R
lapply(list.files(pattern = "\\.qmd$"), rstudioapi::documentOpen)1 Command line developer tools not found
If you don’t yet have Mac OSX command line developer tools, please install it using:
xcode-select --install2 Error: umap-learn not found, or other python packages
If your R does not find the correct python version, it will complain that umap-learn is not installed and ask you to install it. Here are some tips on how to find the correct python version that was installed in the conda environment.
Try selecting the correct conda env in R. In this example the conda environment is named myenv.
library(reticulate)
reticulate::use_conda("myenv")Then check what python you have in R:
reticulate::py_config()
# should read at top:
python: /Users/asbj/miniconda3/envs/myenv/bin/pythonIf that still is not right, you may have an r-reticulate python installation as well and need to perform the steps below.
- Restart R and select python version
- First, find out what path you have to your conda python (in TERMINAL):
which python
/Users/asbj/miniconda3/envs/scRNAseq2021/bin/python- Then in R (after restarting):
reticulate::use_python("/Users/asbj/miniconda3/envs/scRNAseq2021/bin/python", required=T)- Then check again with
py_configif correct version of python is used:
reticulate::py_config()- If you have the correct version now, you should be able to run UMAP without issues.
3 Unable to load stringi.so
You can install stringi in R using:
install.packages('stringi')4 ERROR: Failed building wheel for gevent / MacOSX10.9.sdk missing
This is a problem with the MacOSX compiler, in which conda is unable to find it.
#Download MacOSX10.9.sdk from Github
curl -o MacOSX10.9.sdk.tar.gz "https://github.com/phracker/MacOSX-SDKs/releases/download/11.3/MacOSX10.9.sdk.tar.xz"
#extract
sudo tar -xzf MacOSX10.9.sdk.tar.xz
#copy
sudo cp -r MacOSX10.9.sdk /opt/
#give executable permissions
sudo chmod -R a+rX /opt
#Link the path where conda looks to where the file is
ln -s /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk /opt/MacOSX10.9.sdk5 ERROR: option error has NULL value
This error happens when running code inline. One possible solution is to restart Rstudio and type.
if(interactive()) { options(error = utils::recover)}Please try other solutions listed here. If none of those work, you can click on the wheel engine symbol and check Chunk output in console.
6 R crashes due to memory issues
If R crashes due to memory issues, it may be a good idea to increase the vector size R_MAX_VSIZE. Put in the file .Renviron either in your home directory or the folder you are launching Rstudio from:
R_MAX_VSIZE=70GbOr to whatever value matches your computer, the default size is 16Gb.
7 Docker run fails on Mac apple silicon
Docker run on Apple Mac M1/M2/M3 processors experience this error when running docker run ... on an image not built on Apple silicon.
[s6-init] making user provided files available at /var/run/s6/etc...exited 0.
[s6-init] ensuring user provided files have correct perms...exited 0.
[fix-attrs.d] applying ownership & permissions fixes...
[fix-attrs.d] done.
[cont-init.d] executing container initialization scripts...
[cont-init.d] 01_set_env: executing...
skipping /var/run/s6/container_environment/HOME
skipping /var/run/s6/container_environment/PASSWORD
skipping /var/run/s6/container_environment/RSTUDIO_VERSION
[cont-init.d] 01_set_env: exited 0.
[cont-init.d] 02_userconf: executing...
[cont-init.d] 02_userconf: exited 0.
[cont-init.d] done.
[services.d] starting services
[services.d] done.
TTY detected. Printing informational message about logging configuration. Logging configuration loaded from '/etc/rstudio/logging.conf'. Logging to 'syslog'.
rserver[1195]: ERROR system error 1 (Operation not permitted); OCCURRED AT rstudio::core::Error rstudio::core::system::posix::{anonymous}::restorePrivilegesImpl(uid_t) src/cpp/shared_core/system/PosixSystem.cpp:97; LOGGED FROM: void rstudio::server::pam_auth::{anonymous}::assumeRootPriv() src/cpp/server/ServerPAMAuth.cpp:59
2023-11-28T14:31:03.943703Z [rserver] ERROR system error 1 (Operation not permitted); OCCURRED AT rstudio::core::Error rstudio::core::system::posix::{anonymous}::restorePrivilegesImpl(uid_t) src/cpp/shared_core/system/PosixSystem.cpp:97; LOGGED FROM: void rstudio::server::pam_auth::{anonymous}::assumeRootPriv() src/cpp/server/ServerPAMAuth.cpp:59
rserver[1199]: ERROR system error 1 (Operation not permitted); OCCURRED AT rstudio::core::Error rstudio::core::system::posix::{anonymous}::restorePrivilegesImpl(uid_t) src/cpp/shared_core/system/PosixSystem.cpp:97; LOGGED FROM: rstudio::core::Error rstudio::core::system::launchChildProcess(std::string, std::string, rstudio::core::system::ProcessConfig, rstudio::core::system::ProcessConfigFilter, PidType*) src/cpp/core/system/PosixSystem.cpp:2195In Docker Settings > General, check Use Rosetta for x86/amd64 emulation on Apple Silicon.
8 Open multiple files simultaneously in RStudio
Open all qmd files in the current working directory.