Open ibgui00 opened 6 months ago
We have been running into this issue as well and would appreciate a fix. Installation from source (bioconductor, github) yields the following error message:
clang++ -arch arm64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o CytoML.so cpp11.o parseFlowJoWorkspace.o /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/lib/libcytolib.a /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhdf5lib/lib/libhdf5_cpp.a /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhdf5lib/lib/libhdf5.a -L/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhdf5lib/lib -lcrypto -lcurl -lsz -laec -lz -ldl -lm -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib -lxml2 -lz -lpthread -licucore -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: ignoring duplicate libraries: '-lm', '-lz'
ld: library 'crypto' not found
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [CytoML.so] Error 1
ERROR: compilation failed for package ‘CytoML’
I have tried sourcing CytoML.so
and building CytoML on other machines, but was not successful:
library(CytoML)
then errors with CytoML.so' (not a mach-o file)
I am using the M3 chip and I too am having trouble installing it with the same error.
Using an Apple M1 chip with macOS Sonoma 14.1.1, R version 4.3.3., I also have this problem, also with ld: library 'crypto' not found
. Using the x86_64 version of R does not fix this problem (same error message). Any work-arounds for this?
I have two mac users who also experience the ld: library 'crypto' not found
error (no solution yet). As far as I can tell the 'crypto' package is related to cryptocurrency so this seems really odd (perhaps sketchy?).
Installing OpenSSL and updating PATH resolves this issue on at least some machines.
In terminal:
brew install openssl
In R session:
Sys.setenv(LIBRARY_PATH = '/opt/homebrew/lib')
Sys.setenv(LDFLAGS = '-L/opt/homebrew/lib')
Sys.setenv(CPPFLAGS = '-I/opt/homebrew/include')
If this works consistently, it should enable the package authors to include Apple Silicon install instructions and to provide a macOS arm64 binary on Bioconductor if they choose to.
Installing OpenSSL and updating PATH resolves this issue on at least some machines.
In terminal:
brew install openssl
In R session:
Sys.setenv(LIBRARY_PATH = '/opt/homebrew/lib') Sys.setenv(LDFLAGS = '-L/opt/homebrew/lib') Sys.setenv(CPPFLAGS = '-I/opt/homebrew/include')
If this works consistently, it should enable the package authors to include Apple Silicon install instructions and to provide a macOS arm64 binary on Bioconductor if they choose to.
This worked! Thank you!
@davnovak thanks. That worked for me. Adding the PATHs worked. Interestingly, most of the times that I have brew
dependencies, I can launch R
from the command line and compile from source then. But that did not work for CytoML
.
But manually setting the paths did! So thank you, learned something new.
The installation is incompatible with Apple Silicon Mac. Is anyone aware of how to go around this issue?