I am trying install rentrez in Rstudio and it fails (error below). But I cannot find the config.log to interpret the error. Any help appreciated locating file or installing rentrez. I am doing this with R version R version 3.6.1 (2019-07-05) on Mac OS 10.14.6. Thanks
Error:
install.packages("rentrez") also installing the dependency ‘XML’
>trying URL 'https://cran.rstudio.com/src/contrib/XML_3.98-1.20.tar.gz'
>Content type 'application/x-gzip' length 1600829 bytes (1.5 MB)
downloaded 1.5 MB
>trying URL 'https://cran.rstudio.com/src/contrib/rentrez_1.2.2.tar.gz'
>Content type 'application/x-gzip' length 79029 bytes (77 KB)
downloaded 77 KB
>installing source package ‘XML’ ...
>** package ‘XML’ 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/f0/3d9kdp5j09x5xpv5t0_zq6b80000gn/T/Rtmpp98Wvu/R.INSTALLaf61110a6db/XML':
configure: error: C compiler cannot create executables
Seeconfig.log' for more details ERROR: configuration failed for package ‘XML’
>removing ‘/opt/anaconda3/lib/R/library/XML’ Warning in install.packages : installation of package ‘XML’ had non-zero exit status ERROR: dependency ‘XML’ is not available for package ‘rentrez’
removing ‘/opt/anaconda3/lib/R/library/rentrez’ Warning in install.packages : installation of package ‘rentrez’ had non-zero exit status
The downloaded source packages are in
‘/private/var/folders/f0/3d9kdp5j09x5xpv5t0_zq6b80000gn/T/RtmpxDMasm/downloaded_packages’
Updating HTML index of packages in '.Library' Making 'packages.html' ... done
I have looked for the config.log file in the working directory I am in when I enter the
install.packages("rentrez") command.
I also tried to look for it in /private/var/folders/f0/3d9kdp5j09x5xpv5t0_zq6b80000gn/T/RtmpxDMasm/downloaded_packages’, however RtmpxDMasm/downloaded_packages does not exist. Is it being deleted with the config.log file in the failed install? What should I do next?