Hi Rick,

I uninstalled and reinstalled AFNI a couple of times now. The current status of the problem is as follows.

The command line "export DYLD_LIBRARY_PATH=${DYLD_LIBRARY_PATH}:/opt/X11/lib/flat_namespace" is added in my ".zshrc" file.

The message output by afni_system_check.py -check_all "please set DYLD_LIBRARY_PATH to include /opt/X11/lib/flat_namespace" only appears when using the Zsh shell. If I switch to tcsh, this message does no longer occur when doing the system check.

I also uninstalled the newest R version and switched back to 3.6.3. When I now run "rPkgsInstall -pkgs ALL" the error "load R_io.so" does no longer occur. Instead, the terminal starts to download the updates. Many "warnings" occur while the files are downloaded, but I believe thats due to the fact that I am not using the up-to-date version of R (it is a really long list of warnings, if its helpfull to post it there, let me know). These warnings occur both when running "rPkgsInstall -pkgs ALL" under the tcsh and zsh shell.

The download and installation of "rPkgsInstall -pkgs ALL" then ends with the following message output:

++ Note: @ 11:13:31
This package has been installed on the computer: afex

Warnmeldungen (warning messages):
1: In install.packages(pkgs_miss, dep = TRUE, repos = site) :
installation of package ‘quantreg’ had non-zero exit status
2: In install.packages(pkgs_miss, dep = TRUE, repos = site) :
installation of package ‘glmmTMB’ had non-zero exit status
3: In install.packages(pkgs_miss, dep = TRUE, repos = site) :
installation of package ‘car’ had non-zero exit status
4: In install.packages(pkgs_miss, dep = TRUE, repos = site) :
installation of package ‘afex’ had non-zero exit status


Now what is interesting is the following fact:
This is the output of AFNIs system check while running the Zsh shell (my favorite shell).

========================= summary, please fix: =========================
* just be aware: login shell 'zsh', but our code examples use 'tcsh'
* missing R packages (see rPkgsInstall)
* insufficient data for AFNI bootcamp
* please set DYLD_LIBRARY_PATH to include /opt/X11/lib/flat_namespace

And this is the output when running the tcsh shell.
========================= summary, please fix: =========================
* just be aware: login shell 'zsh', but our code examples use 'tcsh'
* missing R packages (see rPkgsInstall)
* insufficient data for AFNI bootcamp

These summaries appear after I ran "rPkgsInstall -pkgs ALL". There was another topic here where someone had a similiar problem and you wrote that the message "please set DYLD_LIBRARY_PATH to include /opt/X11/lib/flat_namespace" under zsh might just be a bug while running zsh, but that in fact everything is ok. Even if that would be the case, we would still face the problem with the missing R packages (or could that be a bug too?).

Let's sum it up:
- The problem with the "R_io.so" file seems solved.
- The message to incldue the DYLD_LIBRARY path might be a bug related to the usage of zsh.
- What would be your idea to solve the problem with the missing R packages? Are there some other files required for AFNI that might be missing on my computer?


rick reynolds Wrote:
-------------------------------------------------------
> Hi Philipp,
>
> If you really want to use the R packages on that
> mac, it might be necessary to compile AFNI
> locally, which might take some work (the homebrew
> dependencies seem to be a bit of a moving target
> right now). Is that something that you would like
> to consider? Otherwise, is installing 3.6 an
> option?
>
> - rick

I am not sure if my knowledge would allow me to do those changes in AFNI and on my computer. But is that option off the table since I already switched to R 3.6.3 anyway? Please let me know if you have another idea on the "missing R packages (see rPkgsInstall)" output by AFNIs system check, or if you think that this problem is directly related to what you just explained and asked me above, so that I have to compile AFNI locally, whatever this means in detail.

Thanks,
Philipp



Edited 1 time(s). Last edit at 11/05/2021 06:40AM by Philipp.