![]() Installation of package ‘hdf5r’ had non-zero exit statusģ: In install.packages("Seurat", dependencies = TRUE) :Ĥ: In install.packages("Seurat", dependencies = TRUE) : Today I've tried a fresh R install and using install('Seurat', dependencies = TRUE), I still got similar errors:ġ: In install.packages("Seurat", dependencies = TRUE) :Ģ: In install.packages("Seurat", dependencies = TRUE) : Then, I've tried install.packages('sn') and got:ĮRROR: dependency ‘mnormt’ is not available for package ‘sn’ Installation of package ‘metap’ had non-zero exit status Installation of package ‘TFisher’ had non-zero exit status Installation of package ‘sn’ had non-zero exit status I followed the instructions, but I got problems with install.packages('metap'): This can be accomplished with the following commands: - install.packages('BiocManager') BiocManager::install('multtest') install.packages('metap'). ![]() Its output is the message:Įrror: Please install the metap package to use FindConservedMarkers. However, the function FindConservedMarkers stopped working now (in the same tutorial, I didn't modify anything). Last edit at 06:40AM by Philipp.I was following the guided tutorial Stimulated vs Control PBMCs using RStudio. 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.Įdited 1 time(s). I am not sure if my knowledge would allow me to do those changes in AFNI and on my computer. > to consider? Otherwise, is installing 3.6 an > dependencies seem to be a bit of a moving target > locally, which might take some work (the homebrew > mac, it might be necessary to compile AFNI > If you really want to use the R packages on that 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? The message to incldue the DYLD_LIBRARY path might be a bug related to the usage of zsh. ![]() The problem with the "R_io.so" file seems solved. 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?). 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. These summaries appear after I ran "rPkgsInstall -pkgs ALL". * please set DYLD_LIBRARY_PATH to include /opt/X11/lib/flat_namespaceĪnd this is the output when running the tcsh shell. * just be aware: login shell 'zsh', but our code examples use 'tcsh' This is the output of AFNIs system check while running the Zsh shell (my favorite shell). Now what is interesting is the following fact: Installation of package ‘afex’ had non-zero exit status Installation of package ‘car’ had non-zero exit statusĤ: In install.packages(pkgs_miss, dep = TRUE, repos = site) : Installation of package ‘glmmTMB’ had non-zero exit statusģ: In install.packages(pkgs_miss, dep = TRUE, repos = site) : Installation of package ‘quantreg’ had non-zero exit statusĢ: In install.packages(pkgs_miss, dep = TRUE, repos = site) : This package has been installed on the computer: afexġ: In install.packages(pkgs_miss, dep = TRUE, repos = site) : The download and installation of "rPkgsInstall -pkgs ALL" then ends with the following message output: These warnings occur both when running "rPkgsInstall -pkgs ALL" under the tcsh and zsh shell. 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). Instead, the terminal starts to download the updates. When I now run "rPkgsInstall -pkgs ALL" the error "load R_io.so" does no longer occur. I also uninstalled the newest R version and switched back to 3.6.3. If I switch to tcsh, this message does no longer occur when doing the system check. 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. The command line "export DYLD_LIBRARY_PATH=$:/opt/X11/lib/flat_namespace" is added in my ".zshrc" file. The current status of the problem is as follows. I uninstalled and reinstalled AFNI a couple of times now.
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