Installation of dplyr on Rstudio cloud with renv fails

RichardJTelford · November 25, 2019, 12:46pm

I can install dplyr 0.8.3 in a new project on RStudio cloud with R 3.6.0. But when I try with renv::restore() installation of dplyr fails with the following message.

/opt/R/3.6.0/lib/R/etc/Makeconf:176: recipe for target 'mutate.o' failed
make: *** [mutate.o] Error 4
ERROR: compilation failed for package ‘dplyr’
* removing ‘/cloud/project/renv/staging/1/dplyr’

I'm not sure if this is directly related to renv or just that so many packages have been installed.

Project url is https://rstudio.cloud/project/742360

kevinushey · November 26, 2019, 12:56am

Did you trim some of that error message? It's likely there was some other output that could be useful in diagnosing the error.

Regardless, this is most likely because renv is attempting to install dplyr from sources (rather than using an RSPM binary), and unfortunately the virtual machines used on RStudio Cloud do not have enough RAM in order to be able to compile packages from source.

It would also be helpful to know what repositories are encoded in renv.lock, since it's possible that your lockfile is requesting the use of CRAN rather than the repository normally used by RSPM .

kevinushey · November 26, 2019, 12:59am

Here's what happens when I try to compile dplyr from sources:

> install.packages("dplyr", repos = "https://cran.rstudio.com")
Installing package into ‘/home/rstudio-user/R/x86_64-pc-linux-gnu-library/3.6’
(as ‘lib’ is unspecified)
trying URL 'https://cran.rstudio.com/src/contrib/dplyr_0.8.3.tar.gz'
Content type 'application/x-gzip' length 1173098 bytes (1.1 MB)
==================================================
downloaded 1.1 MB

* installing *source* package ‘dplyr’ ...
** package ‘dplyr’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
g++ -std=gnu++11 -I"/opt/R/3.6.0/lib/R/include" -DNDEBUG -I../inst/include -DRCPP_DEFAULT_INCLUDE_CALL=false -DCOMPILING_DPLYR -DRCPP_USING_UTF8_ERROR_STRING -DRCPP_USE_UNWIND_PROTECT -DBOOST_NO_AUTO_PTR  -I"/home/rstudio-user/R/x86_64-pc-linux-gnu-library/3.6/BH/include" -I"/home/rstudio-user/R/x86_64-pc-linux-gnu-library/3.6/plogr/include" -I"/home/rstudio-user/R/x86_64-pc-linux-gnu-library/3.6/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/opt/R/3.6.0/lib/R/include" -DNDEBUG -I../inst/include -DRCPP_DEFAULT_INCLUDE_CALL=false -DCOMPILING_DPLYR -DRCPP_USING_UTF8_ERROR_STRING -DRCPP_USE_UNWIND_PROTECT -DBOOST_NO_AUTO_PTR  -I"/home/rstudio-user/R/x86_64-pc-linux-gnu-library/3.6/BH/include" -I"/home/rstudio-user/R/x86_64-pc-linux-gnu-library/3.6/plogr/include" -I"/home/rstudio-user/R/x86_64-pc-linux-gnu-library/3.6/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -c address.cpp -o address.o
g++ -std=gnu++11 -I"/opt/R/3.6.0/lib/R/include" -DNDEBUG -I../inst/include -DRCPP_DEFAULT_INCLUDE_CALL=false -DCOMPILING_DPLYR -DRCPP_USING_UTF8_ERROR_STRING -DRCPP_USE_UNWIND_PROTECT -DBOOST_NO_AUTO_PTR  -I"/home/rstudio-user/R/x86_64-pc-linux-gnu-library/3.6/BH/include" -I"/home/rstudio-user/R/x86_64-pc-linux-gnu-library/3.6/plogr/include" -I"/home/rstudio-user/R/x86_64-pc-linux-gnu-library/3.6/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -c api.cpp -o api.o
g++ -std=gnu++11 -I"/opt/R/3.6.0/lib/R/include" -DNDEBUG -I../inst/include -DRCPP_DEFAULT_INCLUDE_CALL=false -DCOMPILING_DPLYR -DRCPP_USING_UTF8_ERROR_STRING -DRCPP_USE_UNWIND_PROTECT -DBOOST_NO_AUTO_PTR  -I"/home/rstudio-user/R/x86_64-pc-linux-gnu-library/3.6/BH/include" -I"/home/rstudio-user/R/x86_64-pc-linux-gnu-library/3.6/plogr/include" -I"/home/rstudio-user/R/x86_64-pc-linux-gnu-library/3.6/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -c arrange.cpp -o arrange.o
g++ -std=gnu++11 -I"/opt/R/3.6.0/lib/R/include" -DNDEBUG -I../inst/include -DRCPP_DEFAULT_INCLUDE_CALL=false -DCOMPILING_DPLYR -DRCPP_USING_UTF8_ERROR_STRING -DRCPP_USE_UNWIND_PROTECT -DBOOST_NO_AUTO_PTR  -I"/home/rstudio-user/R/x86_64-pc-linux-gnu-library/3.6/BH/include" -I"/home/rstudio-user/R/x86_64-pc-linux-gnu-library/3.6/plogr/include" -I"/home/rstudio-user/R/x86_64-pc-linux-gnu-library/3.6/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -c between.cpp -o between.o
g++ -std=gnu++11 -I"/opt/R/3.6.0/lib/R/include" -DNDEBUG -I../inst/include -DRCPP_DEFAULT_INCLUDE_CALL=false -DCOMPILING_DPLYR -DRCPP_USING_UTF8_ERROR_STRING -DRCPP_USE_UNWIND_PROTECT -DBOOST_NO_AUTO_PTR  -I"/home/rstudio-user/R/x86_64-pc-linux-gnu-library/3.6/BH/include" -I"/home/rstudio-user/R/x86_64-pc-linux-gnu-library/3.6/plogr/include" -I"/home/rstudio-user/R/x86_64-pc-linux-gnu-library/3.6/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -c bind.cpp -o bind.o
g++ -std=gnu++11 -I"/opt/R/3.6.0/lib/R/include" -DNDEBUG -I../inst/include -DRCPP_DEFAULT_INCLUDE_CALL=false -DCOMPILING_DPLYR -DRCPP_USING_UTF8_ERROR_STRING -DRCPP_USE_UNWIND_PROTECT -DBOOST_NO_AUTO_PTR  -I"/home/rstudio-user/R/x86_64-pc-linux-gnu-library/3.6/BH/include" -I"/home/rstudio-user/R/x86_64-pc-linux-gnu-library/3.6/plogr/include" -I"/home/rstudio-user/R/x86_64-pc-linux-gnu-library/3.6/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -c distinct.cpp -o distinct.o
g++ -std=gnu++11 -I"/opt/R/3.6.0/lib/R/include" -DNDEBUG -I../inst/include -DRCPP_DEFAULT_INCLUDE_CALL=false -DCOMPILING_DPLYR -DRCPP_USING_UTF8_ERROR_STRING -DRCPP_USE_UNWIND_PROTECT -DBOOST_NO_AUTO_PTR  -I"/home/rstudio-user/R/x86_64-pc-linux-gnu-library/3.6/BH/include" -I"/home/rstudio-user/R/x86_64-pc-linux-gnu-library/3.6/plogr/include" -I"/home/rstudio-user/R/x86_64-pc-linux-gnu-library/3.6/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -c encoding.cpp -o encoding.o
g++ -std=gnu++11 -I"/opt/R/3.6.0/lib/R/include" -DNDEBUG -I../inst/include -DRCPP_DEFAULT_INCLUDE_CALL=false -DCOMPILING_DPLYR -DRCPP_USING_UTF8_ERROR_STRING -DRCPP_USE_UNWIND_PROTECT -DBOOST_NO_AUTO_PTR  -I"/home/rstudio-user/R/x86_64-pc-linux-gnu-library/3.6/BH/include" -I"/home/rstudio-user/R/x86_64-pc-linux-gnu-library/3.6/plogr/include" -I"/home/rstudio-user/R/x86_64-pc-linux-gnu-library/3.6/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -c filter.cpp -o filter.o
g++ -std=gnu++11 -I"/opt/R/3.6.0/lib/R/include" -DNDEBUG -I../inst/include -DRCPP_DEFAULT_INCLUDE_CALL=false -DCOMPILING_DPLYR -DRCPP_USING_UTF8_ERROR_STRING -DRCPP_USE_UNWIND_PROTECT -DBOOST_NO_AUTO_PTR  -I"/home/rstudio-user/R/x86_64-pc-linux-gnu-library/3.6/BH/include" -I"/home/rstudio-user/R/x86_64-pc-linux-gnu-library/3.6/plogr/include" -I"/home/rstudio-user/R/x86_64-pc-linux-gnu-library/3.6/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -c group_indices.cpp -o group_indices.o
g++ -std=gnu++11 -I"/opt/R/3.6.0/lib/R/include" -DNDEBUG -I../inst/include -DRCPP_DEFAULT_INCLUDE_CALL=false -DCOMPILING_DPLYR -DRCPP_USING_UTF8_ERROR_STRING -DRCPP_USE_UNWIND_PROTECT -DBOOST_NO_AUTO_PTR  -I"/home/rstudio-user/R/x86_64-pc-linux-gnu-library/3.6/BH/include" -I"/home/rstudio-user/R/x86_64-pc-linux-gnu-library/3.6/plogr/include" -I"/home/rstudio-user/R/x86_64-pc-linux-gnu-library/3.6/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -c hybrid.cpp -o hybrid.o
g++ -std=gnu++11 -I"/opt/R/3.6.0/lib/R/include" -DNDEBUG -I../inst/include -DRCPP_DEFAULT_INCLUDE_CALL=false -DCOMPILING_DPLYR -DRCPP_USING_UTF8_ERROR_STRING -DRCPP_USE_UNWIND_PROTECT -DBOOST_NO_AUTO_PTR  -I"/home/rstudio-user/R/x86_64-pc-linux-gnu-library/3.6/BH/include" -I"/home/rstudio-user/R/x86_64-pc-linux-gnu-library/3.6/plogr/include" -I"/home/rstudio-user/R/x86_64-pc-linux-gnu-library/3.6/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -c init.cpp -o init.o
g++ -std=gnu++11 -I"/opt/R/3.6.0/lib/R/include" -DNDEBUG -I../inst/include -DRCPP_DEFAULT_INCLUDE_CALL=false -DCOMPILING_DPLYR -DRCPP_USING_UTF8_ERROR_STRING -DRCPP_USE_UNWIND_PROTECT -DBOOST_NO_AUTO_PTR  -I"/home/rstudio-user/R/x86_64-pc-linux-gnu-library/3.6/BH/include" -I"/home/rstudio-user/R/x86_64-pc-linux-gnu-library/3.6/plogr/include" -I"/home/rstudio-user/R/x86_64-pc-linux-gnu-library/3.6/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -c join.cpp -o join.o
g++ -std=gnu++11 -I"/opt/R/3.6.0/lib/R/include" -DNDEBUG -I../inst/include -DRCPP_DEFAULT_INCLUDE_CALL=false -DCOMPILING_DPLYR -DRCPP_USING_UTF8_ERROR_STRING -DRCPP_USE_UNWIND_PROTECT -DBOOST_NO_AUTO_PTR  -I"/home/rstudio-user/R/x86_64-pc-linux-gnu-library/3.6/BH/include" -I"/home/rstudio-user/R/x86_64-pc-linux-gnu-library/3.6/plogr/include" -I"/home/rstudio-user/R/x86_64-pc-linux-gnu-library/3.6/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -c join_exports.cpp -o join_exports.o
g++ -std=gnu++11 -I"/opt/R/3.6.0/lib/R/include" -DNDEBUG -I../inst/include -DRCPP_DEFAULT_INCLUDE_CALL=false -DCOMPILING_DPLYR -DRCPP_USING_UTF8_ERROR_STRING -DRCPP_USE_UNWIND_PROTECT -DBOOST_NO_AUTO_PTR  -I"/home/rstudio-user/R/x86_64-pc-linux-gnu-library/3.6/BH/include" -I"/home/rstudio-user/R/x86_64-pc-linux-gnu-library/3.6/plogr/include" -I"/home/rstudio-user/R/x86_64-pc-linux-gnu-library/3.6/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -c mutate.cpp -o mutate.o
g++: internal compiler error: Killed (program cc1plus)
Please submit a full bug report,
with preprocessed source if appropriate.
See <file:///usr/share/doc/gcc-5/README.Bugs> for instructions.
make: *** [mutate.o] Error 4
/opt/R/3.6.0/lib/R/etc/Makeconf:176: recipe for target 'mutate.o' failed
ERROR: compilation failed for package ‘dplyr’
* removing ‘/home/rstudio-user/R/x86_64-pc-linux-gnu-library/3.6/dplyr’
* restoring previous ‘/home/rstudio-user/R/x86_64-pc-linux-gnu-library/3.6/dplyr’
Warning in install.packages :
  installation of package ‘dplyr’ had non-zero exit status

RichardJTelford · November 26, 2019, 1:07am

Thanks for the feedback.
The rev.lock is at https://github.com/richardjtelford/kustkarnor/blob/master/renv.lock
It uses CRAN with URL "https://cloud.r-project.org". Is it possible to change this so the project works both on Rstudio cloud and on the desktop?

This is the full output from when trying to install dplyr

g++ -std=gnu++11 -I"/opt/R/3.6.0/lib/R/include" -DNDEBUG -I../inst/include -DRCPP_DEFAULT_INCLUDE_CALL=false -DCOMPILING_DPLYR -DRCPP_USING_UTF8_ERROR_STRING -DRCPP_USE_UNWIND_PROTECT -DBOOST_NO_AUTO_PTR  -I"/cloud/project/renv/library/R-3.6/x86_64-pc-linux-gnu/BH/include" -I"/cloud/project/renv/library/R-3.6/x86_64-pc-linux-gnu/plogr/include" -I"/cloud/project/renv/library/R-3.6/x86_64-pc-linux-gnu/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/opt/R/3.6.0/lib/R/include" -DNDEBUG -I../inst/include -DRCPP_DEFAULT_INCLUDE_CALL=false -DCOMPILING_DPLYR -DRCPP_USING_UTF8_ERROR_STRING -DRCPP_USE_UNWIND_PROTECT -DBOOST_NO_AUTO_PTR  -I"/cloud/project/renv/library/R-3.6/x86_64-pc-linux-gnu/BH/include" -I"/cloud/project/renv/library/R-3.6/x86_64-pc-linux-gnu/plogr/include" -I"/cloud/project/renv/library/R-3.6/x86_64-pc-linux-gnu/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -c address.cpp -o address.o
g++ -std=gnu++11 -I"/opt/R/3.6.0/lib/R/include" -DNDEBUG -I../inst/include -DRCPP_DEFAULT_INCLUDE_CALL=false -DCOMPILING_DPLYR -DRCPP_USING_UTF8_ERROR_STRING -DRCPP_USE_UNWIND_PROTECT -DBOOST_NO_AUTO_PTR  -I"/cloud/project/renv/library/R-3.6/x86_64-pc-linux-gnu/BH/include" -I"/cloud/project/renv/library/R-3.6/x86_64-pc-linux-gnu/plogr/include" -I"/cloud/project/renv/library/R-3.6/x86_64-pc-linux-gnu/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -c api.cpp -o api.o
g++ -std=gnu++11 -I"/opt/R/3.6.0/lib/R/include" -DNDEBUG -I../inst/include -DRCPP_DEFAULT_INCLUDE_CALL=false -DCOMPILING_DPLYR -DRCPP_USING_UTF8_ERROR_STRING -DRCPP_USE_UNWIND_PROTECT -DBOOST_NO_AUTO_PTR  -I"/cloud/project/renv/library/R-3.6/x86_64-pc-linux-gnu/BH/include" -I"/cloud/project/renv/library/R-3.6/x86_64-pc-linux-gnu/plogr/include" -I"/cloud/project/renv/library/R-3.6/x86_64-pc-linux-gnu/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -c arrange.cpp -o arrange.o
g++ -std=gnu++11 -I"/opt/R/3.6.0/lib/R/include" -DNDEBUG -I../inst/include -DRCPP_DEFAULT_INCLUDE_CALL=false -DCOMPILING_DPLYR -DRCPP_USING_UTF8_ERROR_STRING -DRCPP_USE_UNWIND_PROTECT -DBOOST_NO_AUTO_PTR  -I"/cloud/project/renv/library/R-3.6/x86_64-pc-linux-gnu/BH/include" -I"/cloud/project/renv/library/R-3.6/x86_64-pc-linux-gnu/plogr/include" -I"/cloud/project/renv/library/R-3.6/x86_64-pc-linux-gnu/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -c between.cpp -o between.o
g++ -std=gnu++11 -I"/opt/R/3.6.0/lib/R/include" -DNDEBUG -I../inst/include -DRCPP_DEFAULT_INCLUDE_CALL=false -DCOMPILING_DPLYR -DRCPP_USING_UTF8_ERROR_STRING -DRCPP_USE_UNWIND_PROTECT -DBOOST_NO_AUTO_PTR  -I"/cloud/project/renv/library/R-3.6/x86_64-pc-linux-gnu/BH/include" -I"/cloud/project/renv/library/R-3.6/x86_64-pc-linux-gnu/plogr/include" -I"/cloud/project/renv/library/R-3.6/x86_64-pc-linux-gnu/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -c bind.cpp -o bind.o
g++ -std=gnu++11 -I"/opt/R/3.6.0/lib/R/include" -DNDEBUG -I../inst/include -DRCPP_DEFAULT_INCLUDE_CALL=false -DCOMPILING_DPLYR -DRCPP_USING_UTF8_ERROR_STRING -DRCPP_USE_UNWIND_PROTECT -DBOOST_NO_AUTO_PTR  -I"/cloud/project/renv/library/R-3.6/x86_64-pc-linux-gnu/BH/include" -I"/cloud/project/renv/library/R-3.6/x86_64-pc-linux-gnu/plogr/include" -I"/cloud/project/renv/library/R-3.6/x86_64-pc-linux-gnu/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -c distinct.cpp -o distinct.o
g++ -std=gnu++11 -I"/opt/R/3.6.0/lib/R/include" -DNDEBUG -I../inst/include -DRCPP_DEFAULT_INCLUDE_CALL=false -DCOMPILING_DPLYR -DRCPP_USING_UTF8_ERROR_STRING -DRCPP_USE_UNWIND_PROTECT -DBOOST_NO_AUTO_PTR  -I"/cloud/project/renv/library/R-3.6/x86_64-pc-linux-gnu/BH/include" -I"/cloud/project/renv/library/R-3.6/x86_64-pc-linux-gnu/plogr/include" -I"/cloud/project/renv/library/R-3.6/x86_64-pc-linux-gnu/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -c encoding.cpp -o encoding.o
g++ -std=gnu++11 -I"/opt/R/3.6.0/lib/R/include" -DNDEBUG -I../inst/include -DRCPP_DEFAULT_INCLUDE_CALL=false -DCOMPILING_DPLYR -DRCPP_USING_UTF8_ERROR_STRING -DRCPP_USE_UNWIND_PROTECT -DBOOST_NO_AUTO_PTR  -I"/cloud/project/renv/library/R-3.6/x86_64-pc-linux-gnu/BH/include" -I"/cloud/project/renv/library/R-3.6/x86_64-pc-linux-gnu/plogr/include" -I"/cloud/project/renv/library/R-3.6/x86_64-pc-linux-gnu/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -c filter.cpp -o filter.o
g++ -std=gnu++11 -I"/opt/R/3.6.0/lib/R/include" -DNDEBUG -I../inst/include -DRCPP_DEFAULT_INCLUDE_CALL=false -DCOMPILING_DPLYR -DRCPP_USING_UTF8_ERROR_STRING -DRCPP_USE_UNWIND_PROTECT -DBOOST_NO_AUTO_PTR  -I"/cloud/project/renv/library/R-3.6/x86_64-pc-linux-gnu/BH/include" -I"/cloud/project/renv/library/R-3.6/x86_64-pc-linux-gnu/plogr/include" -I"/cloud/project/renv/library/R-3.6/x86_64-pc-linux-gnu/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -c group_indices.cpp -o group_indices.o
g++ -std=gnu++11 -I"/opt/R/3.6.0/lib/R/include" -DNDEBUG -I../inst/include -DRCPP_DEFAULT_INCLUDE_CALL=false -DCOMPILING_DPLYR -DRCPP_USING_UTF8_ERROR_STRING -DRCPP_USE_UNWIND_PROTECT -DBOOST_NO_AUTO_PTR  -I"/cloud/project/renv/library/R-3.6/x86_64-pc-linux-gnu/BH/include" -I"/cloud/project/renv/library/R-3.6/x86_64-pc-linux-gnu/plogr/include" -I"/cloud/project/renv/library/R-3.6/x86_64-pc-linux-gnu/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -c hybrid.cpp -o hybrid.o
g++ -std=gnu++11 -I"/opt/R/3.6.0/lib/R/include" -DNDEBUG -I../inst/include -DRCPP_DEFAULT_INCLUDE_CALL=false -DCOMPILING_DPLYR -DRCPP_USING_UTF8_ERROR_STRING -DRCPP_USE_UNWIND_PROTECT -DBOOST_NO_AUTO_PTR  -I"/cloud/project/renv/library/R-3.6/x86_64-pc-linux-gnu/BH/include" -I"/cloud/project/renv/library/R-3.6/x86_64-pc-linux-gnu/plogr/include" -I"/cloud/project/renv/library/R-3.6/x86_64-pc-linux-gnu/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -c init.cpp -o init.o
g++ -std=gnu++11 -I"/opt/R/3.6.0/lib/R/include" -DNDEBUG -I../inst/include -DRCPP_DEFAULT_INCLUDE_CALL=false -DCOMPILING_DPLYR -DRCPP_USING_UTF8_ERROR_STRING -DRCPP_USE_UNWIND_PROTECT -DBOOST_NO_AUTO_PTR  -I"/cloud/project/renv/library/R-3.6/x86_64-pc-linux-gnu/BH/include" -I"/cloud/project/renv/library/R-3.6/x86_64-pc-linux-gnu/plogr/include" -I"/cloud/project/renv/library/R-3.6/x86_64-pc-linux-gnu/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -c join.cpp -o join.o
g++ -std=gnu++11 -I"/opt/R/3.6.0/lib/R/include" -DNDEBUG -I../inst/include -DRCPP_DEFAULT_INCLUDE_CALL=false -DCOMPILING_DPLYR -DRCPP_USING_UTF8_ERROR_STRING -DRCPP_USE_UNWIND_PROTECT -DBOOST_NO_AUTO_PTR  -I"/cloud/project/renv/library/R-3.6/x86_64-pc-linux-gnu/BH/include" -I"/cloud/project/renv/library/R-3.6/x86_64-pc-linux-gnu/plogr/include" -I"/cloud/project/renv/library/R-3.6/x86_64-pc-linux-gnu/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -c join_exports.cpp -o join_exports.o
g++ -std=gnu++11 -I"/opt/R/3.6.0/lib/R/include" -DNDEBUG -I../inst/include -DRCPP_DEFAULT_INCLUDE_CALL=false -DCOMPILING_DPLYR -DRCPP_USING_UTF8_ERROR_STRING -DRCPP_USE_UNWIND_PROTECT -DBOOST_NO_AUTO_PTR  -I"/cloud/project/renv/library/R-3.6/x86_64-pc-linux-gnu/BH/include" -I"/cloud/project/renv/library/R-3.6/x86_64-pc-linux-gnu/plogr/include" -I"/cloud/project/renv/library/R-3.6/x86_64-pc-linux-gnu/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -c mutate.cpp -o mutate.o
g++: internal compiler error: Killed (program cc1plus)
Please submit a full bug report,
with preprocessed source if appropriate.
See <file:///usr/share/doc/gcc-5/README.Bugs> for instructions.
make: *** [mutate.o] Error 4
/opt/R/3.6.0/lib/R/etc/Makeconf:176: recipe for target 'mutate.o' failed
ERROR: compilation failed for package ‘dplyr’
* removing ‘/cloud/project/renv/library/R-3.6/x86_64-pc-linux-gnu/dplyr’
Warning in install.packages :
  installation of package ‘dplyr’ had non-zero exit status

kevinushey · November 26, 2019, 1:10am

I suspect you'll be able to work around this issue with something like:

renv::restore(repos = getOption("repos"))

This will force renv to use the binary-providing RSPM CRAN mirror normally used on RStudio Cloud, as opposed to the default RStudio CRAN mirror.

RichardJTelford · November 26, 2019, 1:18am

That gives the same error.

> getOption("repos")
                         CRAN 
"https://cloud.r-project.org"

RichardJTelford · November 26, 2019, 1:11pm

Is there a way to control whether renv uses the binary files rather than tries to install from source? Seems it may be related to https://github.com/rstudio/renv/issues/124

I'm going to try without renv for now

kevinushey · November 26, 2019, 5:47pm

Then you can try explicitly forcing the use of RStudio Cloud's binary repository:

renv::restore(repos = "http://package-proxy")

This is not a bug in renv.

system · December 17, 2019, 5:47pm

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