Can't install dplyr in new project

Yarnabrina · May 14, 2019, 3:26pm

Hi!

I tried to install dplyr in a fresh RStudio Cloud project, and failed.

As far as I can see, all the dependencies are installed successfully.

Complete output of `install.packages("dplyr")`

> install.packages("dplyr")
Installing package into ‘/home/rstudio-user/R/x86_64-pc-linux-gnu-library/3.6’
(as ‘lib’ is unspecified)
also installing the dependencies ‘backports’, ‘digest’, ‘zeallot’, ‘utf8’, ‘vctrs’, ‘cli’, ‘crayon’, ‘fansi’, ‘pillar’, ‘purrr’, ‘assertthat’, ‘glue’, ‘magrittr’, ‘pkgconfig’, ‘R6’, ‘Rcpp’, ‘rlang’, ‘tibble’, ‘tidyselect’, ‘BH’, ‘plogr’

trying URL 'http://package-proxy/src/contrib/backports_1.1.4.tar.gz'
Content type 'application/x-tar' length 56157 bytes (54 KB)
==================================================
downloaded 54 KB

trying URL 'http://package-proxy/src/contrib/digest_0.6.18.tar.gz'
Content type 'application/x-tar' length 200635 bytes (195 KB)
==================================================
downloaded 195 KB

trying URL 'http://package-proxy/src/contrib/zeallot_0.1.0.tar.gz'
Content type 'application/x-tar' length 58452 bytes (57 KB)
==================================================
downloaded 57 KB

trying URL 'http://package-proxy/src/contrib/utf8_1.1.4.tar.gz'
Content type 'application/x-tar' length 213375 bytes (208 KB)
==================================================
downloaded 208 KB

trying URL 'http://package-proxy/src/contrib/vctrs_0.1.0.tar.gz'
Content type 'application/x-tar' length 613623 bytes (599 KB)
==================================================
downloaded 599 KB

trying URL 'http://package-proxy/src/contrib/cli_1.1.0.tar.gz'
Content type 'application/x-tar' length 175994 bytes (171 KB)
==================================================
downloaded 171 KB

trying URL 'http://package-proxy/src/contrib/crayon_1.3.4.tar.gz'
Content type 'application/x-tar' length 749323 bytes (731 KB)
==================================================
downloaded 731 KB

trying URL 'http://package-proxy/src/contrib/fansi_0.4.0.tar.gz'
Content type 'application/x-tar' length 230596 bytes (225 KB)
==================================================
downloaded 225 KB

trying URL 'http://package-proxy/src/contrib/pillar_1.4.0.tar.gz'
Content type 'application/x-tar' length 177288 bytes (173 KB)
==================================================
downloaded 173 KB

trying URL 'http://package-proxy/src/contrib/purrr_0.3.2.tar.gz'
Content type 'application/x-tar' length 422831 bytes (412 KB)
==================================================
downloaded 412 KB

trying URL 'http://package-proxy/src/contrib/assertthat_0.2.1.tar.gz'
Content type 'application/x-tar' length 53331 bytes (52 KB)
==================================================
downloaded 52 KB

trying URL 'http://package-proxy/src/contrib/glue_1.3.1.tar.gz'
Content type 'application/x-tar' length 162221 bytes (158 KB)
==================================================
downloaded 158 KB

trying URL 'http://package-proxy/src/contrib/magrittr_1.5.tar.gz'
Content type 'application/x-tar' length 154794 bytes (151 KB)
==================================================
downloaded 151 KB

trying URL 'http://package-proxy/src/contrib/pkgconfig_2.0.2.tar.gz'
Content type 'application/x-tar' length 17522 bytes (17 KB)
==================================================
downloaded 17 KB

trying URL 'http://package-proxy/src/contrib/R6_2.4.0.tar.gz'
Content type 'application/x-tar' length 56894 bytes (55 KB)
==================================================
downloaded 55 KB

trying URL 'http://package-proxy/src/contrib/Rcpp_1.0.1.tar.gz'
Content type 'application/x-tar' length 4609208 bytes (4.4 MB)
==================================================
downloaded 4.4 MB

trying URL 'http://package-proxy/src/contrib/rlang_0.3.4.tar.gz'
Content type 'application/x-tar' length 1153787 bytes (1.1 MB)
==================================================
downloaded 1.1 MB

trying URL 'http://package-proxy/src/contrib/tibble_2.1.1.tar.gz'
Content type 'application/x-tar' length 325589 bytes (317 KB)
==================================================
downloaded 317 KB

trying URL 'http://package-proxy/src/contrib/tidyselect_0.2.5.tar.gz'
Content type 'application/x-tar' length 419744 bytes (409 KB)
==================================================
downloaded 409 KB

trying URL 'http://package-proxy/src/contrib/BH_1.69.0-1.tar.gz'
Content type 'application/x-tar' length 12043944 bytes (11.5 MB)
==================================================
downloaded 11.5 MB

trying URL 'http://package-proxy/src/contrib/plogr_0.2.0.tar.gz'
Content type 'application/x-tar' length 13059 bytes (12 KB)
==================================================
downloaded 12 KB

trying URL 'http://cran.rstudio.org/src/contrib/dplyr_0.8.1.tar.gz'
Content type 'application/x-gzip' length 1170671 bytes (1.1 MB)
==================================================
downloaded 1.1 MB

* installing *binary* package ‘backports’ ...
* DONE (backports)
* installing *binary* package ‘digest’ ...
* DONE (digest)
* installing *binary* package ‘zeallot’ ...
* DONE (zeallot)
* installing *binary* package ‘utf8’ ...
* DONE (utf8)
* installing *binary* package ‘crayon’ ...
* DONE (crayon)
* installing *binary* package ‘fansi’ ...
* DONE (fansi)
* installing *binary* package ‘assertthat’ ...
* DONE (assertthat)
* installing *binary* package ‘glue’ ...
* DONE (glue)
* installing *binary* package ‘magrittr’ ...
* DONE (magrittr)
* installing *binary* package ‘pkgconfig’ ...
* DONE (pkgconfig)
* installing *binary* package ‘R6’ ...
* DONE (R6)
* installing *binary* package ‘Rcpp’ ...
* DONE (Rcpp)
* installing *binary* package ‘rlang’ ...
* DONE (rlang)
* installing *binary* package ‘BH’ ...
* DONE (BH)
* installing *binary* package ‘plogr’ ...
* DONE (plogr)
* installing *binary* package ‘vctrs’ ...
* DONE (vctrs)
* installing *binary* package ‘cli’ ...
* DONE (cli)
* installing *binary* package ‘purrr’ ...
* DONE (purrr)
* installing *binary* package ‘pillar’ ...
* DONE (pillar)
* installing *binary* package ‘tidyselect’ ...
* DONE (tidyselect)
* installing *binary* package ‘tibble’ ...
* DONE (tibble)
* 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/RtmpHChK7p/downloaded_packages’

Here's the project link: https://rstudio.cloud/spaces/17405/project/350481

Here's the space link: https://rstudio.cloud/spaces/17405/join?access_code=f0wGePsRipNCdLEmvjRdeyZARBFfDTN5MhPkJ5rG

Any help will be appreciated.

(A related request: It'll be really helpful to have a clear guide regarding sharing projects. I failed earlier, and maybe now, following the instructions in the Guide link on the LHS)

philip_khor · May 15, 2019, 11:13am

Happens for me too. This issue doesn't occur if I use R 3.5.3 on RStudio Cloud.

andresrcs · May 15, 2019, 8:53pm

dplyr needs more than 1 GB of RAM for installation and apparently it's not cached yet for R 3.6.0 on Rstudio Cloud

stevenolen · May 16, 2019, 1:46pm

Hi!

I've joined the space shared by @Yarnabrina and opened a temporary copy of the project in question. I was able to install dpylr from the cache:

Additionally, starting a fresh project with 3.6.0 results in installing a binary(cached) version of dpylr and all its dependencies.

This leads me to believe that the problem should now be solved, and that what you are seeing is an outstanding bug in our caching layer which can show itself for up to a day or so after a package is released to CRAN until our package manager (backing the cache) has synced and made the latest version available. We're working toward making this better!

stevenolen · May 17, 2019, 2:51pm

Hi!

Here's our guide for working with rstudio.cloud features: Posit Cloud

If there's something that isn't clearly understood (or missing) in the guide, a new community post may attract the right attention for you!

Yarnabrina · May 24, 2019, 2:51pm

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