I can't install qgraph in Rstudio any which way. please help! I have the latest version of Rstudio (1.2.5) and MacOS Catalina 10.15.4
Here is the code:
> install.packages("qgraph")
also installing the dependencies ‘RcppArmadillo’, ‘graphlayouts’, ‘ggraph’
There are binary versions available but the source versions are later:
binary source needs_compilation
RcppArmadillo 0.9.300.2.0 0.9.870.2.0 TRUE
ggraph 1.0.2 2.0.2 TRUE
qgraph 1.6.1 1.6.5 TRUE
Do you want to install from sources the packages which need compilation?
y/n: y
Package which is only available in source form, and may need compilation of C/C++/Fortran:
‘graphlayouts’
Do you want to attempt to install these from sources?
y/n: y
installing the source packages ‘RcppArmadillo’, ‘graphlayouts’, ‘ggraph’, ‘qgraph’
trying URL 'https://cran.rstudio.com/src/contrib/RcppArmadillo_0.9.870.2.0.tar.gz'
Content type 'application/x-gzip' length 1640152 bytes (1.6 MB)
==================================================
downloaded 1.6 MB
trying URL 'https://cran.rstudio.com/src/contrib/graphlayouts_0.7.0.tar.gz'
Content type 'application/x-gzip' length 2410037 bytes (2.3 MB)
==================================================
downloaded 2.3 MB
trying URL 'https://cran.rstudio.com/src/contrib/ggraph_2.0.2.tar.gz'
Content type 'application/x-gzip' length 3183660 bytes (3.0 MB)
==================================================
downloaded 3.0 MB
trying URL 'https://cran.rstudio.com/src/contrib/qgraph_1.6.5.tar.gz'
Content type 'application/x-gzip' length 230442 bytes (225 KB)
==================================================
downloaded 225 KB
Warning in strptime(xx, f <- "%Y-%m-%d %H:%M:%OS", tz = tz) :
unknown timezone 'zone/tz/2020a.1.0/zoneinfo/America/New_York'
* installing *source* package ‘RcppArmadillo’ ...
** package ‘RcppArmadillo’ successfully unpacked and MD5 sums checked
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether clang++ accepts -g... yes
checking how to run the C++ preprocessor... clang++ -E
checking whether we are using the GNU C++ compiler... (cached) yes
checking whether clang++ accepts -g... (cached) yes
checking whether g++ version is sufficient... almost
configure: WARNING: Compiler self-identifies as being compliant with GNUC extensions but is not g++.
checking for macOS... found
checking for macOS Apple compiler... found
configure: WARNING: OpenMP unavailable and turned off.
checking LAPACK_LIBS... R-supplied partial LAPACK found
configure: WARNING: Some complex-valued LAPACK functions may not be available
configure: creating ./config.status
config.status: creating inst/include/RcppArmadilloConfigGenerated.h
config.status: creating src/Makevars
** libs
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I../inst/include -fPIC -Wall -g -O2 -c RcppArmadillo.cpp -o RcppArmadillo.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I../inst/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I../inst/include -fPIC -Wall -g -O2 -c fastLm.cpp -o fastLm.o
clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o RcppArmadillo.so RcppArmadillo.o RcppExports.o fastLm.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0'
ld: warning: directory not found for option '-L/usr/local/gfortran/lib'
ld: library not found for -lgfortran
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [RcppArmadillo.so] Error 1
ERROR: compilation failed for package ‘RcppArmadillo’
* removing ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo’
Warning in install.packages :
installation of package ‘RcppArmadillo’ had non-zero exit status
Warning in strptime(xx, f <- "%Y-%m-%d %H:%M:%OS", tz = tz) :
unknown timezone 'zone/tz/2020a.1.0/zoneinfo/America/New_York'
ERROR: dependency ‘RcppArmadillo’ is not available for package ‘graphlayouts’
* removing ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/graphlayouts’
Warning in install.packages :
installation of package ‘graphlayouts’ had non-zero exit status
Warning in strptime(xx, f <- "%Y-%m-%d %H:%M:%OS", tz = tz) :
unknown timezone 'zone/tz/2020a.1.0/zoneinfo/America/New_York'
ERROR: dependency ‘graphlayouts’ is not available for package ‘ggraph’
* removing ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/ggraph’
Warning in install.packages :
installation of package ‘ggraph’ had non-zero exit status
Warning in strptime(xx, f <- "%Y-%m-%d %H:%M:%OS", tz = tz) :
unknown timezone 'zone/tz/2020a.1.0/zoneinfo/America/New_York'
ERROR: dependency ‘ggraph’ is not available for package ‘qgraph’
* removing ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/qgraph’
Warning in install.packages :
installation of package ‘qgraph’ had non-zero exit status
The downloaded source packages are in
‘/private/var/folders/sf/t7dh31ls1c7_5m6k107_2xvw0000gn/T/RtmpApriZt/downloaded_packages’