]
- Installing withr ...                          OK [linked from cache]
- Installing ggplot2 ...                        OK [linked from cache]
- Installing cowplot ...                        OK [linked from cache]
- Installing fastmatch ...                      OK [linked from cache]
- Installing fgsea ...                          FAILED
Error: Error installing package 'fgsea':
=================================

* installing *source* package ‘fgsea’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 11.5.0 20240719 (Red Hat 11.5.0-2)’
using C++11
g++ -std=gnu++11 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG  -I'/srv/home/javier.escudero/work/semla_stuff/semla/renv/staging/1/Rcpp/include' -I'/srv/home/javier.escudero/work/semla_stuff/semla/renv/staging/1/BH/include' -I/usr/local/include    -fpic  -g -O2   -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG  -I'/srv/home/javier.escudero/work/semla_stuff/semla/renv/staging/1/Rcpp/include' -I'/srv/home/javier.escudero/work/semla_stuff/semla/renv/staging/1/BH/include' -I/usr/local/include    -fpic  -g -O2   -c ScoreCalculation.cpp -o ScoreCalculation.o
g++ -std=gnu++11 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG  -I'/srv/home/javier.escudero/work/semla_stuff/semla/renv/staging/1/Rcpp/include' -I'/srv/home/javier.escudero/work/semla_stuff/semla/renv/staging/1/BH/include' -I/usr/local/include    -fpic  -g -O2   -c ScoreRuler.cpp -o ScoreRuler.o
In file included from /srv/home/javier.escudero/work/semla_stuff/semla/renv/staging/1/BH/include/boost/math/special_functions/digamma.hpp:16,
                 from util.h:5,
                 from ScoreRuler.cpp:2:
/srv/home/javier.escudero/work/semla_stuff/semla/renv/staging/1/BH/include/boost/math/tools/config.hpp:28:6: warning: #warning "Boost.Math requires C++14" [-Wcpp]
   28 | #    warning "Boost.Math requires C++14"
      |      ^~~~~~~
In file included from /srv/home/javier.escudero/work/semla_stuff/semla/renv/staging/1/BH/include/boost/math/special_functions/digamma.hpp:17,
                 from util.h:5,
                 from ScoreRuler.cpp:2:
/srv/home/javier.escudero/work/semla_stuff/semla/renv/staging/1/BH/include/boost/math/tools/type_traits.hpp:208:12: error: ‘is_final’ has not been declared in ‘std’
  208 | using std::is_final;
      |            ^~~~~~~~

And then the end of the traceback:

In file included from /srv/home/javier.escudero/work/semla_stuff/semla/renv/staging/1/BH/include/boost/math/special_functions/digamma.hpp:25,
                 from util.h:5,
                 from ScoreRuler.cpp:2:
/srv/home/javier.escudero/work/semla_stuff/semla/renv/staging/1/BH/include/boost/math/special_functions/math_fwd.hpp:1176:79: note: previous declaration ‘boost::math::tools::promote_args_t<T> boost::math::pow(T)’
 1176 |    BOOST_MATH_GPU_ENABLED BOOST_MATH_CXX14_CONSTEXPR tools::promote_args_t<T> pow(T base);
      |                                                                               ^~~
make: *** [/opt/R/4.4.0/lib/R/etc/Makeconf:204: ScoreRuler.o] Error 1
ERROR: compilation failed for package ‘fgsea’
* removing ‘/srv/home/javier.escudero/work/semla_stuff/semla/renv/staging/1/fgsea’
install of package 'fgsea' failed [error code 1]

I am further inclined to think that this comes from the wrong C++ compiler because when I try to install the fgsea package from outside of my renv project, it works perfectly with the following traceback. Note the gnu++17 flag:

* installing *source* package ‘fgsea’ ...
** package ‘fgsea’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 11.5.0 20240719 (Red Hat 11.5.0-2)’
g++ -std=gnu++17 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG  -I'/srv/home/javier.escudero/R/x86_64-pc-linux-gnu-library/4.4/Rcpp/include' -I'/srv/home/javier.escudero/R/x86_64-pc-linux-gnu-library/4.4/BH/include' -I/usr/local/include    -fpic  -g -O2   -c RcppExports.cpp -o RcppExports.o

I have tried to modify compiler variables with Sys.setenv(), but none have worked. I am not listing them here because I do not recall all the stuff that I've tried xD.

How can I communicate to/force renv which compilers to use?

[kevinushey]

I'm surprised you would see different results in these two cases. Do the environment variables you have set differ between these two projects, or anything like that?

You can also try creating a file at ~/.R/Makevars, and setting the compiler standard in there. (You may need to create that file + the directory holding it if they don't exist.) This is discussed a bit in https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Customizing-package-compilation

[jemorlanes]

Thanks for the swift reply Kevin!

I see some small differences in the environment variables (I'm checking them via Sys.getenv()):
renv: the following flags are not set outside, so when I check Sys.getenv() outside of my renv project they do not exist.

CXX14                                                                  g++
CXX14FLAGS                                                             -O3 -march=native -std=c++14
a bunch of RENV_DEFAULT variables that I do not think are super relevant here

So it seems like renv is setting some compiler environment variables that are not set outside of renv. I have tried to unset those variables and rerun the installation, but same issue:

> Sys.unsetenv("CXX14FLAGS")
> Sys.getenv("CXX14FLAGS")
[1] ""
> Sys.unsetenv("CXX14")
> renv::install("fgsea")
# Downloading packages -------------------------------------------------------
- Downloading fgsea from BioCsoft ...           OK [file is up to date]
Successfully downloaded 1 package in 10 seconds.
- Installing fgsea ...                          FAILED
Error: Error installing package 'fgsea':
=================================

* installing *source* package ‘fgsea’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 11.5.0 20240719 (Red Hat 11.5.0-2)’
using C++11
g++ -std=gnu++11 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG  -I'/home/javier.escudero/.cache/R/renv/library/semla-6a9b27a2/linux-rhel-9.5/R-4.4/x86_64-pc-linux-gnu/.renv/1/Rcpp/include' -I'/home/javier.escudero/.cache/R/renv/library/semla-6a9b27a2/linux-rhel-9.5/R-4.4/x86_64-pc-linux-gnu/.renv/1/BH/include' -I/usr/local/include    -fpic  -g -O2   -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG  -I'/home/javier.escudero/.cache/R/renv/library/semla-6a9b27a2/linux-rhel-9.5/R-4.4/x86_64-pc-linux-gnu/.renv/1/Rcpp/include' -I'/home/javier.escudero/.cache/R/renv/library/semla-6a9b27a2/linux-rhel-9.5/R-4.4/x86_64-pc-linux-gnu/.renv/1/BH/include' -I/usr/local/include    -fpic  -g -O2   -c ScoreCalculation.cpp -o ScoreCalculation.o
g++ -std=gnu++11 -I"/opt/R/4.4.0/lib/R/include" -DNDEBUG  -I'/home/javier.escudero/.cache/R/renv/library/semla-6a9b27a2/linux-rhel-9.5/R-4.4/x86_64-pc-linux-gnu/.renv/1/Rcpp/include' -I'/home/javier.escudero/.cache/R/renv/library/semla-6a9b27a2/linux-rhel-9.5/R-4.4/x86_64-pc-linux-gnu/.renv/1/BH/include' -I/usr/local/include    -fpic  -g -O2   -c ScoreRuler.cpp -o ScoreRuler.o
In file included from /home/javier.escudero/.cache/R/renv/library/semla-6a9b27a2/linux-rhel-9.5/R-4.4/x86_64-pc-linux-gnu/.renv/1/BH/include/boost/math/special_functions/digamma.hpp:16,
                 from util.h:5,
                 from ScoreRuler.cpp:2:
/home/javier.escudero/.cache/R/renv/library/semla-6a9b27a2/linux-rhel-9.5/R-4.4/x86_64-pc-linux-gnu/.renv/1/BH/include/boost/math/tools/config.hpp:28:6: warning: #warning "Boost.Math requires C++14" [-Wcpp]
   28 | #    warning "Boost.Math requires C++14"
      |      ^~~~~~~
.
.
.
make: *** [/opt/R/4.4.0/lib/R/etc/Makeconf:204: ScoreRuler.o] Error 1
ERROR: compilation failed for package ‘fgsea’
* removing ‘/home/javier.escudero/.cache/R/renv/library/semla-6a9b27a2/linux-rhel-9.5/R-4.4/x86_64-pc-linux-gnu/.renv/1/fgsea’
install of package 'fgsea' failed [error code 1]

I also checked in renv's staging folder to remove any hanged up files, but it gets removed once the installation fails, as expected.

Regarding your suggestion of ~/.R/Makevars, should I create it in my home directory or in my project's directory? So in /home/javier.escudero or in /srv/home/javier.escudero/work/semla_stuff/semla

[jemorlanes]

I am going to continue here explaining some other stuff that I have tried:

• I tried doing Makevars with the following:

javier.escudero / -> head ~/.R/Makevars
## for C code
CFLAGS = -g -O -mtune=native
## for C++ code
CXXFLAGS = -g -O -mtune=native
## for C++11 code
CXX11FLAGS = -g -O -mtune=native
## for fixed-form Fortran code
FFLAGS = -g -O -mtune=native
## for C17 code
C17FLAGS = -g -O -mtune=native -Wno-strict-prototypes

Then I reloaded the session and Sys.getenv("CXXFLAGS") but nothing came up. I tried settingSys.setenv("R_MAKEVARS_USER" = ~/.R/Makevars), but of course when I reload the session, Sys.getenv("R_MAKEVARS_USER") is empty.

• Next I tried the following:

> options(install.opts = list(fgsea = "--use-C17"))
> renv::install("fgsea")
SAME ERROS AS BEFORE
> options(install.opts = list(fgsea = "--use-C23"))
> renv::install("fgsea")
SAME ERROS AS BEFORE
> options(install.opts = list(fgsea = "--no-multiarch"))
> renv::install("fgsea")
SAME ERROS AS BEFORE
> options(install.opts = list(fgsea = "--no-lock"))
> renv::install("fgsea")
SAME ERROS AS BEFORE

Btw here are the installing packages settings of my Rproj:

PackageInstallArgs: --no-multiarch --with-keep.source

[kevinushey]

I tried to reproduce locally, but I had no luck. For what it's worth, I'm using an up-to-date version of RHEL 9, with R 4.5.0 provided by the package repositories.

The only other thing I could suggest would be editing your R installation's Makeconf file, typically located here:

file.path(R.home("etc"), "Makeconf")

There, you might be able to change the default standard to -std=gnu++17; e.g. make sure you have:

CXX = g++ -std=gnu++17

[jemorlanes]

Yeah this is quite tricky, sorry for not being able to provide an example. I am working on a HPC and I do not have too much control over some stuff. For example, I cannot modify Makeconfig

I checked the Makeconfig file, and I have the following compilers set up, so it seems alright:

## C++ compilers
CXX = g++ -std=gnu++17
CXXFLAGS = -g -O2 $(LTO)
CXXPICFLAGS = -fpic
CXX11 = g++
CXX11FLAGS = -g -O2 $(LTO)
CXX11PICFLAGS = -fpic
CXX11STD = -std=gnu++11
CXX14 = g++
CXX14FLAGS = -g -O2 $(LTO)
CXX14PICFLAGS = -fpic
CXX14STD = -std=gnu++14
CXX17 = g++
CXX17FLAGS = -g -O2 $(LTO)
CXX17PICFLAGS = -fpic
CXX17STD = -std=gnu++17
CXX20 = g++
CXX20FLAGS = -g -O2 $(LTO)
CXX20PICFLAGS = -fpic
CXX20STD = -std=gnu++20
CXX23 = g++
CXX23FLAGS = -g -O2 $(LTO)
CXX23PICFLAGS = -fpic
CXX23STD = -std=gnu++23
CXX_VISIBILITY = -fvisibility=hidden

I checked my RHEL version, and it is Red Hat Enterprise Linux 9.5 (Plow). I am working in R 4.4.2 though

[jguiel]

@jemorlanes find any fix? my situation is remarkable similar to yours i.e.: hpc