C Compiler Error on R 3.5.3

[iAmMischa]

Hi,

since the update to R 3.5.3 I can not install some packages, like 'install.packages("git2r")'. Which results in a C Compiler error message (see below).

I also installed this tools https://cran.r-project.org/bin/macosx/tools/ (clang 6.0.0 and gfortran 6.1)

installing the source package 'git2r'

trying URL 'https://cran.rstudio.com/src/contrib/git2r_0.25.2.tar.gz'
Content type 'application/x-gzip' length 1209396 bytes (1.2 MB)
==================================================
downloaded 1.2 MB

During startup - Warning messages:
1: Setting LC_CTYPE failed, using "C" 
2: Setting LC_TIME failed, using "C" 
3: Setting LC_MESSAGES failed, using "C" 
4: Setting LC_MONETARY failed, using "C" 
* installing *source* package 'git2r' ...
** package 'git2r' successfully unpacked and MD5 sums checked
checking build system type... x86_64-apple-darwin18.2.0
checking host system type... x86_64-apple-darwin18.2.0
checking for gcc... gcc
checking whether the C compiler works... no
configure: error: in `/private/var/folders/vg/4nywbj390lq647k3jm3hs1sw0000gn/T/Rtmpdz7Vt9/R.INSTALL4154512d21e/git2r':
configure: error: C compiler cannot create executables
See `config.log' for more details
ERROR: configuration failed for package 'git2r'
* removing '/Library/Frameworks/R.framework/Versions/3.5/Resources/library/git2r'
Warning in install.packages :
  installation of package 'git2r' had non-zero exit status

The downloaded source packages are in
	'/private/var/folders/vg/4nywbj390lq647k3jm3hs1sw0000gn/T/RtmpkXcvqk/downloaded_packages'

My sessionInfo():

R version 3.5.3 (2019-03-11)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.3

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

locale:
[1] C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] compiler_3.5.3 tools_3.5.3    yaml_2.2.0   

[iAmMischa]

Solved this issue, however I'm not sure which point exactly did the trick. I'm on a MacBook which used a time machine backup to restore the system, then I also updated R from 3.4 to 3.5 - so many issues lie somewhere in this migrations.
On the process to make things work again I updated homebrew within terminal, on the way doing so I had to change ownership of many sys folders and persmissions. I also updated the lang settings: https://stackoverflow.com/questions/9689104/installing-r-on-mac-warning-messages-setting-lc-ctype-failed-using-c

After all that (and maybe some steps missing) this error was resolved. I can not provide any more info on that. But now it works on my machine.