dplyr installation no longer working on rstudio.cloud

[Leon]

I am teaching a class right now using https://rstudio.cloud/ and I can no longer run:

install.packages("tidyverse")

In a new project - I (and the students) keep getting non-zero exit status on the dplyr installation. I have tried running;

install.packages("devtools")
devtools::install_github("tidyverse/dplyr")

But this also fails - Is this to do with the recent update to dplyr?

Output:

> install.packages("dplyr")
Installing package into ‘/home/rstudio-user/R/x86_64-pc-linux-gnu-library/3.6’
(as ‘lib’ is unspecified)
trying URL 'http://cran.rstudio.org/src/contrib/dplyr_0.8.5.tar.gz'
Content type 'application/x-gzip' length 1378766 bytes (1.3 MB)
==================================================
downloaded 1.3 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’
Warning in install.packages :
  installation of package ‘dplyr’ had non-zero exit status

The downloaded source packages are in
	‘/tmp/RtmpEwkCBA/downloaded_packages’
> library("dplyr")
Error in library("dplyr") : there is no package called ‘dplyr’

[mishabalyasin]

That's an unfortunate timing, but the root cause is because dplyr has been updated to 0.8.5 2 days ago and it hasn't been yet cached in pre-compiled form. Compiling it from source requires more than 1 Gb of RAM that you don't have on RStudio Cloud. I'm not sure what's the process of putting pre-compiled package in there, but it'll probably trickle down today/tomorrow.

[Leon]

Thanks for your reply @mishabalyasin - Unfortunate timing is an understatement with 40 students and a loaded teaching program, but that's data science life I guess...

[andresrcs]

You could use the walk-around from this related post

Problem installing dplyr on RStudio Cloud

Thanks! The "base project" solution is one that I had not considered...and it worked! I didn't have a base project created, so I set one of the earlier projects (that had dplyr installed, along with most of the other packages) as the base created a new project (which uses the space's base project as the starting point) named the new project "base_project", and deleted all the unnecessary files closed "base_project" and then set it as the base project for the space created a new project, and voila, dplyr is installed Thanks again!

[andy_kipp]

Hi there,

I posted a work around over here:

install.packages('dplyr') fails on new project

Hi there. We're working on getting the updated version of dplyr built and cached. In the mean time, you can install the archived version using the remotes package: remotes::install_version('dplyr', '0.8.3', repos = 'https://demo.rstudiopm.com/cran/__linux__/xenial/latest')

[Leon]

Thanks @andy_kipp! We got through the day - Just need it up and running for next Monday morning

We did experience some weird git behaviour, don't know if it's associated. The git tab in the environment pane did not appear upon git initialisation and also, some students were experiencing authentication issues despite seemingly having done the setup correct?

[Robby]

The binary version of the dplyr package is now cached, so you should be able to install it now.

[Leon]

Excellent @Robby - This works now. I'm still facing quirks with the git tab not appearing in the environment pane and nor the .gitignore-file after initialising git in a fresh project and then logging out/in?

I issue the following commands in the terminal on a fresh project on rstudio.cloud as per instruction on GitHub, when creating a new repo:

echo "# 2020_leonjessen" > README.md
git init
git add README.md
git commit -m "first commit"
git remote add origin https://github.com/rforbiodatascience/2020_leonjessen.git
git push -u origin master

Running git push -u origin master results in prompting for user/pass and this error appearing:
error: cannot run rpostback-askpass: No such file or directory

If I just ignore this and go to the repo https://github.com/rforbiodatascience/2020_leonjessen, it however looks fine.

But alas, the git tab and .gitignore-file remain illusive?

[Robby]

Does using the "New Project from Git Repo" in the Cloud interface work for you?

[Leon]

It does, but I want the students to use the commandline version

Oddly, I can fix the issue, by clicking the three dots in the upper right corner and then choose Relaunch Project and then hit OK. Once the project has been relaunched, I can see the git tab and the .gitignore-file

[Robby]

It's less than ideal, but the behavior you're seeing is similar to what you'd see if you're using the desktop RStudio IDE - you have to close & reopen the project for the git tab to show up after you initialize git. So in Cloud, if you just refresh the browser (or go back to the Projects listing and re-open the project), you should see the git tab.

[Leon]

For some reason, simply refreshing or clicking out/in on the project doesn't cut it. The Relaunch approach seems to do the trick