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Can not install Cyclops on Mac 10.8

Developers
#1

Hi ALL,

I was trying to install Cyclops on Mac version 10.8. Here are the errors I got:

library(devtools)
install_github(“ohdsi/Cyclops”)
Downloading github repo ohdsi/Cyclops@master
Installing Cyclops
‘/Library/Frameworks/R.framework/Resources/bin/R’ --vanilla CMD INSTALL
‘/private/var/folders/h9/916cb9hj6tq1nvnvtfpb4c901544sj/T/Rtmp4paLaK/devtools7ef7ed57634/OHDSI-Cyclops-57327d5’
–library=’/Library/Frameworks/R.framework/Versions/3.1/Resources/library’
–install-tests

  • installing source package ‘Cyclops’ …
    ** libs
    I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Icyclops -DR_BUILD -DDOUBLE_PRECISION -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppEigen/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppParallel/include" -c IsSorted.cpp -o IsSorted.o
    /bin/sh: I/Library/Frameworks/R.framework/Resources/include: No such file or directory
    make: [IsSorted.o] Error 127 (ignored)
    I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Icyclops -DR_BUILD -DDOUBLE_PRECISION -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppEigen/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppParallel/include" -c RcppCyclopsInterface.cpp -o RcppCyclopsInterface.o
    /bin/sh: I/Library/Frameworks/R.framework/Resources/include: No such file or directory
    make: [RcppCyclopsInterface.o] Error 127 (ignored)
    I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Icyclops -DR_BUILD -DDOUBLE_PRECISION -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppEigen/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppParallel/include" -c RcppExports.cpp -o RcppExports.o
    /bin/sh: I/Library/Frameworks/R.framework/Resources/include: No such file or directory
    make: [RcppExports.o] Error 127 (ignored)
    I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Icyclops -DR_BUILD -DDOUBLE_PRECISION -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppEigen/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppParallel/include" -c RcppIsSorted.cpp -o RcppIsSorted.o
    /bin/sh: I/Library/Frameworks/R.framework/Resources/include: No such file or directory
    make: [RcppIsSorted.o] Error 127 (ignored)
    I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Icyclops -DR_BUILD -DDOUBLE_PRECISION -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppEigen/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppParallel/include" -c RcppModelData.cpp -o RcppModelData.o
    /bin/sh: I/Library/Frameworks/R.framework/Resources/include: No such file or directory
    make: [RcppModelData.o] Error 127 (ignored)
    I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Icyclops -DR_BUILD -DDOUBLE_PRECISION -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppEigen/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppParallel/include" -c cyclops/CcdInterface.cpp -o cyclops/CcdInterface.o
    /bin/sh: I/Library/Frameworks/R.framework/Resources/include: No such file or directory
    make: [cyclops/CcdInterface.o] Error 127 (ignored)
    I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Icyclops -DR_BUILD -DDOUBLE_PRECISION -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppEigen/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppParallel/include" -c cyclops/CompressedDataMatrix.cpp -o cyclops/CompressedDataMatrix.o
    /bin/sh: I/Library/Frameworks/R.framework/Resources/include: No such file or directory
    make: [cyclops/CompressedDataMatrix.o] Error 127 (ignored)
    I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Icyclops -DR_BUILD -DDOUBLE_PRECISION -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppEigen/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppParallel/include" -c cyclops/CyclicCoordinateDescent.cpp -o cyclops/CyclicCoordinateDescent.o
    /bin/sh: I/Library/Frameworks/R.framework/Resources/include: No such file or directory
    make: [cyclops/CyclicCoordinateDescent.o] Error 127 (ignored)
    I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Icyclops -DR_BUILD -DDOUBLE_PRECISION -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppEigen/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppParallel/include" -c cyclops/ModelData.cpp -o cyclops/ModelData.o
    /bin/sh: I/Library/Frameworks/R.framework/Resources/include: No such file or directory
    make: [cyclops/ModelData.o] Error 127 (ignored)
    I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Icyclops -DR_BUILD -DDOUBLE_PRECISION -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppEigen/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppParallel/include" -c cyclops/SqlModelData.cpp -o cyclops/SqlModelData.o
    /bin/sh: I/Library/Frameworks/R.framework/Resources/include: No such file or directory
    make: [cyclops/SqlModelData.o] Error 127 (ignored)
    I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Icyclops -DR_BUILD -DDOUBLE_PRECISION -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppEigen/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppParallel/include" -c cyclops/Timer.cpp -o cyclops/Timer.o
    /bin/sh: I/Library/Frameworks/R.framework/Resources/include: No such file or directory
    make: [cyclops/Timer.o] Error 127 (ignored)
    I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Icyclops -DR_BUILD -DDOUBLE_PRECISION -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppEigen/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppParallel/include" -c cyclops/drivers/AbstractCrossValidationDriver.cpp -o cyclops/drivers/AbstractCrossValidationDriver.o
    /bin/sh: I/Library/Frameworks/R.framework/Resources/include: No such file or directory
    make: [cyclops/drivers/AbstractCrossValidationDriver.o] Error 127 (ignored)
    I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Icyclops -DR_BUILD -DDOUBLE_PRECISION -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppEigen/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppParallel/include" -c cyclops/drivers/AbstractDriver.cpp -o cyclops/drivers/AbstractDriver.o
    /bin/sh: I/Library/Frameworks/R.framework/Resources/include: No such file or directory
    make: [cyclops/drivers/AbstractDriver.o] Error 127 (ignored)
    I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Icyclops -DR_BUILD -DDOUBLE_PRECISION -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppEigen/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppParallel/include" -c cyclops/drivers/AbstractSelector.cpp -o cyclops/drivers/AbstractSelector.o
    /bin/sh: I/Library/Frameworks/R.framework/Resources/include: No such file or directory
    make: [cyclops/drivers/AbstractSelector.o] Error 127 (ignored)
    I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Icyclops -DR_BUILD -DDOUBLE_PRECISION -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppEigen/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppParallel/include" -c cyclops/drivers/AutoSearchCrossValidationDriver.cpp -o cyclops/drivers/AutoSearchCrossValidationDriver.o
    /bin/sh: I/Library/Frameworks/R.framework/Resources/include: No such file or directory
    make: [cyclops/drivers/AutoSearchCrossValidationDriver.o] Error 127 (ignored)
    I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Icyclops -DR_BUILD -DDOUBLE_PRECISION -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppEigen/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppParallel/include" -c cyclops/drivers/BootstrapDriver.cpp -o cyclops/drivers/BootstrapDriver.o
    /bin/sh: I/Library/Frameworks/R.framework/Resources/include: No such file or directory
    make: [cyclops/drivers/BootstrapDriver.o] Error 127 (ignored)
    I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Icyclops -DR_BUILD -DDOUBLE_PRECISION -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppEigen/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppParallel/include" -c cyclops/drivers/BootstrapSelector.cpp -o cyclops/drivers/BootstrapSelector.o
    /bin/sh: I/Library/Frameworks/R.framework/Resources/include: No such file or directory
    make: [cyclops/drivers/BootstrapSelector.o] Error 127 (ignored)
    I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Icyclops -DR_BUILD -DDOUBLE_PRECISION -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppEigen/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppParallel/include" -c cyclops/drivers/CrossValidationSelector.cpp -o cyclops/drivers/CrossValidationSelector.o
    /bin/sh: I/Library/Frameworks/R.framework/Resources/include: No such file or directory
    make: [cyclops/drivers/CrossValidationSelector.o] Error 127 (ignored)
    I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Icyclops -DR_BUILD -DDOUBLE_PRECISION -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppEigen/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppParallel/include" -c cyclops/drivers/GridSearchCrossValidationDriver.cpp -o cyclops/drivers/GridSearchCrossValidationDriver.o
    /bin/sh: I/Library/Frameworks/R.framework/Resources/include: No such file or directory
    make: [cyclops/drivers/GridSearchCrossValidationDriver.o] Error 127 (ignored)
    I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Icyclops -DR_BUILD -DDOUBLE_PRECISION -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppEigen/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppParallel/include" -c cyclops/drivers/HierarchyAutoSearchCrossValidationDriver.cpp -o cyclops/drivers/HierarchyAutoSearchCrossValidationDriver.o
    /bin/sh: I/Library/Frameworks/R.framework/Resources/include: No such file or directory
    make: [cyclops/drivers/HierarchyAutoSearchCrossValidationDriver.o] Error 127 (ignored)
    I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Icyclops -DR_BUILD -DDOUBLE_PRECISION -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppEigen/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppParallel/include" -c cyclops/drivers/HierarchyGridSearchCrossValidationDriver.cpp -o cyclops/drivers/HierarchyGridSearchCrossValidationDriver.o
    /bin/sh: I/Library/Frameworks/R.framework/Resources/include: No such file or directory
    make: [cyclops/drivers/HierarchyGridSearchCrossValidationDriver.o] Error 127 (ignored)
    I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Icyclops -DR_BUILD -DDOUBLE_PRECISION -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppEigen/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppParallel/include" -c cyclops/drivers/ProportionSelector.cpp -o cyclops/drivers/ProportionSelector.o
    /bin/sh: I/Library/Frameworks/R.framework/Resources/include: No such file or directory
    make: [cyclops/drivers/ProportionSelector.o] Error 127 (ignored)
    I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Icyclops -DR_BUILD -DDOUBLE_PRECISION -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppEigen/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppParallel/include" -c cyclops/engine/AbstractModelSpecifics.cpp -o cyclops/engine/AbstractModelSpecifics.o
    /bin/sh: I/Library/Frameworks/R.framework/Resources/include: No such file or directory
    make: [cyclops/engine/AbstractModelSpecifics.o] Error 127 (ignored)
    I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Icyclops -DR_BUILD -DDOUBLE_PRECISION -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppEigen/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppParallel/include" -c cyclops/io/InputReader.cpp -o cyclops/io/InputReader.o
    /bin/sh: I/Library/Frameworks/R.framework/Resources/include: No such file or directory
    make: [cyclops/io/InputReader.o] Error 127 (ignored)
    I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Icyclops -DR_BUILD -DDOUBLE_PRECISION -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppEigen/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppParallel/include" -c cyclops/priors/CovariatePrior.cpp -o cyclops/priors/CovariatePrior.o
    /bin/sh: I/Library/Frameworks/R.framework/Resources/include: No such file or directory
    make: [cyclops/priors/CovariatePrior.o] Error 127 (ignored)
    I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Icyclops -DR_BUILD -DDOUBLE_PRECISION -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppEigen/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppParallel/include" -c utils/HParSearch.cpp -o utils/HParSearch.o
    /bin/sh: I/Library/Frameworks/R.framework/Resources/include: No such file or directory
    make: [utils/HParSearch.o] Error 127 (ignored)
    I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Icyclops -DR_BUILD -DDOUBLE_PRECISION -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppEigen/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppParallel/include" -c tinythread/tinythread.cpp -o tinythread/tinythread.o
    /bin/sh: I/Library/Frameworks/R.framework/Resources/include: No such file or directory
    make: [tinythread/tinythread.o] Error 127 (ignored)
    -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 -L/usr/local/lib -o Cyclops.so IsSorted.o RcppCyclopsInterface.o RcppExports.o RcppIsSorted.o RcppModelData.o cyclops/CcdInterface.o cyclops/CompressedDataMatrix.o cyclops/CyclicCoordinateDescent.o cyclops/ModelData.o cyclops/SqlModelData.o cyclops/Timer.o cyclops/drivers/AbstractCrossValidationDriver.o cyclops/drivers/AbstractDriver.o cyclops/drivers/AbstractSelector.o cyclops/drivers/AutoSearchCrossValidationDriver.o cyclops/drivers/BootstrapDriver.o cyclops/drivers/BootstrapSelector.o cyclops/drivers/CrossValidationSelector.o cyclops/drivers/GridSearchCrossValidationDriver.o cyclops/drivers/HierarchyAutoSearchCrossValidationDriver.o cyclops/drivers/HierarchyGridSearchCrossValidationDriver.o cyclops/drivers/ProportionSelector.o cyclops/engine/AbstractModelSpecifics.o cyclops/io/InputReader.o cyclops/priors/CovariatePrior.o utils/HParSearch.o tinythread/tinythread.o -F/Library/Frameworks/R.framework/… -framework R -Wl,-framework -Wl,CoreFoundation
    /bin/sh: -dynamiclib: command not found
    make: *** [Cyclops.so] Error 127
    ERROR: compilation failed for package ‘Cyclops’
  • removing ‘/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Cyclops’
    Error: Command failed (1)
#2

@yonghui

I just tested this on my Mac using the following:

  • Mac OSX 10.10.2
  • R for Mac OS X GUI (R 3.1.1 GUI 1.65)

Here are the contents of the directory that the build is reporting as missing for you:

$ ls /Library/Frameworks/R.framework/Resources/include/
R.h Rconfig.h Rembedded.h Rinternals.h Rversion.h libintl.h
R_ext Rdefines.h Rinterface.h Rmath.h S.h

I was able to get the install to work locally using this configuration. The only reported warning concerns unused variables:

In file included from cyclops/engine/AbstractModelSpecifics.cpp:13:
In file included from cyclops/engine/ModelSpecifics.h:1906:
In file included from cyclops/engine/ModelSpecifics.hpp:25:
cyclops/engine/Ranges.h:638:22: warning: unused variable ‘K’ [-Wunused-variable]
const size_t K = mat.getNumberOfRows();
^
cyclops/engine/Ranges.h:660:22: warning: unused variable ‘K’ [-Wunused-variable]
const size_t K = mat.getNumberOfRows();
^
2 warnings generated.

Bill

#3

Thanks for your post. I checked the folder that was reported missing during installation, they are all there:

bash-3.2$ ls /Library/Frameworks/R.framework/Resources/include
R.h R_ext Rconfig.h Rdefines.h Rembedded.h Rinterface.h Rinternals.h Rmath.h Rversion.h S.h libintl.h
bash-3.2$

It seems for some reason, the include path string was not correctly generated.
‘I/Library/Frameworks/R.framework/Resources/include’

instead of
‘/Library/Frameworks/R.framework/Resources/include’

#4

yonghui I can’t reproduce your error since I don’t have a Mac, but I can at least say that the problem is almost certainly with the backend producing the compiliation commands. I.e. one of the commands is the following:

I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Icyclops -DR_BUILD -DDOUBLE_PRECISION -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppEigen/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppParallel/include" -c IsSorted.cpp -o IsSorted.o

That is what your shell is executing. But the first part (i.e. ‘I/Library/Frameworks/R.framework/Resources/include’) is being interpreted as a program. So even if you changed that to the correct path it would still be an error. The first thing on that line should be ‘g++’ or something like that (g++ is the name of the gnu c++ compiler).

You do have a c++ compiler installed right?

#5

Yes. I tried two versions of c++. The current version on my Mac is:

bash-3.2$ /usr/bin/gcc --version
gcc (Homebrew gcc49 4.9.0) 4.9.0
Copyright © 2014 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

bash-3.2$ /usr/bin/g++ --version
g++ (Homebrew gcc49 4.9.0) 4.9.0
Copyright © 2014 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

I will double check the environment variables related to g++.

Installing cyclops on gnu linux
#6

It might be something weird with Cyclops, but there are also many levels to the compilation build tools. You might do a sanity check by downloading Rcpp (which is pretty simple) from here:

Click on the download link on the right and extract it somewhere and then start up R in that unzipped folder. Finally run the following command:

remove.packages("Rcpp") # If necessary
install.packages(getwd(), repos = NULL, type = "source")

If that doesn’t work, the problem is deeper than Cyclops and if that does work, then the problem is probably with devtools or Cyclops.

#7

Actually now that I think about it, you might first want to try to install Cyclops in the same way. I.e. download the zip file from here

https://github.com/ohdsi/cyclops

In this case don’t run the command above, but instead go into the folder and just run:

library(devtools)
install()

I’m not sure why that would be any different, but it might be easier to localize the problem with the source tree handy.

#8

A final thing to try is to do the previous post’s instructions in the Rcpp directory. I.e. use devtools to install Rcpp. After doing all these things you should at least be able to localize the issue a bit better.

Also if any of this isn’t making sense, just ping me and I can try to explain better. Good luck!

#9

The problem was fixed by editing the file ‘Makevars’:

CXX_STD = /usr/bin/g++
PKG_CPPFLAGS = -std=c++11 -I. -Icyclops -DR_BUILD -DDOUBLE_PRECISION

I downloaded the zip package according to the suggestion from Tom.
Then, modify the file ‘Makevars’.
Finally, the installation was finished by:

library(devtools)
install()

Thanks for your help, Tom, William.
Cheers.

#10

My Mac builds this using clang++:

clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Icyclops -DR_BUILD -DDOUBLE_PRECISION -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppEigen/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppParallel/include" -fPIC -Wall -mtune=core2 -g -O2 -c cyclops/engine/AbstractModelSpecifics.cpp -o cyclops/engine/AbstractModelSpecifics.o

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