Problem installing from trunk about cytoml HOT 6 CLOSED

You need to install the latest RProtoBufLib and cytolib

from cytoml.

Thank you, this did the trick:
install_github("RGLab/RProtoBufLib", ref="trunk")
install_github("RGLab/cytolib", ref="trunk")
install_github("RGLab/flowWorkspace", ref="trunk")

from cytoml.

Actually, the flowWorkspace package still gives me an error:

clang++ -std=gnu++11 -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 flowWorkspace.so R_API.o R_GatingHierarchy.o R_GatingSet.o RcppExports.o getSingleCellExpression.o setCounts.o /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RProtoBufLib/lib/GatingSet.pb.o /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RProtoBufLib/lib/libprotobuf.a -lxml2 -lz -lpthread -licucore -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: ignoring file /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RProtoBufLib/lib/GatingSet.pb.o, file was built for unsupported file format ( 0x7F 0x45 0x4C 0x46 0x02 0x01 0x01 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 ) which is not the architecture being linked (x86_64): /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RProtoBufLib/lib/GatingSet.pb.o
if [ uname -s = 'Darwin' ]; then install_name_tool -change /usr/local/clang4/lib/libc++.1.dylib /usr/lib/libc++.1.dylib flowWorkspace.so; fi
installing to /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/libs
** R
** inst
** tests
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Error: package or namespace load failed for ‘flowWorkspace’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/libs/flowWorkspace.so':
dlopen(/Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/libs/flowWorkspace.so, 6): Symbol not found: __ZN2pb11ellipseGate17default_instance_E
Referenced from: /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/libs/flowWorkspace.so
Expected in: flat namespace
in /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/libs/flowWorkspace.so
Error: loading failed
Execution halted

from cytoml.

Sorry, included the object file in repo by mistake. Try to re-install RProtoBufLib from github.

from cytoml.

Ok, I was able to install the libraries from github. I now have:
flowWorkspace version 3.27.6
openCyto version 1.17.2
flowCore version 1.45.2

My original problem was not being able to import a Gating-ML 2.0 file from Cytobank into R, the error: Error in FUN(X[[i]], ...) :
Don't know how to inverse transformation: logtGml2

I was hoping the updated libraries would be able to deal with that, but the error persists.

from cytoml.

see #30

from cytoml.