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install R modules step fails on DescTools #357

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pdurbin opened this issue May 28, 2024 · 2 comments
Open

install R modules step fails on DescTools #357

pdurbin opened this issue May 28, 2024 · 2 comments

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@pdurbin
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pdurbin commented May 28, 2024 •
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I just tried running the ec2 create script with no arguments as of 2d7f797 but it fails with the following:

TASK [dataverse : install R modules] *******************************************
changed: [localhost] => (item=R2HTML)
changed: [localhost] => (item=rjson)
failed: [localhost] (item=DescTools)

Here is the complete output: install-fail-2d7f797.txt

It tried to run it again at the command line and got the same error (maybe this output is a bit more readable):

[root@ip-172-31-91-40 ~]# R --version
R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-redhat-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under the terms of the
GNU General Public License versions 2 or 3.
For more information about these matters see
https://www.gnu.org/licenses/.

[root@ip-172-31-91-40 ~]# /usr/bin/Rscript -e 'install.packages("DescTools", repos=c("https://cloud.r-project.org/"))'
Installing package into ‘/usr/lib64/R/library’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/DescTools_0.99.54.tar.gz'
Content type 'application/x-gzip' length 2654274 bytes (2.5 MB)
==================================================
downloaded 2.5 MB

* installing *source* package ‘DescTools’ ...
** package ‘DescTools’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (GCC) 8.5.0 20210514 (Red Hat 8.5.0-20)’
using Fortran compiler: ‘GNU Fortran (GCC) 8.5.0 20210514 (Red Hat 8.5.0-20)’
using C++ compiler: ‘g++ (GCC) 8.5.0 20210514 (Red Hat 8.5.0-20)’
using C++17
gcc -I"/usr/include/R" -DNDEBUG  -I'/usr/lib64/R/library/Rcpp/include' -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c ADinf.c -o ADinf.o
gcc -I"/usr/include/R" -DNDEBUG  -I'/usr/lib64/R/library/Rcpp/include' -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c AnDarl.c -o AnDarl.o
g++ -std=gnu++17 -I"/usr/include/R" -DNDEBUG  -I'/usr/lib64/R/library/Rcpp/include' -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection   -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/usr/include/R" -DNDEBUG  -I'/usr/lib64/R/library/Rcpp/include' -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection   -c aux_fct.cpp -o aux_fct.o
aux_fct.cpp: In function ‘Rcpp::List n_pow_sum(Rcpp::NumericVector)’:
aux_fct.cpp:205:23: error: ‘reduce’ is not a member of ‘std’
   double mean =  std::reduce(x.begin(), x.end(), 0.0, std::plus<double>()) / x.size();
                       ^~~~~~
aux_fct.cpp:205:23: note: suggested alternative: ‘replace’
   double mean =  std::reduce(x.begin(), x.end(), 0.0, std::plus<double>()) / x.size();
                       ^~~~~~
                       replace
make: *** [/usr/lib64/R/etc/Makeconf:204: aux_fct.o] Error 1
make: *** Waiting for unfinished jobs....
ERROR: compilation failed for package ‘DescTools’
* removing ‘/usr/lib64/R/library/DescTools’

The downloaded source packages are in
	‘/tmp/RtmpoxV6UK/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages("DescTools", repos = c("https://cloud.r-project.org/")) :
  installation of package ‘DescTools’ had non-zero exit status
[root@ip-172-31-91-40 ~]#

I see that g++ (GCC) 8.5.0 is used but from https://stackoverflow.com/questions/76397816/error-with-stdreduce-method-in-c17-using-gnu-g17-and-clang-17-20-com and https://stackoverflow.com/questions/61564006/compilation-error-while-using-reduce-and-stdexecution-in-c it seems like we might need version 9.1? 🤷
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@pdurbin @donsizemore