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I'm trying to get R installed as a kernel for jupyter notebook. I am follwing the instructions at: https://irkernel.github.io/installation/ but when I try to install IRkernel I get:

also installing the dependency 'uuid'

trying URL 'https://cran.mtu.edu/src/contrib/uuid_0.1-4.tar.gz'
Content type 'application/x-gzip' length 49544 bytes (48 KB)
==================================================
downloaded 48 KB

trying URL 'https://cran.mtu.edu/src/contrib/IRkernel_1.1.tar.gz'
Content type 'application/x-gzip' length 52805 bytes (51 KB)
==================================================
downloaded 51 KB

* installing *source* package 'uuid' ...
** package 'uuid' successfully unpacked and MD5 sums checked
** using staged installation
checking for gcc... x86_64-apple-darwin13.4.0-clang
checking whether the C compiler works... no
configure: error: in `/private/var/folders/y2/38gkkc0s7d52_mr_s6zfj7m80000gq/T/Rtmpru6fsM/R.INSTALL92f935860c3f/uuid':
configure: error: C compiler cannot create executables
See `config.log' for more details
ERROR: configuration failed for package 'uuid'
* removing '/anaconda3/lib/R/library/uuid'
ERROR: dependency 'uuid' is not available for package 'IRkernel'
* removing '/anaconda3/lib/R/library/IRkernel'

The downloaded source packages are in
    '/private/var/folders/y2/38gkkc0s7d52_mr_s6zfj7m80000gq/T/Rtmpg79DeD/downloaded_packages'
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning messages:
1: In install.packages("IRkernel") :
  installation of package 'uuid' had non-zero exit status
2: In install.packages("IRkernel") :
  installation of package 'IRkernel' had non-zero exit status

Can someone please tell me the problem?emphasized text

ihf
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  • Did you try any of solutions out there for your issue, such as [here](https://github.com/conda-forge/compilers-feedstock/issues/11), [here](https://stackoverflow.com/q/53637414/8508004), [here](https://apple.stackexchange.com/questions/216573/cant-compile-source-code-on-mac), or [here](https://community.rstudio.com/t/cannot-install-many-r-packages-on-mac-10-13-6-please-help/45382/2)? – Wayne Mar 02 '20 at 01:44
  • OK, I have now gone through and tried all of these and I still cannot get it to work. I don't understand why it says the c compiler does not work when I can compile c code using gcc. install.packages('IRkernel') continues to fail as above. – ihf Mar 05 '20 at 02:47
  • I just tried running R as su and then doing the install.packages('IRkernel') and it failed but with a different `error. checking whether we are cross compiling... configure: error: in `/private/tmp/Rtmp7TEBDr/R.INSTALL1011130127de2/uuid': configure: error: cannot run C compiled programs. If you meant to cross compile, use `--host'.` – ihf Mar 05 '20 at 03:07
  • Do you know if the point it is failing at now is after the point it was originally failing at? In other words are you making progress because with sudo it got past `checking whether the C compiler works`? Can you use conda to try this process, like [here](https://anaconda.org/r/r-irkernel)? – Wayne Mar 05 '20 at 16:55
  • I'm not sure what precisely is wrong with my "base" conda environment but I just tried again with another conda env and it worked. I can now use the R Kernel in a Jupyter Notebook. – ihf Mar 06 '20 at 22:40
  • Glad it to hear you were able to get it working. – Wayne Mar 07 '20 at 19:01

0 Answers0