tidyverse not installing/loading: specifically, haven due to [DfReader.o] Error 4

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Hi everyone!

Installation of tidyverse and loading is failing. Specifically, it's the haven package with the following error. I've tried session restart and relaunching the project several times---didn't work.

* installing *source* package ‘haven’ ...
** package ‘haven’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG  -I'/home/rstudio-user/R/x86_64-pc-linux-gnu-library/4.0/cpp11/include' -I/usr/local/include  -Ireadstat -DHAVE_ZLIB -fpic  -g -O2  -c tagged_na.c -o tagged_na.o
gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG  -I'/home/rstudio-user/R/x86_64-pc-linux-gnu-library/4.0/cpp11/include' -I/usr/local/include  -Ireadstat -DHAVE_ZLIB -fpic  -g -O2  -c readstat/readstat_parser.c -o readstat/readstat_parser.o
gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG  -I'/home/rstudio-user/R/x86_64-pc-linux-gnu-library/4.0/cpp11/include' -I/usr/local/include  -Ireadstat -DHAVE_ZLIB -fpic  -g -O2  -c readstat/readstat_metadata.c -o readstat/readstat_metadata.o
gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG  -I'/home/rstudio-user/R/x86_64-pc-linux-gnu-library/4.0/cpp11/include' -I/usr/local/include  -Ireadstat -DHAVE_ZLIB -fpic  -g -O2  -c readstat/readstat_io_unistd.c -o readstat/readstat_io_unistd.o
gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG  -I'/home/rstudio-user/R/x86_64-pc-linux-gnu-library/4.0/cpp11/include' -I/usr/local/include  -Ireadstat -DHAVE_ZLIB -fpic  -g -O2  -c readstat/readstat_bits.c -o readstat/readstat_bits.o
gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG  -I'/home/rstudio-user/R/x86_64-pc-linux-gnu-library/4.0/cpp11/include' -I/usr/local/include  -Ireadstat -DHAVE_ZLIB -fpic  -g -O2  -c readstat/readstat_variable.c -o readstat/readstat_variable.o
gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG  -I'/home/rstudio-user/R/x86_64-pc-linux-gnu-library/4.0/cpp11/include' -I/usr/local/include  -Ireadstat -DHAVE_ZLIB -fpic  -g -O2  -c readstat/readstat_writer.c -o readstat/readstat_writer.o
gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG  -I'/home/rstudio-user/R/x86_64-pc-linux-gnu-library/4.0/cpp11/include' -I/usr/local/include  -Ireadstat -DHAVE_ZLIB -fpic  -g -O2  -c readstat/readstat_error.c -o readstat/readstat_error.o
gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG  -I'/home/rstudio-user/R/x86_64-pc-linux-gnu-library/4.0/cpp11/include' -I/usr/local/include  -Ireadstat -DHAVE_ZLIB -fpic  -g -O2  -c readstat/readstat_convert.c -o readstat/readstat_convert.o
gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG  -I'/home/rstudio-user/R/x86_64-pc-linux-gnu-library/4.0/cpp11/include' -I/usr/local/include  -Ireadstat -DHAVE_ZLIB -fpic  -g -O2  -c readstat/CKHashTable.c -o readstat/CKHashTable.o
gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG  -I'/home/rstudio-user/R/x86_64-pc-linux-gnu-library/4.0/cpp11/include' -I/usr/local/include  -Ireadstat -DHAVE_ZLIB -fpic  -g -O2  -c readstat/readstat_malloc.c -o readstat/readstat_malloc.o
gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG  -I'/home/rstudio-user/R/x86_64-pc-linux-gnu-library/4.0/cpp11/include' -I/usr/local/include  -Ireadstat -DHAVE_ZLIB -fpic  -g -O2  -c readstat/readstat_value.c -o readstat/readstat_value.o
gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG  -I'/home/rstudio-user/R/x86_64-pc-linux-gnu-library/4.0/cpp11/include' -I/usr/local/include  -Ireadstat -DHAVE_ZLIB -fpic  -g -O2  -c readstat/sas/readstat_xport_write.c -o readstat/sas/readstat_xport_write.o
gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG  -I'/home/rstudio-user/R/x86_64-pc-linux-gnu-library/4.0/cpp11/include' -I/usr/local/include  -Ireadstat -DHAVE_ZLIB -fpic  -g -O2  -c readstat/sas/readstat_sas7bcat_read.c -o readstat/sas/readstat_sas7bcat_read.o
gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG  -I'/home/rstudio-user/R/x86_64-pc-linux-gnu-library/4.0/cpp11/include' -I/usr/local/include  -Ireadstat -DHAVE_ZLIB -fpic  -g -O2  -c readstat/sas/readstat_sas7bdat_write.c -o readstat/sas/readstat_sas7bdat_write.o
gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG  -I'/home/rstudio-user/R/x86_64-pc-linux-gnu-library/4.0/cpp11/include' -I/usr/local/include  -Ireadstat -DHAVE_ZLIB -fpic  -g -O2  -c readstat/sas/readstat_sas7bcat_write.c -o readstat/sas/readstat_sas7bcat_write.o
gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG  -I'/home/rstudio-user/R/x86_64-pc-linux-gnu-library/4.0/cpp11/include' -I/usr/local/include  -Ireadstat -DHAVE_ZLIB -fpic  -g -O2  -c readstat/sas/ieee.c -o readstat/sas/ieee.o
gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG  -I'/home/rstudio-user/R/x86_64-pc-linux-gnu-library/4.0/cpp11/include' -I/usr/local/include  -Ireadstat -DHAVE_ZLIB -fpic  -g -O2  -c readstat/sas/readstat_xport_read.c -o readstat/sas/readstat_xport_read.o
gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG  -I'/home/rstudio-user/R/x86_64-pc-linux-gnu-library/4.0/cpp11/include' -I/usr/local/include  -Ireadstat -DHAVE_ZLIB -fpic  -g -O2  -c readstat/sas/readstat_sas.c -o readstat/sas/readstat_sas.o
gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG  -I'/home/rstudio-user/R/x86_64-pc-linux-gnu-library/4.0/cpp11/include' -I/usr/local/include  -Ireadstat -DHAVE_ZLIB -fpic  -g -O2  -c readstat/sas/readstat_sas_rle.c -o readstat/sas/readstat_sas_rle.o
gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG  -I'/home/rstudio-user/R/x86_64-pc-linux-gnu-library/4.0/cpp11/include' -I/usr/local/include  -Ireadstat -DHAVE_ZLIB -fpic  -g -O2  -c readstat/sas/readstat_xport.c -o readstat/sas/readstat_xport.o
gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG  -I'/home/rstudio-user/R/x86_64-pc-linux-gnu-library/4.0/cpp11/include' -I/usr/local/include  -Ireadstat -DHAVE_ZLIB -fpic  -g -O2  -c readstat/sas/readstat_sas7bdat_read.c -o readstat/sas/readstat_sas7bdat_read.o
gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG  -I'/home/rstudio-user/R/x86_64-pc-linux-gnu-library/4.0/cpp11/include' -I/usr/local/include  -Ireadstat -DHAVE_ZLIB -fpic  -g -O2  -c readstat/spss/readstat_spss_parse.c -o readstat/spss/readstat_spss_parse.o
gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG  -I'/home/rstudio-user/R/x86_64-pc-linux-gnu-library/4.0/cpp11/include' -I/usr/local/include  -Ireadstat -DHAVE_ZLIB -fpic  -g -O2  -c readstat/spss/readstat_sav_read.c -o readstat/spss/readstat_sav_read.o
gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG  -I'/home/rstudio-user/R/x86_64-pc-linux-gnu-library/4.0/cpp11/include' -I/usr/local/include  -Ireadstat -DHAVE_ZLIB -fpic  -g -O2  -c readstat/spss/readstat_por_read.c -o readstat/spss/readstat_por_read.o
gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG  -I'/home/rstudio-user/R/x86_64-pc-linux-gnu-library/4.0/cpp11/include' -I/usr/local/include  -Ireadstat -DHAVE_ZLIB -fpic  -g -O2  -c readstat/spss/readstat_sav.c -o readstat/spss/readstat_sav.o
gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG  -I'/home/rstudio-user/R/x86_64-pc-linux-gnu-library/4.0/cpp11/include' -I/usr/local/include  -Ireadstat -DHAVE_ZLIB -fpic  -g -O2  -c readstat/spss/readstat_zsav_compress.c -o readstat/spss/readstat_zsav_compress.o
gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG  -I'/home/rstudio-user/R/x86_64-pc-linux-gnu-library/4.0/cpp11/include' -I/usr/local/include  -Ireadstat -DHAVE_ZLIB -fpic  -g -O2  -c readstat/spss/readstat_sav_parse_timestamp.c -o readstat/spss/readstat_sav_parse_timestamp.o
gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG  -I'/home/rstudio-user/R/x86_64-pc-linux-gnu-library/4.0/cpp11/include' -I/usr/local/include  -Ireadstat -DHAVE_ZLIB -fpic  -g -O2  -c readstat/spss/readstat_zsav_read.c -o readstat/spss/readstat_zsav_read.o
gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG  -I'/home/rstudio-user/R/x86_64-pc-linux-gnu-library/4.0/cpp11/include' -I/usr/local/include  -Ireadstat -DHAVE_ZLIB -fpic  -g -O2  -c readstat/spss/readstat_sav_write.c -o readstat/spss/readstat_sav_write.o
gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG  -I'/home/rstudio-user/R/x86_64-pc-linux-gnu-library/4.0/cpp11/include' -I/usr/local/include  -Ireadstat -DHAVE_ZLIB -fpic  -g -O2  -c readstat/spss/readstat_por_write.c -o readstat/spss/readstat_por_write.o
gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG  -I'/home/rstudio-user/R/x86_64-pc-linux-gnu-library/4.0/cpp11/include' -I/usr/local/include  -Ireadstat -DHAVE_ZLIB -fpic  -g -O2  -c readstat/spss/readstat_spss.c -o readstat/spss/readstat_spss.o
gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG  -I'/home/rstudio-user/R/x86_64-pc-linux-gnu-library/4.0/cpp11/include' -I/usr/local/include  -Ireadstat -DHAVE_ZLIB -fpic  -g -O2  -c readstat/spss/readstat_por.c -o readstat/spss/readstat_por.o
gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG  -I'/home/rstudio-user/R/x86_64-pc-linux-gnu-library/4.0/cpp11/include' -I/usr/local/include  -Ireadstat -DHAVE_ZLIB -fpic  -g -O2  -c readstat/spss/readstat_zsav_write.c -o readstat/spss/readstat_zsav_write.o
gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG  -I'/home/rstudio-user/R/x86_64-pc-linux-gnu-library/4.0/cpp11/include' -I/usr/local/include  -Ireadstat -DHAVE_ZLIB -fpic  -g -O2  -c readstat/spss/readstat_sav_compress.c -o readstat/spss/readstat_sav_compress.o
gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG  -I'/home/rstudio-user/R/x86_64-pc-linux-gnu-library/4.0/cpp11/include' -I/usr/local/include  -Ireadstat -DHAVE_ZLIB -fpic  -g -O2  -c readstat/spss/readstat_sav_parse.c -o readstat/spss/readstat_sav_parse.o
gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG  -I'/home/rstudio-user/R/x86_64-pc-linux-gnu-library/4.0/cpp11/include' -I/usr/local/include  -Ireadstat -DHAVE_ZLIB -fpic  -g -O2  -c readstat/spss/readstat_por_parse.c -o readstat/spss/readstat_por_parse.o
gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG  -I'/home/rstudio-user/R/x86_64-pc-linux-gnu-library/4.0/cpp11/include' -I/usr/local/include  -Ireadstat -DHAVE_ZLIB -fpic  -g -O2  -c readstat/stata/readstat_dta_read.c -o readstat/stata/readstat_dta_read.o
gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG  -I'/home/rstudio-user/R/x86_64-pc-linux-gnu-library/4.0/cpp11/include' -I/usr/local/include  -Ireadstat -DHAVE_ZLIB -fpic  -g -O2  -c readstat/stata/readstat_dta.c -o readstat/stata/readstat_dta.o
gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG  -I'/home/rstudio-user/R/x86_64-pc-linux-gnu-library/4.0/cpp11/include' -I/usr/local/include  -Ireadstat -DHAVE_ZLIB -fpic  -g -O2  -c readstat/stata/readstat_dta_parse_timestamp.c -o readstat/stata/readstat_dta_parse_timestamp.o
gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG  -I'/home/rstudio-user/R/x86_64-pc-linux-gnu-library/4.0/cpp11/include' -I/usr/local/include  -Ireadstat -DHAVE_ZLIB -fpic  -g -O2  -c readstat/stata/readstat_dta_write.c -o readstat/stata/readstat_dta_write.o
g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG  -I'/home/rstudio-user/R/x86_64-pc-linux-gnu-library/4.0/cpp11/include' -I/usr/local/include  -Ireadstat -DHAVE_ZLIB -fpic  -g -O2  -c DfReader.cpp -o DfReader.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.
/opt/R/4.0.3/lib/R/etc/Makeconf:181: recipe for target 'DfReader.o' failed
make: *** [DfReader.o] Error 4
ERROR: compilation failed for package ‘haven’
* removing ‘/home/rstudio-user/R/x86_64-pc-linux-gnu-library/4.0/haven’
Warning in install.packages :
  installation of package ‘haven’ had non-zero exit status

The downloaded source packages are in
	‘/tmp/Rtmpaq2909/downloaded_packages’

I'm an instructor trying to set up a base project for my students, so if things don't work smoothly, I'll have to revert to the local installations. Any idea how to resolve this?

Cheers,

2

I created a new project, switched from R 4.1 (the new default) to the 4.0.3 version you are using, and started the tidyverse installation. Once all the other packages were installed as binary files it started compiling haven from source. No problems.

Haven was just updated today, so if you are still having problems just wait a bit for the binary to be available.

As an instructor preparing for fall term, I share your pain!

3

This happens from time to time when a new package version is out, the reason is that the package requires more than 1GB of memory to compile (the default RStudio Cloud memory limit), the way RStudio Cloud addresses this issue is by caching precompiled binaries of the packages but it could take some time for the cache to update to the current package version.

Alternatively, you could try installing a previous version this way:

remotes::install_version("package_name", version = "x.x.x", repos = 'https://packagemanager.rstudio.com/cran/__linux__/xenial/latest') # For projects created with Ubuntu 20 change the repo to "focal" instead of "xenial".
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