conda install error

[jianshu93]

Hello Team,

It seems under conda environment, it cannot be installed:

installing source package ‘polyclip’ ...
** using staged installation
compiling under C++11
checking whether the C++ compiler works... no
configure: error: in /tmp/RtmpX79Rc1/R.INSTALL7dc05967a6f2/polyclip': configure: error: C++ compiler cannot create executables See config.log' for more details
ERROR: configuration failed for package ‘polyclip’

• removing ‘/condo/ieg/jianshu/miniconda3_new2/lib/R/library/polyclip’
  Warning message:
  In i.p(...) :
  installation of package ‘/tmp/Rtmp8cATiW/file7d4f6b03cf34/polyclip_1.10-4.tar.gz’ had non-zero exit status

I do have everything including gcc, g++, C++, c++, CC, CC in my conda environment.

Thanks,

Jianshu

[baddstats]

The message says that the C++ compiler cannot create executable files. This probably means there is a problem with file permissions.

The message also says "See config.log" for more details. Perhaps this would provide further information, such as the pathname of the directory where C++ was trying to create files.

[rubak]

@jianshu93 this could be related to the permission problem in #14. A workaround that seems to work for some people is in this comment.

[jianshu93]

Hello，

Thanks for the response. However，it is a computer cluster，which I do not have sudo access but only a conda environment with R installed，I can have access to everything in this environment. I do not understand why C++ compliler is not available. I do have system level installation and conda level. I will add the config log file you mentioned soon.

Thanks，

Jianshu

[rubak]

You don't necessarily need sudo access. The workaround I mentioned is:

wget https://cran.r-project.org/src/contrib/polyclip_1.10-4.tar.gz
tar -zxvf polyclip_1.10-4.tar.gz
Rscript -e "library('devtools'); devtools::install('polyclip')"

[jianshu93]

Thanks!

Oh I missed it. I will try and get back.

Jianshu

[dbrookeUAB]

You don't necessarily need sudo access. The workaround I mentioned is:

wget https://cran.r-project.org/src/contrib/polyclip_1.10-4.tar.gz
tar -zxvf polyclip_1.10-4.tar.gz
Rscript -e "library('devtools'); devtools::install('polyclip')"

This may be the most helpful github comment of all time.