We have a C++ library (libEDM.a) that integrates Eigen. The library is standalone as a core API to be wrapped with Rcpp and pybind11 for user interfaces.
Since Eigen is called internally from the library, we do not use RcppEigen in the Rcpp wrapper.
This works fine on linux and OSX R package builds, and the mingw-32 (arch - i386) build for R (using devtools::check_win_release).
However, for the (arch - x64) build with mingw-64, the linker fails to find Eigen references in the C++ libEDM.a, vis (from winbuilder):
d:/Compiler/gcc-4.9.3/mingw_64/bin/g++ -m64 -shared -s -static-libgcc -o rEDMNew.dll tmp.def CCM.o ComputeError.o DataFrame.o Embed.o EmbedDim.o Multiview.o PredictInterval.o PredictNL.o RcppEDMCommon.o RcppExports.o SMap.o Simplex.o -L./cppEDM/src/ -lEDM -Ld:/Compiler/gcc-4.9.3/local330/lib/x64 -Ld:/Compiler/gcc-4.9.3/local330/lib -LD:/RCompile/recent/R-3.6.1/bin/x64 -lR
./cppEDM/src//libEDM.a(SMap.o):SMap.cc:(.text+0x245d): undefined reference to `Eigen::internal::first_aligned_impl<16, Eigen::CwiseUnaryOp<Eigen::internal::scalar_abs2_op<double>, Eigen::Block<Eigen::Block<Eigen::Block<Eigen::Matrix<double, -1, -1, 0, -1, -1>, -1, 1, true>, -1, 1, false> const, -1, 1, false> const>, true>::run(Eigen::CwiseUnaryOp<Eigen::internal::scalar_abs2_op<double>, Eigen::Block<Eigen::Block<Eigen::Block<Eigen::Matrix<double, -1, -1, 0, -1, -1>, -1, 1, true>, -1, 1, false> const, -1, 1, false> const> const&)'
A wrinkle for the mingw-64 is the addition of -Wa,-mbig-obj flag passed to the linker, as it seems Eigen templates with mingw-64 exceed the number of sections allowed.
Perhaps it is a mingw-64 linker/option issue, as the mingw-32 and other builds seem to work fine?
Update:
It seems that the linker configuration and Eigen are stuck in some kind of recursive search. Using Rtools35 on a Windows 10 box with R 3.4.3, and the following Makevars.win:
PKG_CPPFLAGS = -I./cppEDM/src -I../
PKG_LIBS = -L./cppEDM/src/ -lEDM
CXX_STD = CXX11
$(SHLIB): cppEDM/src/libEDM.a
cppEDM/src/libEDM.a:
#(cd cppEDM/src && $(MAKE) -f makefile.mingw \
CC="$(CC)" CFLAGS="-Wa,-mbig-obj -std=c++11 -DCCM_THREADED -DMULTIVIEW_VALUES_OVERLOAD -I../ $(CPICFLAGS)" AR="$(AR)" RANLIB="$(RANLIB)")
The build has two phases. First the Rcpp interface code is compiled by the canonical Makefile, then the libEDM.a is built in cppEDM/src, which is then linked against the Rcpp objects for the final library.
The i386 build seems fine, creates and installs rEDMNew.dll as noted below. The x64 build appears to build without incident, and then takes about 20 minutes to create rEDMNew.dll in the src/-x64/ directory. However, it then seems stalled, CPU running ~50% for hours... and the rEDMNew.dll not installed.
Any ideas? Perhaps a linker flag?
I presume that x64 build failure is a CRAN disqualification. This is the last hurdle, but seems like a big one.
C:.\EDM\rEDM_cpp_dev>R CMD INSTALL rEDMNew
In R CMD INSTALL
* installing to library './R/win-library/3.4'
* installing *source* package 'rEDMNew' ...
** libs
*** arch - i386
c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/PROGRA~1/R/R-34~1.4/include" -DNDEBUG -I./cppEDM/src -I../ -I"./R/win-library/3.4/Rcpp/include" -O2 -Wall -mtune=generic -c CCM.cpp -o CCM.o
c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/PROGRA~1/R/R-34~1.4/include" -DNDEBUG -I./cppEDM/src -I../ -I"./R/win-library/3.4/Rcpp/include" -O2 -Wall -mtune=generic -c ComputeError.cpp -o ComputeError.o
c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/PROGRA~1/R/R-34~1.4/include" -DNDEBUG -I./cppEDM/src -I../ -I"./R/win-library/3.4/Rcpp/include" -O2 -Wall -mtune=generic -c DataFrame.cpp -o DataFrame.o
c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/PROGRA~1/R/R-34~1.4/include" -DNDEBUG -I./cppEDM/src -I../ -I"./R/win-library/3.4/Rcpp/include" -O2 -Wall -mtune=generic -c Embed.cpp -o Embed.o
c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/PROGRA~1/R/R-34~1.4/include" -DNDEBUG -I./cppEDM/src -I../ -I"./R/win-library/3.4/Rcpp/include" -O2 -Wall -mtune=generic -c EmbedDim.cpp -o EmbedDim.o
c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/PROGRA~1/R/R-34~1.4/include" -DNDEBUG -I./cppEDM/src -I../ -I"./R/win-library/3.4/Rcpp/include" -O2 -Wall -mtune=generic -c Multiview.cpp -o Multiview.o
c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/PROGRA~1/R/R-34~1.4/include" -DNDEBUG -I./cppEDM/src -I../ -I"./R/win-library/3.4/Rcpp/include" -O2 -Wall -mtune=generic -c PredictInterval.cpp -o PredictInterval.o
c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/PROGRA~1/R/R-34~1.4/include" -DNDEBUG -I./cppEDM/src -I../ -I"./R/win-library/3.4/Rcpp/include" -O2 -Wall -mtune=generic -c PredictNL.cpp -o PredictNL.o
c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/PROGRA~1/R/R-34~1.4/include" -DNDEBUG -I./cppEDM/src -I../ -I"./R/win-library/3.4/Rcpp/include" -O2 -Wall -mtune=generic -c RcppEDMCommon.cpp -o RcppEDMCommon.o
c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/PROGRA~1/R/R-34~1.4/include" -DNDEBUG -I./cppEDM/src -I../ -I"./R/win-library/3.4/Rcpp/include" -O2 -Wall -mtune=generic -c RcppExports.cpp -o RcppExports.o
c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/PROGRA~1/R/R-34~1.4/include" -DNDEBUG -I./cppEDM/src -I../ -I"./R/win-library/3.4/Rcpp/include" -O2 -Wall -mtune=generic -c SMap.cpp -o SMap.o
c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/PROGRA~1/R/R-34~1.4/include" -DNDEBUG -I./cppEDM/src -I../ -I"./R/win-library/3.4/Rcpp/include" -O2 -Wall -mtune=generic -c Simplex.cpp -o Simplex.o
make[1]: Entering directory './src-i386/cppEDM/src'
c:/Rtools/mingw_32/bin/gcc -c Common.cc -Wa,-mbig-obj -std=c++11 -DCCM_THREADED -DMULTIVIEW_VALUES_OVERLOAD -I../
c:/Rtools/mingw_32/bin/gcc -c AuxFunc.cc -Wa,-mbig-obj -std=c++11 -DCCM_THREADED -DMULTIVIEW_VALUES_OVERLOAD -I../
c:/Rtools/mingw_32/bin/gcc -c DateTimeUtil.cc -Wa,-mbig-obj -std=c++11 -DCCM_THREADED -DMULTIVIEW_VALUES_OVERLOAD -I../
c:/Rtools/mingw_32/bin/gcc -c Parameter.cc -Wa,-mbig-obj -std=c++11 -DCCM_THREADED -DMULTIVIEW_VALUES_OVERLOAD -I../
c:/Rtools/mingw_32/bin/gcc -c Embed.cc -Wa,-mbig-obj -std=c++11 -DCCM_THREADED -DMULTIVIEW_VALUES_OVERLOAD -I../
c:/Rtools/mingw_32/bin/gcc -c Interface.cc -Wa,-mbig-obj -std=c++11 -DCCM_THREADED -DMULTIVIEW_VALUES_OVERLOAD -I../
c:/Rtools/mingw_32/bin/gcc -c Neighbors.cc -Wa,-mbig-obj -std=c++11 -DCCM_THREADED -DMULTIVIEW_VALUES_OVERLOAD -I../
c:/Rtools/mingw_32/bin/gcc -c Simplex.cc -Wa,-mbig-obj -std=c++11 -DCCM_THREADED -DMULTIVIEW_VALUES_OVERLOAD -I../
c:/Rtools/mingw_32/bin/gcc -c Eval.cc -Wa,-mbig-obj -std=c++11 -DCCM_THREADED -DMULTIVIEW_VALUES_OVERLOAD -I../
c:/Rtools/mingw_32/bin/gcc -c CCM.cc -Wa,-mbig-obj -std=c++11 -DCCM_THREADED -DMULTIVIEW_VALUES_OVERLOAD -I../
c:/Rtools/mingw_32/bin/gcc -c Multiview.cc -Wa,-mbig-obj -std=c++11 -DCCM_THREADED -DMULTIVIEW_VALUES_OVERLOAD -I../
c:/Rtools/mingw_32/bin/gcc -c SMap.cc -Wa,-mbig-obj -std=c++11 -DCCM_THREADED -DMULTIVIEW_VALUES_OVERLOAD -I../
c:/Rtools/mingw_32/bin/ar -rcs libEDM.a Common.o AuxFunc.o DateTimeUtil.o Parameter.o Embed.o Interface.o Neighbors.o Simplex.o Eval.o CCM.o Multiview.o SMap.o
cp libEDM.a ../lib/
make[1]: Leaving directory './src-i386/cppEDM/src'
c:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o rEDMNew.dll tmp.def CCM.o ComputeError.o DataFrame.o Embed.o EmbedDim.o Multiview.o PredictInterval.o Pred
ictNL.o RcppEDMCommon.o RcppExports.o SMap.o Simplex.o -L./cppEDM/src/ -lEDM -LC:/PROGRA~1/R/R-34~1.4/bin/i386 -lR
installing to ./R/win-library/3.4/rEDMNew/libs/i386
*** arch - x64
c:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/PROGRA~1/R/R-34~1.4/include" -DNDEBUG -I./cppEDM/src -I../ -I"./R/win-library/3.4/Rcpp/include" -O2 -Wall -mtune=generic -c CCM.cpp -o CCM.o
c:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/PROGRA~1/R/R-34~1.4/include" -DNDEBUG -I./cppEDM/src -I../ -I"./R/win-library/3.4/Rcpp/include" -O2 -Wall -mtune=generic -c ComputeError.cpp -o ComputeError.o
c:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/PROGRA~1/R/R-34~1.4/include" -DNDEBUG -I./cppEDM/src -I../ -I"./R/win-library/3.4/Rcpp/include" -O2 -Wall -mtune=generic -c DataFrame.cpp -o DataFrame.o
c:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/PROGRA~1/R/R-34~1.4/include" -DNDEBUG -I./cppEDM/src -I../ -I"./R/win-library/3.4/Rcpp/include" -O2 -Wall -mtune=generic -c Embed.cpp -o Embed.o
c:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/PROGRA~1/R/R-34~1.4/include" -DNDEBUG -I./cppEDM/src -I../ -I"./R/win-library/3.4/Rcpp/include" -O2 -Wall -mtune=generic -c EmbedDim.cpp -o EmbedDim.o
c:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/PROGRA~1/R/R-34~1.4/include" -DNDEBUG -I./cppEDM/src -I../ -I"./R/win-library/3.4/Rcpp/include" -O2 -Wall -mtune=generic -c Multiview.cpp -o Multiview.o
c:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/PROGRA~1/R/R-34~1.4/include" -DNDEBUG -I./cppEDM/src -I../ -I"./R/win-library/3.4/Rcpp/include" -O2 -Wall -mtune=generic -c PredictInterval.cpp -o PredictInterval.o
c:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/PROGRA~1/R/R-34~1.4/include" -DNDEBUG -I./cppEDM/src -I../ -I"./R/win-library/3.4/Rcpp/include" -O2 -Wall -mtune=generic -c PredictNL.cpp -o PredictNL.o
c:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/PROGRA~1/R/R-34~1.4/include" -DNDEBUG -I./cppEDM/src -I../ -I"./R/win-library/3.4/Rcpp/include" -O2 -Wall -mtune=generic -c RcppEDMCommon.cpp -o RcppEDMCommon.o
c:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/PROGRA~1/R/R-34~1.4/include" -DNDEBUG -I./cppEDM/src -I../ -I"./R/win-library/3.4/Rcpp/include" -O2 -Wall -mtune=generic -c RcppExports.cpp -o RcppExports.o
c:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/PROGRA~1/R/R-34~1.4/include" -DNDEBUG -I./cppEDM/src -I../ -I"./R/win-library/3.4/Rcpp/include" -O2 -Wall -mtune=generic -c SMap.cpp -o SMap.o
c:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/PROGRA~1/R/R-34~1.4/include" -DNDEBUG -I./cppEDM/src -I../ -I"./R/win-library/3.4/Rcpp/include" -O2 -Wall -mtune=generic -c Simplex.cpp -o Simplex.o
make[1]: Entering directory './src-x64/cppEDM/src'
c:/Rtools/mingw_64/bin/gcc -c Common.cc -Wa,-mbig-obj -std=c++11 -DCCM_THREADED -DMULTIVIEW_VALUES_OVERLOAD -I../
c:/Rtools/mingw_64/bin/gcc -c AuxFunc.cc -Wa,-mbig-obj -std=c++11 -DCCM_THREADED -DMULTIVIEW_VALUES_OVERLOAD -I../
c:/Rtools/mingw_64/bin/gcc -c DateTimeUtil.cc -Wa,-mbig-obj -std=c++11 -DCCM_THREADED -DMULTIVIEW_VALUES_OVERLOAD -I../
c:/Rtools/mingw_64/bin/gcc -c Parameter.cc -Wa,-mbig-obj -std=c++11 -DCCM_THREADED -DMULTIVIEW_VALUES_OVERLOAD -I../
c:/Rtools/mingw_64/bin/gcc -c Embed.cc -Wa,-mbig-obj -std=c++11 -DCCM_THREADED -DMULTIVIEW_VALUES_OVERLOAD -I../
c:/Rtools/mingw_64/bin/gcc -c Interface.cc -Wa,-mbig-obj -std=c++11 -DCCM_THREADED -DMULTIVIEW_VALUES_OVERLOAD -I../
c:/Rtools/mingw_64/bin/gcc -c Neighbors.cc -Wa,-mbig-obj -std=c++11 -DCCM_THREADED -DMULTIVIEW_VALUES_OVERLOAD -I../
c:/Rtools/mingw_64/bin/gcc -c Simplex.cc -Wa,-mbig-obj -std=c++11 -DCCM_THREADED -DMULTIVIEW_VALUES_OVERLOAD -I../
c:/Rtools/mingw_64/bin/gcc -c Eval.cc -Wa,-mbig-obj -std=c++11 -DCCM_THREADED -DMULTIVIEW_VALUES_OVERLOAD -I../
c:/Rtools/mingw_64/bin/gcc -c CCM.cc -Wa,-mbig-obj -std=c++11 -DCCM_THREADED -DMULTIVIEW_VALUES_OVERLOAD -I../
c:/Rtools/mingw_64/bin/gcc -c Multiview.cc -Wa,-mbig-obj -std=c++11 -DCCM_THREADED -DMULTIVIEW_VALUES_OVERLOAD -I../
c:/Rtools/mingw_64/bin/gcc -c SMap.cc -Wa,-mbig-obj -std=c++11 -DCCM_THREADED -DMULTIVIEW_VALUES_OVERLOAD -I../
c:/Rtools/mingw_64/bin/ar -rcs libEDM.a Common.o AuxFunc.o DateTimeUtil.o Parameter.o Embed.o Interface.o Neighbors.o Simplex.o Eval.o CCM.o Multiview.o SMap.o
cp libEDM.a ../lib/
make[1]: Leaving directory './src-x64/cppEDM/src'
c:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o rEDMNew.dll tmp.def CCM.o ComputeError.o DataFrame.o Embed.o EmbedDim.o Multiview.o PredictInterval.o Pred
ictNL.o RcppEDMCommon.o RcppExports.o SMap.o Simplex.o -L./cppEDM/src/ -lEDM -LC:/PROGRA~1/R/R-34~1.4/bin/x64 -lR
-- This is where it just grinds away...
Apologies if I've transgressed a social norm by editing this post. Seemed like a logical thing to do rather than starting a new one.
Related
I'm trying to install rJava, an xlsx package dependency, but I'm having issues getting it to work. Every time I run the install.packages function, I get a long output culminating in the error:
"ld: library not found for -lpcre2-8"
What exactly can I do to circumvent this?
relevant info:
RStudio 2022.07.2+576 "Spotted Wakerobin"
R 4.2.2 "Innocent and Trusting"
Java 1.8.0_352 (arm64) "Azul Systems, Inc." - "Zulu 8.66.0.15"
Below are the function call and warnings/error I got in the R console. I noticed several warnings throughout after the "checking" phase.
Function call:
install.packages("rJava",type='source')
Warnings and error:
1 warning generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/Library/Java/JavaVirtualMachines/zulu-8.jdk/Contents/Home/jre/../include -I/Library/Java/JavaVirtualMachines/zulu-8.jdk/Contents/Home/jre/../include/darwin -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c arrayc.c -o arrayc.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/Library/Java/JavaVirtualMachines/zulu-8.jdk/Contents/Home/jre/../include -I/Library/Java/JavaVirtualMachines/zulu-8.jdk/Contents/Home/jre/../include/darwin -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c callJNI.c -o callJNI.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/Library/Java/JavaVirtualMachines/zulu-8.jdk/Contents/Home/jre/../include -I/Library/Java/JavaVirtualMachines/zulu-8.jdk/Contents/Home/jre/../include/darwin -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c callback.c -o callback.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/Library/Java/JavaVirtualMachines/zulu-8.jdk/Contents/Home/jre/../include -I/Library/Java/JavaVirtualMachines/zulu-8.jdk/Contents/Home/jre/../include/darwin -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c fields.c -o fields.o
fields.c:91:13: warning: unused variable 'c' [-Wunused-variable]
char *c = clnam;
^
fields.c:149:9: warning: unused variable 'clnam' [-Wunused-variable]
char *clnam = 0, *detsig = 0;
^
2 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/Library/Java/JavaVirtualMachines/zulu-8.jdk/Contents/Home/jre/../include -I/Library/Java/JavaVirtualMachines/zulu-8.jdk/Contents/Home/jre/../include/darwin -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c init.c -o init.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/Library/Java/JavaVirtualMachines/zulu-8.jdk/Contents/Home/jre/../include -I/Library/Java/JavaVirtualMachines/zulu-8.jdk/Contents/Home/jre/../include/darwin -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c jri_glue.c -o jri_glue.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/Library/Java/JavaVirtualMachines/zulu-8.jdk/Contents/Home/jre/../include -I/Library/Java/JavaVirtualMachines/zulu-8.jdk/Contents/Home/jre/../include/darwin -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c loader.c -o loader.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/Library/Java/JavaVirtualMachines/zulu-8.jdk/Contents/Home/jre/../include -I/Library/Java/JavaVirtualMachines/zulu-8.jdk/Contents/Home/jre/../include/darwin -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c otables.c -o otables.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/Library/Java/JavaVirtualMachines/zulu-8.jdk/Contents/Home/jre/../include -I/Library/Java/JavaVirtualMachines/zulu-8.jdk/Contents/Home/jre/../include/darwin -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c rJava.c -o rJava.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/Library/Java/JavaVirtualMachines/zulu-8.jdk/Contents/Home/jre/../include -I/Library/Java/JavaVirtualMachines/zulu-8.jdk/Contents/Home/jre/../include/darwin -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c registration.c -o registration.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/Library/Java/JavaVirtualMachines/zulu-8.jdk/Contents/Home/jre/../include -I/Library/Java/JavaVirtualMachines/zulu-8.jdk/Contents/Home/jre/../include/darwin -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c tools.c -o tools.o
clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o rJava.so Rglue.o arrayc.o callJNI.o callback.o fields.o init.o jri_glue.o loader.o otables.o rJava.o registration.o tools.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
(cd ../jri && make)
make -C src JRI.jar
/Library/Java/JavaVirtualMachines/zulu-8.jdk/Contents/Home/bin/javac -target 1.4 -source 1.4 -d . ../Mutex.java ../RBool.java ../RConsoleOutputStream.java ../REXP.java ../RFactor.java ../RList.java ../RMainLoopCallbacks.java ../RVector.java ../Rengine.java ../package-info.java
warning: [options] bootstrap class path not set in conjunction with -source 1.4
warning: [options] source value 1.4 is obsolete and will be removed in a future release
warning: [options] target value 1.4 is obsolete and will be removed in a future release
warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.
4 warnings
if [ -n "/Library/Java/JavaVirtualMachines/zulu-8.jdk/Contents/Home/bin/javah" ]; then /Library/Java/JavaVirtualMachines/zulu-8.jdk/Contents/Home/bin/javah -d . -classpath . org.rosuda.JRI.Rengine; fi
clang -arch arm64 -c -o Rengine.o Rengine.c -g -Iinclude -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -DHAVE_CONFIG_H -falign-functions=64 -Wall -g -O2 -I/Library/Java/JavaVirtualMachines/zulu-8.jdk/Contents/Home/jre/../include -I/Library/Java/JavaVirtualMachines/zulu-8.jdk/Contents/Home/jre/../include/darwin -fno-common -I/Library/Java/JavaVirtualMachines/zulu-8.jdk/Contents/Home/jre/../include -I/Library/Java/JavaVirtualMachines/zulu-8.jdk/Contents/Home/jre/../include/darwin -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include
clang -arch arm64 -c -o jri.o jri.c -g -Iinclude -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -DHAVE_CONFIG_H -falign-functions=64 -Wall -g -O2 -I/Library/Java/JavaVirtualMachines/zulu-8.jdk/Contents/Home/jre/../include -I/Library/Java/JavaVirtualMachines/zulu-8.jdk/Contents/Home/jre/../include/darwin -fno-common -I/Library/Java/JavaVirtualMachines/zulu-8.jdk/Contents/Home/jre/../include -I/Library/Java/JavaVirtualMachines/zulu-8.jdk/Contents/Home/jre/../include/darwin -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include
clang -arch arm64 -c -o Rcallbacks.o Rcallbacks.c -g -Iinclude -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -DHAVE_CONFIG_H -falign-functions=64 -Wall -g -O2 -I/Library/Java/JavaVirtualMachines/zulu-8.jdk/Contents/Home/jre/../include -I/Library/Java/JavaVirtualMachines/zulu-8.jdk/Contents/Home/jre/../include/darwin -fno-common -I/Library/Java/JavaVirtualMachines/zulu-8.jdk/Contents/Home/jre/../include -I/Library/Java/JavaVirtualMachines/zulu-8.jdk/Contents/Home/jre/../include/darwin -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include
clang -arch arm64 -c -o Rinit.o Rinit.c -g -Iinclude -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -DHAVE_CONFIG_H -falign-functions=64 -Wall -g -O2 -I/Library/Java/JavaVirtualMachines/zulu-8.jdk/Contents/Home/jre/../include -I/Library/Java/JavaVirtualMachines/zulu-8.jdk/Contents/Home/jre/../include/darwin -fno-common -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include
clang -arch arm64 -c -o globals.o globals.c -g -Iinclude -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -DHAVE_CONFIG_H -falign-functions=64 -Wall -g -O2 -I/Library/Java/JavaVirtualMachines/zulu-8.jdk/Contents/Home/jre/../include -I/Library/Java/JavaVirtualMachines/zulu-8.jdk/Contents/Home/jre/../include/darwin -fno-common -I/Library/Java/JavaVirtualMachines/zulu-8.jdk/Contents/Home/jre/../include -I/Library/Java/JavaVirtualMachines/zulu-8.jdk/Contents/Home/jre/../include/darwin
clang -arch arm64 -c -o rjava.o rjava.c -g -Iinclude -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -DHAVE_CONFIG_H -falign-functions=64 -Wall -g -O2 -I/Library/Java/JavaVirtualMachines/zulu-8.jdk/Contents/Home/jre/../include -I/Library/Java/JavaVirtualMachines/zulu-8.jdk/Contents/Home/jre/../include/darwin -fno-common -I/Library/Java/JavaVirtualMachines/zulu-8.jdk/Contents/Home/jre/../include -I/Library/Java/JavaVirtualMachines/zulu-8.jdk/Contents/Home/jre/../include/darwin
clang -arch arm64 -o libjri.jnilib Rengine.o jri.o Rcallbacks.o Rinit.o globals.o rjava.o -dynamiclib -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Java/JavaVirtualMachines/zulu-8.jdk/Contents/Home/jre/lib/server -ljvm -L/opt/R/arm64/lib -F/Library/Frameworks/R.framework/.. -framework R -L/opt/R/arm64/lib -lpcre2-8 -llzma -lbz2 -lz -licucore -ldl -lm -liconv
ld: library not found for -lpcre2-8
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make[2]: *** [libjri.jnilib] Error 1
make[1]: *** [src/JRI.jar] Error 2
make: *** [jri] Error 2
ERROR: compilation failed for package ‘rJava’
* removing ‘/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/rJava’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/rJava’
Warning in install.packages :
installation of package ‘rJava’ had non-zero exit status
The downloaded source packages are in
‘/private/var/folders/bw/15yqlzdd3gbd_r0trwcsy8h40000gn/T/RtmpZj51Iw/downloaded_packages’
lpcre2-8 is only needed to compile JRI, if you don't need it, you can use --disable-jri to install rJava without JRI. If you need JRI, either compile pcre2 yourself or download it from https://mac.R-project.org/libs-4/.
Have a look at the raised issue here: https://github.com/s-u/rJava/issues/153
I have been trying to install "openxlsx" library in R. I have R 3.4.0 and tried installing "openxlsx" from cran and from package archive (local folder) as well but none of them let me install this package. Below is the log message. Can someone please help.
> install.packages("C:/Users/rgowriga/Downloads/openxlsx_4.0.17.tar.gz", repos = NULL, type = "source")
'\\...\rgowriga$\Documents'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported. Defaulting to Windows directory.
* installing *source* package 'openxlsx' ...
** package 'openxlsx' successfully unpacked and MD5 sums checked
** libs
*** arch - i386
C:/PF/Rtools/mingw_32/bin/g++ -I"C:/PROGRA~1/R/R-34~1.0/include" -DNDEBUG -I"C:/Program Files/R/R-3.4.0/library/Rcpp/include" -I"d:/Compiler/gcc-4.9.3/local330/include" -O2 -Wall -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/PF/Rtools/mingw_32/bin/g++ -I"C:/PROGRA~1/R/R-34~1.0/include" -DNDEBUG -I"C:/Program Files/R/R-3.4.0/library/Rcpp/include" -I"d:/Compiler/gcc-4.9.3/local330/include" -O2 -Wall -mtune=core2 -c helper_functions.cpp -o helper_functions.o
C:/PF/Rtools/mingw_32/bin/g++ -I"C:/PROGRA~1/R/R-34~1.0/include" -DNDEBUG -I"C:/Program Files/R/R-3.4.0/library/Rcpp/include" -I"d:/Compiler/gcc-4.9.3/local330/include" -O2 -Wall -mtune=core2 -c load_workbook.cpp -o load_workbook.o
C:/PF/Rtools/mingw_32/bin/gcc -I"C:/PROGRA~1/R/R-34~1.0/include" -DNDEBUG -I"C:/Program Files/R/R-3.4.0/library/Rcpp/include" -I"d:/Compiler/gcc-4.9.3/local330/include" -O3 -Wall -std=gnu99 -mtune=core2 -c openxlsx_init.c -o openxlsx_init.o
C:/PF/Rtools/mingw_32/bin/g++ -I"C:/PROGRA~1/R/R-34~1.0/include" -DNDEBUG -I"C:/Program Files/R/R-3.4.0/library/Rcpp/include" -I"d:/Compiler/gcc-4.9.3/local330/include" -O2 -Wall -mtune=core2 -c read_workbook.cpp -o read_workbook.o
C:/PF/Rtools/mingw_32/bin/g++ -I"C:/PROGRA~1/R/R-34~1.0/include" -DNDEBUG -I"C:/Program Files/R/R-3.4.0/library/Rcpp/include" -I"d:/Compiler/gcc-4.9.3/local330/include" -O2 -Wall -mtune=core2 -c write_data.cpp -o write_data.o
C:/PF/Rtools/mingw_32/bin/g++ -I"C:/PROGRA~1/R/R-34~1.0/include" -DNDEBUG -I"C:/Program Files/R/R-3.4.0/library/Rcpp/include" -I"d:/Compiler/gcc-4.9.3/local330/include" -O2 -Wall -mtune=core2 -c write_file.cpp -o write_file.o
C:/PF/Rtools/mingw_32/bin/g++ -I"C:/PROGRA~1/R/R-34~1.0/include" -DNDEBUG -I"C:/Program Files/R/R-3.4.0/library/Rcpp/include" -I"d:/Compiler/gcc-4.9.3/local330/include" -O2 -Wall -mtune=core2 -c write_file_2.cpp -o write_file_2.o
C:/PF/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o openxlsx.dll tmp.def RcppExports.o helper_functions.o load_workbook.o openxlsx_init.o read_workbook.o write_data.o write_file.o write_file_2.o -Ld:/Compiler/gcc-4.9.3/local330/lib/i386 -Ld:/Compiler/gcc-4.9.3/local330/lib -LC:/PROGRA~1/R/R-34~1.0/bin/i386 -lR
installing to C:/Program Files/R/R-3.4.0/library/openxlsx/libs/i386
*** arch - x64
C:/PF/Rtools/mingw_32/bin/g++ -I"C:/PROGRA~1/R/R-34~1.0/include" -DNDEBUG -I"C:/Program Files/R/R-3.4.0/library/Rcpp/include" -I"d:/Compiler/gcc-4.9.3/local330/include" -O2 -Wall -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/PF/Rtools/mingw_32/bin/g++ -I"C:/PROGRA~1/R/R-34~1.0/include" -DNDEBUG -I"C:/Program Files/R/R-3.4.0/library/Rcpp/include" -I"d:/Compiler/gcc-4.9.3/local330/include" -O2 -Wall -mtune=core2 -c helper_functions.cpp -o helper_functions.o
C:/PF/Rtools/mingw_32/bin/g++ -I"C:/PROGRA~1/R/R-34~1.0/include" -DNDEBUG -I"C:/Program Files/R/R-3.4.0/library/Rcpp/include" -I"d:/Compiler/gcc-4.9.3/local330/include" -O2 -Wall -mtune=core2 -c load_workbook.cpp -o load_workbook.o
C:/PF/Rtools/mingw_32/bin/gcc -I"C:/PROGRA~1/R/R-34~1.0/include" -DNDEBUG -I"C:/Program Files/R/R-3.4.0/library/Rcpp/include" -I"d:/Compiler/gcc-4.9.3/local330/include" -O2 -Wall -std=gnu99 -mtune=core2 -c openxlsx_init.c -o openxlsx_init.o
C:/PF/Rtools/mingw_32/bin/g++ -I"C:/PROGRA~1/R/R-34~1.0/include" -DNDEBUG -I"C:/Program Files/R/R-3.4.0/library/Rcpp/include" -I"d:/Compiler/gcc-4.9.3/local330/include" -O2 -Wall -mtune=core2 -c read_workbook.cpp -o read_workbook.o
C:/PF/Rtools/mingw_32/bin/g++ -I"C:/PROGRA~1/R/R-34~1.0/include" -DNDEBUG -I"C:/Program Files/R/R-3.4.0/library/Rcpp/include" -I"d:/Compiler/gcc-4.9.3/local330/include" -O2 -Wall -mtune=core2 -c write_data.cpp -o write_data.o
C:/PF/Rtools/mingw_32/bin/g++ -I"C:/PROGRA~1/R/R-34~1.0/include" -DNDEBUG -I"C:/Program Files/R/R-3.4.0/library/Rcpp/include" -I"d:/Compiler/gcc-4.9.3/local330/include" -O2 -Wall -mtune=core2 -c write_file.cpp -o write_file.o
C:/PF/Rtools/mingw_32/bin/g++ -I"C:/PROGRA~1/R/R-34~1.0/include" -DNDEBUG -I"C:/Program Files/R/R-3.4.0/library/Rcpp/include" -I"d:/Compiler/gcc-4.9.3/local330/include" -O2 -Wall -mtune=core2 -c write_file_2.cpp -o write_file_2.o
C:/PF/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o openxlsx.dll tmp.def RcppExports.o helper_functions.o load_workbook.o openxlsx_init.o read_workbook.o write_data.o write_file.o write_file_2.o -Ld:/Compiler/gcc-4.9.3/local330/lib/x64 -Ld:/Compiler/gcc-4.9.3/local330/lib -LC:/PROGRA~1/R/R-34~1.0/bin/x64 -lR
C:/PROGRA~1/R/R-34~1.0/bin/x64/R.dll: file not recognized: File format not recognized
collect2.exe: error: ld returned 1 exit status
no DLL was created
ERROR: compilation failed for package 'openxlsx'
* removing 'C:/Program Files/R/R-3.4.0/library/openxlsx'
Warning in install.packages :
running command '"C:/PROGRA~1/R/R-34~1.0/bin/i386/R" CMD INSTALL -l "C:\Program Files\R\R-3.4.0\library" "C:/Users/rgowriga/Downloads/openxlsx_4.0.17.tar.gz"' had status 1
Warning in install.packages :
installation of package ‘C:/Users/rgowriga/Downloads/openxlsx_4.0.17.tar.gz’ had non-zero exit status
I'm currently trying to set up continuous integration for a bookdown-project
The project bundles dependencies with packrat, so Travis CI needs to build the required packages from source. This seems to go okay for many packages, but the build is failing for data.table.
I am using the current version of data.table (1.11.8) and R (3.5.1)
Maybe I specified the wrong Version of C-compilers in my Makevars
What else could I check to get this working?
...
Installing curl (3.2) ...
OK (built source)
Installing data.table (1.11.8) ...
[1] "Command failed (1)\n\nFailed to run system command:\n\n\t'/home/travis/R-bin/lib/R/bin/R' --vanilla CMD INSTALL '/tmp/RtmpiHzV25/data.table' --library='/home/travis/build/henningsway/Advanced-R-Solutions/packrat/lib/x86_64-pc-linux-gnu/3.5.1' --install-tests --no-docs --no-multiarch --no-demo \n\nThe command failed with output:\n* installing *source* package 'data.table' ...\n** package 'data.table' successfully unpacked and MD5 sums checked\n** libs\nclang -I\"/home/travis/R-bin/lib/R/include\" -DNDEBUG -I/home/travis/R-bin/include -fopenmp -fpic -g -O2 -c assign.c -o assign.o\nclang -I\"/home/travis/R-bin/lib/R/include\" -DNDEBUG -I/home/travis/R-bin/include -fopenmp -fpic -g -O2 -c between.c -o between.o\nclang -I\"/home/travis/R-bin/lib/R/include\" -DNDEBUG -I/home/travis/R-bin/include -fopenmp -fpic -g -O2 -c bmerge.c -o bmerge.o\nclang -I\"/home/travis/R-bin/lib/R/include\" -DNDEBUG -I/home/travis/R-bin/include -fopenmp -fpic -g -O2 -c chmatch.c -o chmatch.o\nclang -I\"/home/travis/R-bin/lib/R/include\" -DNDEBUG -I/home/travis/R-bin/include -fopenmp -fpic -g -O2 -c dogroups.c -o dogroups.o\nclang -I\"/home/travis/R-bin/lib/R/include\" -DNDEBUG -I/home/travis/R-bin/include -fopenmp -fpic -g -O2 -c fastmean.c -o fastmean.o\nclang -I\"/home/travis/R-bin/lib/R/include\" -DNDEBUG -I/home/travis/R-bin/include -fopenmp -fpic -g -O2 -c fcast.c -o fcast.o\nclang -I\"/home/travis/R-bin/lib/R/include\" -DNDEBUG -I/home/travis/R-bin/include -fopenmp -fpic -g -O2 -c fmelt.c -o fmelt.o\nclang -I\"/home/travis/R-bin/lib/R/include\" -DNDEBUG -I/home/travis/R-bin/include -fopenmp -fpic -g -O2 -c forder.c -o forder.o\nclang -I\"/home/travis/R-bin/lib/R/include\" -DNDEBUG -I/home/travis/R-bin/include -fopenmp -fpic -g -O2 -c frank.c -o frank.o\nclang -I\"/home/travis/R-bin/lib/R/include\" -DNDEBUG -I/home/travis/R-bin/include -fopenmp -fpic -g -O2 -c fread.c -o fread.o\nclang -I\"/home/travis/R-bin/lib/R/include\" -DNDEBUG -I/home/travis/R-bin/include -fopenmp -fpic -g -O2 -c freadR.c -o freadR.o\nclang -I\"/home/travis/R-bin/lib/R/include\" -DNDEBUG -I/home/travis/R-bin/include -fopenmp -fpic -g -O2 -c fsort.c -o fsort.o\nclang -I\"/home/travis/R-bin/lib/R/include\" -DNDEBUG -I/home/travis/R-bin/include -fopenmp -fpic -g -O2 -c fwrite.c -o fwrite.o\nclang -I\"/home/travis/R-bin/lib/R/include\" -DNDEBUG -I/home/travis/R-bin/include -fopenmp -fpic -g -O2 -c fwriteR.c -o fwriteR.o\nclang -I\"/home/travis/R-bin/lib/R/include\" -DNDEBUG -I/home/travis/R-bin/include -fopenmp -fpic -g -O2 -c gsumm.c -o gsumm.o\nclang -I\"/home/travis/R-bin/lib/R/include\" -DNDEBUG -I/home/travis/R-bin/include -fopenmp -fpic -g -O2 -c ijoin.c -o ijoin.o\nclang -I\"/home/travis/R-bin/lib/R/include\" -DNDEBUG -I/home/travis/R-bin/include -fopenmp -fpic -g -O2 -c init.c -o init.o\nclang -I\"/home/travis/R-bin/lib/R/include\" -DNDEBUG -I/home/travis/R-bin/include -fopenmp -fpic -g -O2 -c inrange.c -o inrange.o\nclang -I\"/home/travis/R-bin/lib/R/include\" -DNDEBUG -I/home/travis/R-bin/include -fopenmp -fpic -g -O2 -c nqrecreateindices.c -o nqrecreateindices.o\nclang -I\"/home/travis/R-bin/lib/R/include\" -DNDEBUG -I/home/travis/R-bin/include -fopenmp -fpic -g -O2 -c openmp-utils.c -o openmp-utils.o\nclang -I\"/home/travis/R-bin/lib/R/include\" -DNDEBUG -I/home/travis/R-bin/include -fopenmp -fpic -g -O2 -c quickselect.c -o quickselect.o\nclang -I\"/home/travis/R-bin/lib/R/include\" -DNDEBUG -I/home/travis/R-bin/include -fopenmp -fpic -g -O2 -c rbindlist.c -o rbindlist.o\nclang -I\"/home/travis/R-bin/lib/R/include\" -DNDEBUG -I/home/travis/R-bin/include -fopenmp -fpic -g -O2 -c reorder.c -o reorder.o\nclang -I\"/home/travis/R-bin/lib/R/include\" -DNDEBUG -I/home/travis/R-bin/include -fopenmp -fpic -g -O2 -c shift.c -o shift.o\nclang -I\"/home/travis/R-bin/lib/R/include\" -DNDEBUG -I/home/travis/R-bin/include -fopenmp -fpic -g -O2 -c subset.c -o subset.o\nclang -I\"/home/travis/R-bin/lib/R/include\" -DNDEBUG -I/home/travis/R-bin/include -fopenmp -fpic -g -O2 -c transpose.c -o transpose.o\nclang -I\"/home/travis/R-bin/lib/R/include\" -DNDEBUG -I/home/travis/R-bin/include -fopenmp -fpic -g -O2 -c uniqlist.c -o uniqlist.o\nclang -I\"/home/travis/R-bin/lib/R/include\" -DNDEBUG -I/home/travis/R-bin/include -fopenmp -fpic -g -O2 -c vecseq.c -o vecseq.o\nclang -I\"/home/travis/R-bin/lib/R/include\" -DNDEBUG -I/home/travis/R-bin/include -fopenmp -fpic -g -O2 -c wrappers.c -o wrappers.o\nclang -shared -L/home/travis/R-bin/lib/R/lib -L/home/travis/R-bin/lib -o data.table.so assign.o between.o bmerge.o chmatch.o dogroups.o fastmean.o fcast.o fmelt.o forder.o frank.o fread.o freadR.o fsort.o fwrite.o fwriteR.o gsumm.o ijoin.o init.o inrange.o nqrecreateindices.o openmp-utils.o quickselect.o rbindlist.o reorder.o shift.o subset.o transpose.o uniqlist.o vecseq.o wrappers.o -fopenmp -L/home/travis/R-bin/lib/R/lib -lR\nmv data.table.so datatable.so\nif [ \"\" != \"Windows_NT\" ] && [ `uname -s` = 'Darwin' ]; then install_name_tool -id datatable.so datatable.so; fi\ninstalling to /home/travis/build/henningsway/Advanced-R-Solutions/packrat/lib/x86_64-pc-linux-gnu/3.5.1/data.table/libs\n** R\n** inst\n** tests\n** byte-compile and prepare package for lazy loading\n** help\n*** installing help indices\n** building package indices\n** installing vignettes\n** testing if installed package can be loaded\nError: package or namespace load failed for 'data.table' in dyn.load(file, DLLpath = DLLpath, ...):\n unable to load shared object '/home/travis/build/henningsway/Advanced-R-Solutions/packrat/lib/x86_64-pc-linux-gnu/3.5.1/data.table/libs/datatable.so':\n libomp.so: cannot open shared object file: No such file or directory\nError: loading failed\nExecution halted\nERROR: loading failed\n* removing '/home/travis/build/henningsway/Advanced-R-Solutions/packrat/lib/x86_64-pc-linux-gnu/3.5.1/data.table'"
Error: Command failed (1)
Failed to run system command:
'/home/travis/R-bin/lib/R/bin/R' --vanilla CMD INSTALL '/tmp/RtmpiHzV25/data.table' --library='/home/travis/build/henningsway/Advanced-R-Solutions/packrat/lib/x86_64-pc-linux-gnu/3.5.1' --install-tests --no-docs --no-multiarch --no-demo
The command failed with output:
* installing *source* package 'data.table' ...
** package 'data.table' successfully unpacked and MD5 sums checked
** libs
clang -I"/home/travis/R-bin/lib/R/include" -DNDEBUG -I/home/travis/R-bin/include -fopenmp -fpic -g -O2 -c assign.c -o assign.o
clang -I"/home/travis/R-bin/lib/R/include" -DNDEBUG -I/home/travis/R-bin/include -fopenmp -fpic -g -O2 -c between.c -o between.o
clang -I"/home/travis/R-bin/lib/R/include" -DNDEBUG -I/home/travis/R-bin/include -fopenmp -fpic -g -O2 -c bmerge.c -o bmerge.o
clang -I"/home/travis/R-bin/lib/R/include" -DNDEBUG -I/home/travis/R-bin/include -fopenmp -fpic -g -O2 -c chmatch.c -o chmatch.o
clang -I"/home/
Execution halted
The command "R -e "0" --args --bootstrap-packrat" failed and exited with 1 during .
Your build has been stopped.
Setting CC=gcc actually solved the data.table-compilation problem for me.
(I think setting some other arguments for clang would have also been an option, as indicated in #jaaps comment above)
Context
I'm working on Rstudio Server on an HDI cluster to work faster on large datasets but i encountered a problem.
When i'm trying to install packages, i get this error (example with package sparklyr)
> install.packages("sparklyr", repos = "http://cran.us.r-project.org")
Warning in install.packages :
unable to access index for repository https://mran.microsoft.com/snapshot/2017-03-15/src/contrib:
Line starting '<head><title>Documen ...' is malformed!
Installing package into ‘/home/sshuser4/R/x86_64-pc-linux-gnu-library/3.3’
(as ‘lib’ is unspecified)
also installing the dependencies ‘httpuv’, ‘jsonlite’, ‘shiny’
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0100 417k 100 417k 0 0 2838k 0 --:--:-- --:--:-- --:--:-- 2840k
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0100 1071k 100 1071k 0 0 6323k 0 --:--:-- --:--:-- --:--:-- 6337k
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0100 2276k 100 2276k 0 0 10.6M 0 --:--:-- --:--:-- --:--:-- 10.6M
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
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* installing *source* package ‘httpuv’ ...
** package ‘httpuv’ successfully unpacked and MD5 sums checked
** libs
I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -I./libuv/include -I./http-parser -I./sha1 -I./base64 -DU_STATIC_IMPLEMENTATION -I"/home/sshuser4/R/x86_64-pc-linux-gnu-library/3.3/Rcpp/include" -c RcppExports.cpp -o RcppExports.o
sh: I/usr/lib64/microsoft-r/3.3/lib64/R/include: No such file or directory
/usr/lib64/microsoft-r/3.3/lib64/R/etc/Makeconf:141: recipe for target 'RcppExports.o' failed
make: [RcppExports.o] Error 127 (ignored)
I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -I./libuv/include -I./http-parser -I./sha1 -I./base64 -DU_STATIC_IMPLEMENTATION -I"/home/sshuser4/R/x86_64-pc-linux-gnu-library/3.3/Rcpp/include" -c filedatasource-unix.cpp -o filedatasource-unix.o
sh: I/usr/lib64/microsoft-r/3.3/lib64/R/include: No such file or directory
/usr/lib64/microsoft-r/3.3/lib64/R/etc/Makeconf:141: recipe for target 'filedatasource-unix.o' failed
make: [filedatasource-unix.o] Error 127 (ignored)
I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -I./libuv/include -I./http-parser -I./sha1 -I./base64 -DU_STATIC_IMPLEMENTATION -I"/home/sshuser4/R/x86_64-pc-linux-gnu-library/3.3/Rcpp/include" -c filedatasource-win.cpp -o filedatasource-win.o
sh: I/usr/lib64/microsoft-r/3.3/lib64/R/include: No such file or directory
/usr/lib64/microsoft-r/3.3/lib64/R/etc/Makeconf:141: recipe for target 'filedatasource-win.o' failed
make: [filedatasource-win.o] Error 127 (ignored)
I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -I./libuv/include -I./http-parser -I./sha1 -I./base64 -DU_STATIC_IMPLEMENTATION -I"/home/sshuser4/R/x86_64-pc-linux-gnu-library/3.3/Rcpp/include" -c http.cpp -o http.o
sh: I/usr/lib64/microsoft-r/3.3/lib64/R/include: No such file or directory
/usr/lib64/microsoft-r/3.3/lib64/R/etc/Makeconf:141: recipe for target 'http.o' failed
make: [http.o] Error 127 (ignored)
I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -I./libuv/include -I./http-parser -I./sha1 -I./base64 -DU_STATIC_IMPLEMENTATION -I"/home/sshuser4/R/x86_64-pc-linux-gnu-library/3.3/Rcpp/include" -c httpuv.cpp -o httpuv.o
sh: I/usr/lib64/microsoft-r/3.3/lib64/R/include: No such file or directory
/usr/lib64/microsoft-r/3.3/lib64/R/etc/Makeconf:141: recipe for target 'httpuv.o' failed
make: [httpuv.o] Error 127 (ignored)
gcc -std=gnu99 -I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -I./libuv/include -I./http-parser -I./sha1 -I./base64 -DU_STATIC_IMPLEMENTATION -I"/home/sshuser4/R/x86_64-pc-linux-gnu-library/3.3/Rcpp/include" -fpic -DU_STATIC_IMPLEMENTATION -O2 -g -c md5.c -o md5.o
gcc -std=gnu99 -I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -I./libuv/include -I./http-parser -I./sha1 -I./base64 -DU_STATIC_IMPLEMENTATION -I"/home/sshuser4/R/x86_64-pc-linux-gnu-library/3.3/Rcpp/include" -fpic -DU_STATIC_IMPLEMENTATION -O2 -g -c register.c -o register.o
gcc -std=gnu99 -I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -I./libuv/include -I./http-parser -I./sha1 -I./base64 -DU_STATIC_IMPLEMENTATION -I"/home/sshuser4/R/x86_64-pc-linux-gnu-library/3.3/Rcpp/include" -fpic -DU_STATIC_IMPLEMENTATION -O2 -g -c set_invalid_parameter.c -o set_invalid_parameter.o
I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -I./libuv/include -I./http-parser -I./sha1 -I./base64 -DU_STATIC_IMPLEMENTATION -I"/home/sshuser4/R/x86_64-pc-linux-gnu-library/3.3/Rcpp/include" -c uvutil.cpp -o uvutil.o
sh: I/usr/lib64/microsoft-r/3.3/lib64/R/include: No such file or directory
/usr/lib64/microsoft-r/3.3/lib64/R/etc/Makeconf:141: recipe for target 'uvutil.o' failed
I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -I./libuv/include -I./http-parser -I./sha1 -I./base64 -DU_STATIC_IMPLEMENTATION -I"/home/sshuser4/R/x86_64-pc-linux-gnu-library/3.3/Rcpp/include" -c websockets-base.cpp -o websockets-base.o
make: [uvutil.o] Error 127 (ignored)
sh: I/usr/lib64/microsoft-r/3.3/lib64/R/include: No such file or directory
/usr/lib64/microsoft-r/3.3/lib64/R/etc/Makeconf:141: recipe for target 'websockets-base.o' failed
I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -I./libuv/include -I./http-parser -I./sha1 -I./base64 -DU_STATIC_IMPLEMENTATION -I"/home/sshuser4/R/x86_64-pc-linux-gnu-library/3.3/Rcpp/include" -c websockets-hixie76.cpp -o websockets-hixie76.o
make: [websockets-base.o] Error 127 (ignored)
sh: I/usr/lib64/microsoft-r/3.3/lib64/R/include: No such file or directory
/usr/lib64/microsoft-r/3.3/lib64/R/etc/Makeconf:141: recipe for target 'websockets-hixie76.o' failed
I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -I./libuv/include -I./http-parser -I./sha1 -I./base64 -DU_STATIC_IMPLEMENTATION -I"/home/sshuser4/R/x86_64-pc-linux-gnu-library/3.3/Rcpp/include" -c websockets-hybi03.cpp -o websockets-hybi03.o
make: [websockets-hixie76.o] Error 127 (ignored)
sh: I/usr/lib64/microsoft-r/3.3/lib64/R/include: No such file or directory
/usr/lib64/microsoft-r/3.3/lib64/R/etc/Makeconf:141: recipe for target 'websockets-hybi03.o' failed
I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -I./libuv/include -I./http-parser -I./sha1 -I./base64 -DU_STATIC_IMPLEMENTATION -I"/home/sshuser4/R/x86_64-pc-linux-gnu-library/3.3/Rcpp/include" -c websockets-ietf.cpp -o websockets-ietf.o
make: [websockets-hybi03.o] Error 127 (ignored)
sh: I/usr/lib64/microsoft-r/3.3/lib64/R/include: No such file or directory
/usr/lib64/microsoft-r/3.3/lib64/R/etc/Makeconf:141: recipe for target 'websockets-ietf.o' failed
I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -I./libuv/include -I./http-parser -I./sha1 -I./base64 -DU_STATIC_IMPLEMENTATION -I"/home/sshuser4/R/x86_64-pc-linux-gnu-library/3.3/Rcpp/include" -c websockets.cpp -o websockets.o
make: [websockets-ietf.o] Error 127 (ignored)
sh: I/usr/lib64/microsoft-r/3.3/lib64/R/include: No such file or directory
/usr/lib64/microsoft-r/3.3/lib64/R/etc/Makeconf:141: recipe for target 'websockets.o' failed
make --directory=libuv \
CC="gcc -std=gnu99" CFLAGS="-DU_STATIC_IMPLEMENTATION -O2 -g -fpic" AR="ar" RANLIB="ranlib" \
HAVE_DTRACE=0 \
libuv.a
make: [websockets.o] Error 127 (ignored)
make[1]: Entering directory '/tmp/RtmpPak08O/R.INSTALL692e63c7b08a/httpuv/src/libuv'
mkdir -p src/unix
touch src/unix/.buildstamp
gcc -std=gnu99 --std=c89 -pedantic -Wall -Wextra -Wno-unused-parameter -D_GNU_SOURCE -I/tmp/RtmpPak08O/R.INSTALL692e63c7b08a/httpuv/src/libuv/include -I/tmp/RtmpPak08O/R.INSTALL692e63c7b08a/httpuv/src/libuv/include/uv-private -I/tmp/RtmpPak08O/R.INSTALL692e63c7b08a/httpuv/src/libuv/src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DU_STATIC_IMPLEMENTATION -O2 -g -fpic -c src/unix/async.c -o src/unix/async.o
gcc -std=gnu99 --std=c89 -pedantic -Wall -Wextra -Wno-unused-parameter -D_GNU_SOURCE -I/tmp/RtmpPak08O/R.INSTALL692e63c7b08a/httpuv/src/libuv/include -I/tmp/RtmpPak08O/R.INSTALL692e63c7b08a/httpuv/src/libuv/include/uv-private -I/tmp/RtmpPak08O/R.INSTALL692e63c7b08a/httpuv/src/libuv/src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DU_STATIC_IMPLEMENTATION -O2 -g -fpic -c src/unix/core.c -o src/unix/core.o
gcc -std=gnu99 --std=c89 -pedantic -Wall -Wextra -Wno-unused-parameter -D_GNU_SOURCE -I/tmp/RtmpPak08O/R.INSTALL692e63c7b08a/httpuv/src/libuv/include -I/tmp/RtmpPak08O/R.INSTALL692e63c7b08a/httpuv/src/libuv/include/uv-private -I/tmp/RtmpPak08O/R.INSTALL692e63c7b08a/httpuv/src/libuv/src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DU_STATIC_IMPLEMENTATION -O2 -g -fpic -c src/unix/dl.c -o src/unix/dl.o
gcc -std=gnu99 --std=c89 -pedantic -Wall -Wextra -Wno-unused-parameter -D_GNU_SOURCE -I/tmp/RtmpPak08O/R.INSTALL692e63c7b08a/httpuv/src/libuv/include -I/tmp/RtmpPak08O/R.INSTALL692e63c7b08a/httpuv/src/libuv/include/uv-private -I/tmp/RtmpPak08O/R.INSTALL692e63c7b08a/httpuv/src/libuv/src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DU_STATIC_IMPLEMENTATION -O2 -g -fpic -c src/unix/error.c -o src/unix/error.o
gcc -std=gnu99 --std=c89 -pedantic -Wall -Wextra -Wno-unused-parameter -D_GNU_SOURCE -I/tmp/RtmpPak08O/R.INSTALL692e63c7b08a/httpuv/src/libuv/include -I/tmp/RtmpPak08O/R.INSTALL692e63c7b08a/httpuv/src/libuv/include/uv-private -I/tmp/RtmpPak08O/R.INSTALL692e63c7b08a/httpuv/src/libuv/src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DU_STATIC_IMPLEMENTATION -O2 -g -fpic -c src/unix/fs.c -o src/unix/fs.o
gcc -std=gnu99 --std=c89 -pedantic -Wall -Wextra -Wno-unused-parameter -D_GNU_SOURCE -I/tmp/RtmpPak08O/R.INSTALL692e63c7b08a/httpuv/src/libuv/include -I/tmp/RtmpPak08O/R.INSTALL692e63c7b08a/httpuv/src/libuv/include/uv-private -I/tmp/RtmpPak08O/R.INSTALL692e63c7b08a/httpuv/src/libuv/src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DU_STATIC_IMPLEMENTATION -O2 -g -fpic -c src/unix/getaddrinfo.c -o src/unix/getaddrinfo.o
gcc -std=gnu99 --std=c89 -pedantic -Wall -Wextra -Wno-unused-parameter -D_GNU_SOURCE -I/tmp/RtmpPak08O/R.INSTALL692e63c7b08a/httpuv/src/libuv/include -I/tmp/RtmpPak08O/R.INSTALL692e63c7b08a/httpuv/src/libuv/include/uv-private -I/tmp/RtmpPak08O/R.INSTALL692e63c7b08a/httpuv/src/libuv/src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DU_STATIC_IMPLEMENTATION -O2 -g -fpic -c src/unix/loop.c -o src/unix/loop.o
gcc -std=gnu99 --std=c89 -pedantic -Wall -Wextra -Wno-unused-parameter -D_GNU_SOURCE -I/tmp/RtmpPak08O/R.INSTALL692e63c7b08a/httpuv/src/libuv/include -I/tmp/RtmpPak08O/R.INSTALL692e63c7b08a/httpuv/src/libuv/include/uv-private -I/tmp/RtmpPak08O/R.INSTALL692e63c7b08a/httpuv/src/libuv/src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DU_STATIC_IMPLEMENTATION -O2 -g -fpic -c src/unix/loop-watcher.c -o src/unix/loop-watcher.o
gcc -std=gnu99 --std=c89 -pedantic -Wall -Wextra -Wno-unused-parameter -D_GNU_SOURCE -I/tmp/RtmpPak08O/R.INSTALL692e63c7b08a/httpuv/src/libuv/include -I/tmp/RtmpPak08O/R.INSTALL692e63c7b08a/httpuv/src/libuv/include/uv-private -I/tmp/RtmpPak08O/R.INSTALL692e63c7b08a/httpuv/src/libuv/src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DU_STATIC_IMPLEMENTATION -O2 -g -fpic -c src/unix/pipe.c -o src/unix/pipe.o
gcc -std=gnu99 --std=c89 -pedantic -Wall -Wextra -Wno-unused-parameter -D_GNU_SOURCE -I/tmp/RtmpPak08O/R.INSTALL692e63c7b08a/httpuv/src/libuv/include -I/tmp/RtmpPak08O/R.INSTALL692e63c7b08a/httpuv/src/libuv/include/uv-private -I/tmp/RtmpPak08O/R.INSTALL692e63c7b08a/httpuv/src/libuv/src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DU_STATIC_IMPLEMENTATION -O2 -g -fpic -c src/unix/poll.c -o src/unix/poll.o
gcc -std=gnu99 --std=c89 -pedantic -Wall -Wextra -Wno-unused-parameter -D_GNU_SOURCE -I/tmp/RtmpPak08O/R.INSTALL692e63c7b08a/httpuv/src/libuv/include -I/tmp/RtmpPak08O/R.INSTALL692e63c7b08a/httpuv/src/libuv/include/uv-private -I/tmp/RtmpPak08O/R.INSTALL692e63c7b08a/httpuv/src/libuv/src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DU_STATIC_IMPLEMENTATION -O2 -g -fpic -c src/unix/process.c -o src/unix/process.o
gcc -std=gnu99 --std=c89 -pedantic -Wall -Wextra -Wno-unused-parameter -D_GNU_SOURCE -I/tmp/RtmpPak08O/R.INSTALL692e63c7b08a/httpuv/src/libuv/include -I/tmp/RtmpPak08O/R.INSTALL692e63c7b08a/httpuv/src/libuv/include/uv-private -I/tmp/RtmpPak08O/R.INSTALL692e63c7b08a/httpuv/src/libuv/src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DU_STATIC_IMPLEMENTATION -O2 -g -fpic -c src/unix/signal.c -o src/unix/signal.o
gcc -std=gnu99 --std=c89 -pedantic -Wall -Wextra -Wno-unused-parameter -D_GNU_SOURCE -I/tmp/RtmpPak08O/R.INSTALL692e63c7b08a/httpuv/src/libuv/include -I/tmp/RtmpPak08O/R.INSTALL692e63c7b08a/httpuv/src/libuv/include/uv-private -I/tmp/RtmpPak08O/R.INSTALL692e63c7b08a/httpuv/src/libuv/src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DU_STATIC_IMPLEMENTATION -O2 -g -fpic -c src/unix/stream.c -o src/unix/stream.o
gcc -std=gnu99 --std=c89 -pedantic -Wall -Wextra -Wno-unused-parameter -D_GNU_SOURCE -I/tmp/RtmpPak08O/R.INSTALL692e63c7b08a/httpuv/src/libuv/include -I/tmp/RtmpPak08O/R.INSTALL692e63c7b08a/httpuv/src/libuv/include/uv-private -I/tmp/RtmpPak08O/R.INSTALL692e63c7b08a/httpuv/src/libuv/src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DU_STATIC_IMPLEMENTATION -O2 -g -fpic -c src/unix/tcp.c -o src/unix/tcp.o
gcc -std=gnu99 --std=c89 -pedantic -Wall -Wextra -Wno-unused-parameter -D_GNU_SOURCE -I/tmp/RtmpPak08O/R.INSTALL692e63c7b08a/httpuv/src/libuv/include -I/tmp/RtmpPak08O/R.INSTALL692e63c7b08a/httpuv/src/libuv/include/uv-private -I/tmp/RtmpPak08O/R.INSTALL692e63c7b08a/httpuv/src/libuv/src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DU_STATIC_IMPLEMENTATION -O2 -g -fpic -c src/unix/thread.c -o src/unix/thread.o
gcc -std=gnu99 --std=c89 -pedantic -Wall -Wextra -Wno-unused-parameter -D_GNU_SOURCE -I/tmp/RtmpPak08O/R.INSTALL692e63c7b08a/httpuv/src/libuv/include -I/tmp/RtmpPak08O/R.INSTALL692e63c7b08a/httpuv/src/libuv/include/uv-private -I/tmp/RtmpPak08O/R.INSTALL692e63c7b08a/httpuv/src/libuv/src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DU_STATIC_IMPLEMENTATION -O2 -g -fpic -c src/unix/threadpool.c -o src/unix/threadpool.o
gcc -std=gnu99 --std=c89 -pedantic -Wall -Wextra -Wno-unused-parameter -D_GNU_SOURCE -I/tmp/RtmpPak08O/R.INSTALL692e63c7b08a/httpuv/src/libuv/include -I/tmp/RtmpPak08O/R.INSTALL692e63c7b08a/httpuv/src/libuv/include/uv-private -I/tmp/RtmpPak08O/R.INSTALL692e63c7b08a/httpuv/src/libuv/src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DU_STATIC_IMPLEMENTATION -O2 -g -fpic -c src/unix/timer.c -o src/unix/timer.o
gcc -std=gnu99 --std=c89 -pedantic -Wall -Wextra -Wno-unused-parameter -D_GNU_SOURCE -I/tmp/RtmpPak08O/R.INSTALL692e63c7b08a/httpuv/src/libuv/include -I/tmp/RtmpPak08O/R.INSTALL692e63c7b08a/httpuv/src/libuv/include/uv-private -I/tmp/RtmpPak08O/R.INSTALL692e63c7b08a/httpuv/src/libuv/src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DU_STATIC_IMPLEMENTATION -O2 -g -fpic -c src/unix/tty.c -o src/unix/tty.o
gcc -std=gnu99 --std=c89 -pedantic -Wall -Wextra -Wno-unused-parameter -D_GNU_SOURCE -I/tmp/RtmpPak08O/R.INSTALL692e63c7b08a/httpuv/src/libuv/include -I/tmp/RtmpPak08O/R.INSTALL692e63c7b08a/httpuv/src/libuv/include/uv-private -I/tmp/RtmpPak08O/R.INSTALL692e63c7b08a/httpuv/src/libuv/src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DU_STATIC_IMPLEMENTATION -O2 -g -fpic -c src/unix/udp.c -o src/unix/udp.o
mkdir -p src
touch src/.buildstamp
gcc -std=gnu99 --std=c89 -pedantic -Wall -Wextra -Wno-unused-parameter -D_GNU_SOURCE -I/tmp/RtmpPak08O/R.INSTALL692e63c7b08a/httpuv/src/libuv/include -I/tmp/RtmpPak08O/R.INSTALL692e63c7b08a/httpuv/src/libuv/include/uv-private -I/tmp/RtmpPak08O/R.INSTALL692e63c7b08a/httpuv/src/libuv/src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DU_STATIC_IMPLEMENTATION -O2 -g -fpic -c src/fs-poll.c -o src/fs-poll.o
gcc -std=gnu99 --std=c89 -pedantic -Wall -Wextra -Wno-unused-parameter -D_GNU_SOURCE -I/tmp/RtmpPak08O/R.INSTALL692e63c7b08a/httpuv/src/libuv/include -I/tmp/RtmpPak08O/R.INSTALL692e63c7b08a/httpuv/src/libuv/include/uv-private -I/tmp/RtmpPak08O/R.INSTALL692e63c7b08a/httpuv/src/libuv/src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DU_STATIC_IMPLEMENTATION -O2 -g -fpic -c src/uv-common.c -o src/uv-common.o
gcc -std=gnu99 --std=c89 -pedantic -Wall -Wextra -Wno-unused-parameter -D_GNU_SOURCE -I/tmp/RtmpPak08O/R.INSTALL692e63c7b08a/httpuv/src/libuv/include -I/tmp/RtmpPak08O/R.INSTALL692e63c7b08a/httpuv/src/libuv/include/uv-private -I/tmp/RtmpPak08O/R.INSTALL692e63c7b08a/httpuv/src/libuv/src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DU_STATIC_IMPLEMENTATION -O2 -g -fpic -c src/inet.c -o src/inet.o
gcc -std=gnu99 --std=c89 -pedantic -Wall -Wextra -Wno-unused-parameter -D_GNU_SOURCE -I/tmp/RtmpPak08O/R.INSTALL692e63c7b08a/httpuv/src/libuv/include -I/tmp/RtmpPak08O/R.INSTALL692e63c7b08a/httpuv/src/libuv/include/uv-private -I/tmp/RtmpPak08O/R.INSTALL692e63c7b08a/httpuv/src/libuv/src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DU_STATIC_IMPLEMENTATION -O2 -g -fpic -c src/version.c -o src/version.o
gcc -std=gnu99 --std=c89 -pedantic -Wall -Wextra -Wno-unused-parameter -D_GNU_SOURCE -I/tmp/RtmpPak08O/R.INSTALL692e63c7b08a/httpuv/src/libuv/include -I/tmp/RtmpPak08O/R.INSTALL692e63c7b08a/httpuv/src/libuv/include/uv-private -I/tmp/RtmpPak08O/R.INSTALL692e63c7b08a/httpuv/src/libuv/src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DU_STATIC_IMPLEMENTATION -O2 -g -fpic -c src/unix/linux-core.c -o src/unix/linux-core.o
gcc -std=gnu99 --std=c89 -pedantic -Wall -Wextra -Wno-unused-parameter -D_GNU_SOURCE -I/tmp/RtmpPak08O/R.INSTALL692e63c7b08a/httpuv/src/libuv/include -I/tmp/RtmpPak08O/R.INSTALL692e63c7b08a/httpuv/src/libuv/include/uv-private -I/tmp/RtmpPak08O/R.INSTALL692e63c7b08a/httpuv/src/libuv/src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DU_STATIC_IMPLEMENTATION -O2 -g -fpic -c src/unix/linux-inotify.c -o src/unix/linux-inotify.o
gcc -std=gnu99 --std=c89 -pedantic -Wall -Wextra -Wno-unused-parameter -D_GNU_SOURCE -I/tmp/RtmpPak08O/R.INSTALL692e63c7b08a/httpuv/src/libuv/include -I/tmp/RtmpPak08O/R.INSTALL692e63c7b08a/httpuv/src/libuv/include/uv-private -I/tmp/RtmpPak08O/R.INSTALL692e63c7b08a/httpuv/src/libuv/src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DU_STATIC_IMPLEMENTATION -O2 -g -fpic -c src/unix/linux-syscalls.c -o src/unix/linux-syscalls.o
gcc -std=gnu99 --std=c89 -pedantic -Wall -Wextra -Wno-unused-parameter -D_GNU_SOURCE -I/tmp/RtmpPak08O/R.INSTALL692e63c7b08a/httpuv/src/libuv/include -I/tmp/RtmpPak08O/R.INSTALL692e63c7b08a/httpuv/src/libuv/include/uv-private -I/tmp/RtmpPak08O/R.INSTALL692e63c7b08a/httpuv/src/libuv/src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DU_STATIC_IMPLEMENTATION -O2 -g -fpic -c src/unix/proctitle.c -o src/unix/proctitle.o
ar rcs libuv.a src/unix/async.o src/unix/core.o src/unix/dl.o src/unix/error.o src/unix/fs.o src/unix/getaddrinfo.o src/unix/loop.o src/unix/loop-watcher.o src/unix/pipe.o src/unix/poll.o src/unix/process.o src/unix/signal.o src/unix/stream.o src/unix/tcp.o src/unix/thread.o src/unix/threadpool.o src/unix/timer.o src/unix/tty.o src/unix/udp.o src/fs-poll.o src/uv-common.o src/inet.o src/version.o src/unix/linux-core.o src/unix/linux-inotify.o src/unix/linux-syscalls.o src/unix/proctitle.o
make[1]: Leaving directory '/tmp/RtmpPak08O/R.INSTALL692e63c7b08a/httpuv/src/libuv'
make --directory=http-parser \
CC="gcc -std=gnu99" CFLAGS="-DU_STATIC_IMPLEMENTATION -O2 -g -fpic" AR="ar" RANLIB="ranlib" \
http_parser.o
make[1]: Entering directory '/tmp/RtmpPak08O/R.INSTALL692e63c7b08a/httpuv/src/http-parser'
gcc -std=gnu99 -I. -DHTTP_PARSER_STRICT=0 -DU_STATIC_IMPLEMENTATION -O2 -g -fpic -O3 -c http_parser.c
make[1]: Leaving directory '/tmp/RtmpPak08O/R.INSTALL692e63c7b08a/httpuv/src/http-parser'
(cd sha1 && gcc -std=gnu99 -DU_STATIC_IMPLEMENTATION -O2 -g -fpic -c sha1.c -o sha1.o)
(cd base64 && -I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -I./libuv/include -I./http-parser -I./sha1 -I./base64 -DU_STATIC_IMPLEMENTATION -I"/home/sshuser4/R/x86_64-pc-linux-gnu-library/3.3/Rcpp/include" -c base64.cpp -o base64.o)
sh: -I/usr/lib64/microsoft-r/3.3/lib64/R/include: No such file or directory
Makevars:47: recipe for target 'base64.o' failed
make: *** [base64.o] Error 127
ERROR: compilation failed for package ‘httpuv’
* removing ‘/home/sshuser4/R/x86_64-pc-linux-gnu-library/3.3/httpuv’
Warning in install.packages :
installation of package ‘httpuv’ had non-zero exit status
* installing *source* package ‘jsonlite’ ...
** package ‘jsonlite’ successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -Iyajl/api -DU_STATIC_IMPLEMENTATION -fpic -DU_STATIC_IMPLEMENTATION -O2 -g -c base64.c -o base64.o
gcc -std=gnu99 -I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -Iyajl/api -DU_STATIC_IMPLEMENTATION -fpic -DU_STATIC_IMPLEMENTATION -O2 -g -c collapse_array.c -o collapse_array.o
gcc -std=gnu99 -I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -Iyajl/api -DU_STATIC_IMPLEMENTATION -fpic -DU_STATIC_IMPLEMENTATION -O2 -g -c collapse_object.c -o collapse_object.o
gcc -std=gnu99 -I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -Iyajl/api -DU_STATIC_IMPLEMENTATION -fpic -DU_STATIC_IMPLEMENTATION -O2 -g -c collapse_pretty.c -o collapse_pretty.o
gcc -std=gnu99 -I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -Iyajl/api -DU_STATIC_IMPLEMENTATION -fpic -DU_STATIC_IMPLEMENTATION -O2 -g -c escape_chars.c -o escape_chars.o
gcc -std=gnu99 -I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -Iyajl/api -DU_STATIC_IMPLEMENTATION -fpic -DU_STATIC_IMPLEMENTATION -O2 -g -c integer64_to_na.c -o integer64_to_na.o
gcc -std=gnu99 -I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -Iyajl/api -DU_STATIC_IMPLEMENTATION -fpic -DU_STATIC_IMPLEMENTATION -O2 -g -c is_datelist.c -o is_datelist.o
gcc -std=gnu99 -I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -Iyajl/api -DU_STATIC_IMPLEMENTATION -fpic -DU_STATIC_IMPLEMENTATION -O2 -g -c is_recordlist.c -o is_recordlist.o
gcc -std=gnu99 -I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -Iyajl/api -DU_STATIC_IMPLEMENTATION -fpic -DU_STATIC_IMPLEMENTATION -O2 -g -c is_scalarlist.c -o is_scalarlist.o
gcc -std=gnu99 -I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -Iyajl/api -DU_STATIC_IMPLEMENTATION -fpic -DU_STATIC_IMPLEMENTATION -O2 -g -c modp_numtoa.c -o modp_numtoa.o
gcc -std=gnu99 -I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -Iyajl/api -DU_STATIC_IMPLEMENTATION -fpic -DU_STATIC_IMPLEMENTATION -O2 -g -c null_to_na.c -o null_to_na.o
gcc -std=gnu99 -I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -Iyajl/api -DU_STATIC_IMPLEMENTATION -fpic -DU_STATIC_IMPLEMENTATION -O2 -g -c num_to_char.c -o num_to_char.o
gcc -std=gnu99 -I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -Iyajl/api -DU_STATIC_IMPLEMENTATION -fpic -DU_STATIC_IMPLEMENTATION -O2 -g -c parse.c -o parse.o
gcc -std=gnu99 -I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -Iyajl/api -DU_STATIC_IMPLEMENTATION -fpic -DU_STATIC_IMPLEMENTATION -O2 -g -c prettify.c -o prettify.o
gcc -std=gnu99 -I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -Iyajl/api -DU_STATIC_IMPLEMENTATION -fpic -DU_STATIC_IMPLEMENTATION -O2 -g -c push_parser.c -o push_parser.o
gcc -std=gnu99 -I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -Iyajl/api -DU_STATIC_IMPLEMENTATION -fpic -DU_STATIC_IMPLEMENTATION -O2 -g -c r-base64.c -o r-base64.o
gcc -std=gnu99 -I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -Iyajl/api -DU_STATIC_IMPLEMENTATION -fpic -DU_STATIC_IMPLEMENTATION -O2 -g -c register.c -o register.o
gcc -std=gnu99 -I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -Iyajl/api -DU_STATIC_IMPLEMENTATION -fpic -DU_STATIC_IMPLEMENTATION -O2 -g -c row_collapse.c -o row_collapse.o
gcc -std=gnu99 -I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -Iyajl/api -DU_STATIC_IMPLEMENTATION -fpic -DU_STATIC_IMPLEMENTATION -O2 -g -c transpose_list.c -o transpose_list.o
gcc -std=gnu99 -I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -Iyajl/api -DU_STATIC_IMPLEMENTATION -fpic -DU_STATIC_IMPLEMENTATION -O2 -g -c validate.c -o validate.o
gcc -std=gnu99 -I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -Iyajl/api -DU_STATIC_IMPLEMENTATION -fpic -DU_STATIC_IMPLEMENTATION -O2 -g -c yajl/yajl.c -o yajl/yajl.o
gcc -std=gnu99 -I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -Iyajl/api -DU_STATIC_IMPLEMENTATION -fpic -DU_STATIC_IMPLEMENTATION -O2 -g -c yajl/yajl_alloc.c -o yajl/yajl_alloc.o
gcc -std=gnu99 -I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -Iyajl/api -DU_STATIC_IMPLEMENTATION -fpic -DU_STATIC_IMPLEMENTATION -O2 -g -c yajl/yajl_buf.c -o yajl/yajl_buf.o
gcc -std=gnu99 -I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -Iyajl/api -DU_STATIC_IMPLEMENTATION -fpic -DU_STATIC_IMPLEMENTATION -O2 -g -c yajl/yajl_encode.c -o yajl/yajl_encode.o
gcc -std=gnu99 -I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -Iyajl/api -DU_STATIC_IMPLEMENTATION -fpic -DU_STATIC_IMPLEMENTATION -O2 -g -c yajl/yajl_gen.c -o yajl/yajl_gen.o
gcc -std=gnu99 -I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -Iyajl/api -DU_STATIC_IMPLEMENTATION -fpic -DU_STATIC_IMPLEMENTATION -O2 -g -c yajl/yajl_lex.c -o yajl/yajl_lex.o
gcc -std=gnu99 -I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -Iyajl/api -DU_STATIC_IMPLEMENTATION -fpic -DU_STATIC_IMPLEMENTATION -O2 -g -c yajl/yajl_parser.c -o yajl/yajl_parser.o
gcc -std=gnu99 -I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -Iyajl/api -DU_STATIC_IMPLEMENTATION -fpic -DU_STATIC_IMPLEMENTATION -O2 -g -c yajl/yajl_tree.c -o yajl/yajl_tree.o
ar rcs libstatyajl.a yajl/yajl.o yajl/yajl_alloc.o yajl/yajl_buf.o yajl/yajl_encode.o yajl/yajl_gen.o yajl/yajl_lex.o yajl/yajl_parser.o yajl/yajl_tree.o
gcc -std=gnu99 -shared -L/usr/lib64/microsoft-r/3.3/lib64/R/lib -o jsonlite.so base64.o collapse_array.o collapse_object.o collapse_pretty.o escape_chars.o integer64_to_na.o is_datelist.o is_recordlist.o is_scalarlist.o modp_numtoa.o null_to_na.o num_to_char.o parse.o prettify.o push_parser.o r-base64.o register.o row_collapse.o transpose_list.o validate.o -L. -lstatyajl -L/usr/lib64/microsoft-r/3.3/lib64/R/lib -lR
installing to /home/sshuser4/R/x86_64-pc-linux-gnu-library/3.3/jsonlite/libs
** R
** inst
** preparing package for lazy loading
Error in unloadNamespace(pkg_name) :
namespace ‘jsonlite’ is imported by ‘RevoScaleR’, ‘MicrosoftML’, ‘CompatibilityAPI’ so cannot be unloaded
* removing ‘/home/sshuser4/R/x86_64-pc-linux-gnu-library/3.3/jsonlite’
Warning in install.packages :
installation of package ‘jsonlite’ had non-zero exit status
ERROR: dependency ‘httpuv’ is not available for package ‘shiny’
* removing ‘/home/sshuser4/R/x86_64-pc-linux-gnu-library/3.3/shiny’
Warning in install.packages :
installation of package ‘shiny’ had non-zero exit status
ERROR: dependency ‘shiny’ is not available for package ‘sparklyr’
* removing ‘/home/sshuser4/R/x86_64-pc-linux-gnu-library/3.3/sparklyr’
Warning in install.packages :
installation of package ‘sparklyr’ had non-zero exit status
The downloaded source packages are in
‘/tmp/RtmpgVHekU/downloaded_packages’
I don't know why it takes so long and why it doesn't work.
To fix this problem, i have to first install curl and httr and then use devtools install.version and fine which version is available. For information, i'm working with Rstudio server 3.3 installed on an Azure HDI cluster.
Update
I'm able to install some packages but some are still failing to be installed. i got something like this sometimes:
In file included from /home/sshuser/R/x86_64-pc-linux-gnu-library/3.3/Rcpp/include/RcppCommon.h:70:0,
from /home/sshuser/R/x86_64-pc-linux-gnu-library/3.3/Rcpp/include/Rcpp.h:27,
from XlsxWorkBook.cpp:1:
/home/sshuser/R/x86_64-pc-linux-gnu-library/3.3/Rcpp/include/Rcpp/utils/tinyformat.h:136:0: warning: "TINYFORMAT_NO_VARIADIC_TEMPLATES" redefined
#define TINYFORMAT_NO_VARIADIC_TEMPLATES
^
<command-line>:0:0: note: this is the location of the previous definition
Sometimes i get something like this:
ERROR: dependencies ‘RJDBC’, ‘rJava’ are not available for package ‘RH2’
* removing ‘/home/sshuser/R/x86_64-pc-linux-gnu-library/3.3/RH2’
I have been trying to install the R package, Kernlab from source, but I have been running into problems. At first, I had some error related to gfortran, so I downloaded the GNU fortran compiler from http://r.research.att.com/tools/
Then when I type the following command: R CMD INSTALL kernlab_0.9-12.tar.gz
I get the following error:
installing to /Library/Frameworks/R.framework/Versions/2.13/Resources/library/kernlab/libs/x86_64
** R
** data
** inst
** preparing package for lazy loading
Error in .walkClassGraph(ClassDef, "contains", where, attr(ext, "conflicts")) :
the "superClass" list for class "list", includes an undefined class "input"
Error in .walkClassGraph(ClassDef, "contains", where, attr(ext, "conflicts")) :
the "superClass" list for class "numeric", includes an undefined class "output"
Error : evaluation nested too deeply: infinite recursion / options(expressions=)?
Error in setClassUnion("listI", c("list", "numeric", "vector", "integer", :
unable to create union class: could not set members "list", "numeric"
Error : unable to load R code in package 'kernlab'
ERROR: lazy loading failed for package ‘kernlab’
* removing ‘/Library/Frameworks/R.framework/Versions/2.13/Resources/library/kernlab’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/2.13/Resources/library/kernlab’
Does anyone know how to solve this error? PS. For the GNU fortran compiler I downloaded, it says that is for Xcode version up to 3.2.5; and I have Xcode version 3.2.6. Is this the source of my error, or am I looking in the wrong direction?
It must be something with your system. On my Linux box, kernlab_0.9-12 installs fine:
edd#max:/tmp$ R CMD INSTALL kernlab_0.9-12.tar.gz
* installing to library ‘/usr/local/lib/R/site-library’
* installing *source* package ‘kernlab’ ...
** libs
g++-4.4 -I/usr/share/R/include -fpic -O3 -pipe -c brweight.cpp -o brweight.o
g++-4.4 -I/usr/share/R/include -fpic -O3 -pipe -c ctable.cpp -o ctable.o
g++-4.4 -I/usr/share/R/include -fpic -O3 -pipe -c cweight.cpp -o cweight.o
gcc-4.4 -I/usr/share/R/include -fpic -O3 -g0 -Wall -pipe -pedantic -std=gnu99 -c dbreakpt.c -o dbreakpt.o
gcc-4.4 -I/usr/share/R/include -fpic -O3 -g0 -Wall -pipe -pedantic -std=gnu99 -c dcauchy.c -o dcauchy.o
gcc-4.4 -I/usr/share/R/include -fpic -O3 -g0 -Wall -pipe -pedantic -std=gnu99 -c dgpnrm.c -o dgpnrm.o
gcc-4.4 -I/usr/share/R/include -fpic -O3 -g0 -Wall -pipe -pedantic -std=gnu99 -c dgpstep.c -o dgpstep.o
gcc-4.4 -I/usr/share/R/include -fpic -O3 -g0 -Wall -pipe -pedantic -std=gnu99 -c dprecond.c -o dprecond.o
gcc-4.4 -I/usr/share/R/include -fpic -O3 -g0 -Wall -pipe -pedantic -std=gnu99 -c dprsrch.c -o dprsrch.o
gcc-4.4 -I/usr/share/R/include -fpic -O3 -g0 -Wall -pipe -pedantic -std=gnu99 -c dspcg.c -o dspcg.o
gcc-4.4 -I/usr/share/R/include -fpic -O3 -g0 -Wall -pipe -pedantic -std=gnu99 -c dtron.c -o dtron.o
gcc-4.4 -I/usr/share/R/include -fpic -O3 -g0 -Wall -pipe -pedantic -std=gnu99 -c dtrpcg.c -o dtrpcg.o
dtrpcg.c: In function ‘dtrpcg’:
dtrpcg.c:157: warning: value computed is not used
gcc-4.4 -I/usr/share/R/include -fpic -O3 -g0 -Wall -pipe -pedantic -std=gnu99 -c dtrqsol.c -o dtrqsol.o
g++-4.4 -I/usr/share/R/include -fpic -O3 -pipe -c esa.cpp -o esa.o
g++-4.4 -I/usr/share/R/include -fpic -O3 -pipe -c expdecayweight.cpp -o expdecayweight.o
g++-4.4 -I/usr/share/R/include -fpic -O3 -pipe -c inductionsort.cpp -o inductionsort.o
g++-4.4 -I/usr/share/R/include -fpic -O3 -pipe -c kspectrumweight.cpp -o kspectrumweight.o
g++-4.4 -I/usr/share/R/include -fpic -O3 -pipe -c lcp.cpp -o lcp.o
gcc-4.4 -I/usr/share/R/include -fpic -O3 -g0 -Wall -pipe -pedantic -std=gnu99 -c misc.c -o misc.o
g++-4.4 -I/usr/share/R/include -fpic -O3 -pipe -c msufsort.cpp -o msufsort.o
gcc-4.4 -I/usr/share/R/include -fpic -O3 -g0 -Wall -pipe -pedantic -std=gnu99 -c solvebqp.c -o solvebqp.o
gcc-4.4 -I/usr/share/R/include -fpic -O3 -g0 -Wall -pipe -pedantic -std=gnu99 -c stringk.c -o stringk.o
g++-4.4 -I/usr/share/R/include -fpic -O3 -pipe -c stringkernel.cpp -o stringkernel.o
g++-4.4 -I/usr/share/R/include -fpic -O3 -pipe -c svm.cpp -o svm.o
g++-4.4 -I/usr/share/R/include -fpic -O3 -pipe -c wkasailcp.cpp -o wkasailcp.o
g++-4.4 -I/usr/share/R/include -fpic -O3 -pipe -c wmsufsort.cpp -o wmsufsort.o
g++ -shared -o kernlab.so brweight.o ctable.o cweight.o dbreakpt.o dcauchy.o dgpnrm.o dgpstep.o dprecond.o dprsrch.o dspcg.o dtron.o dtrpcg.o dtrqsol.o esa.o expdecayweight.o inductionsort.o kspectrumweight.o lcp.o misc.o msufsort.o solvebqp.o stringk.o stringkernel.o svm.o wkasailcp.o wmsufsort.o -llapack -lblas -lgfortran -lm -L/usr/lib64/R/lib -lR
installing to /usr/local/lib/R/site-library/kernlab/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a new generic function for "terms" in "kernlab"
Creating a new generic function for "fitted" in "kernlab"
Creating a new generic function for "coef" in "kernlab"
Creating a new generic function for "predict" in "kernlab"
Creating a new generic function for "plot" in "kernlab"
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
* DONE (kernlab)
edd#max:/tmp$
Moreover, it has nothing to do with gfortran as the package seems to contain only C and C++ files.
I doubt that a minor version shift in Xcode is the source of your problem (with the unstated version of fortran ... and the unstated version of R), but why not just install the Mac binary?
http://cran.r-project.org/bin/macosx/leopard/contrib/r-release/kernlab_0.9-12.tgz