Problem when installing Monocle 3

[YiqunCao]

Hi, I followed the instruction to install Monocle 3 till the last step, it stucked as follows for overnight. What could be the reason? Thank you! Elaine

devtools::install_github("cole-trapnell-lab/monocle-release", ref="monocle3_alpha")

Downloading GitHub repo cole-trapnell-lab/monocle-release@monocle3_alpha from URL https://api.github.com/repos/cole-trapnell-lab/monocle-release/zipball/monocle3_alpha Installing monocle '/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet CMD INSTALL \ '/private/var/folders/x2/6bjjdwtj0ms6wdvzqr_45xg00000gn/T/RtmpcNyq8B/devtools58af68e089f5/cole-trapnell-lab-monocle-release-e6785b2' \ --library='/Library/Frameworks/R.framework/Versions/3.5/Resources/library' --install-tests

installing source package ‘monocle’ ... libs clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include -std=c++11 -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include -std=c++11 -fPIC -Wall -g -O2 -c clustering.cpp -o clustering.o clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include -std=c++11 -fPIC -Wall -g -O2 -c landmark_selection.cpp -o landmark_selection.o landmark_selection.cpp:235:7: warning: unused variable 'num_proc' [-Wunused-variable] int num_proc = stoi(str_num_proc); ^ 1 warning generated. clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o monocle.so RcppExports.o clustering.o landmark_selection.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/monocle/libs R data moving datasets to lazyload DB inst tests ** byte-compile and prepare package for lazy loading

[Xiaojieqiu]

Have you got any luck since then? I cannot figure out the issue based on this message

[qinzhu]

Encountered the same problem on a MacOS 10.12.6 machine... Any suggestions?

[Xiaojieqiu]

hey @qinzhu have you tried to install it by git clone the monocle-release repo and then build and install the monocle-3alpha branch after you git checkout to that branch?

[qinzhu]

Yes I have tried, still stuck...

[Xiaojieqiu]

Could you please let me know what did you do exactly? I can take a close into it. We tested the workflow from a fresh machine before we release the tutorial and didn't have the issue you mentioned on our hand.

[qinzhu]

I think this might be a machine-specific problem. I tested the installation on another mac with pretty much same system. It works out on that machine...