Installation from CRAN Fails on OSX 10.13.6 during shared object creation.

[astrophys]

I'm on OSX 10.13.6 using R-3.4.2. When I try installing it from CRAN, it tries to link the stdout from R into the shared object. The first bit of output "Looking for libraries in : ~/.R/3.4.2-lib. i.e.

> install.packages("text2vec")
Installing package into ‘/Users/user/.R/3.4.2-lib’
(as ‘lib’ is unspecified)
trying URL 'https://cran.mtu.edu/src/contrib/text2vec_0.5.1.tar.gz'
Content type 'application/x-gzip' length 3486448 bytes (3.3 MB)
==================================================
downloaded 3.3 MB

Looking for libraries in : ~/.R/3.4.2-lib....
Warning in strptime(xx, f <- "%Y-%m-%d %H:%M:%OS", tz = tz) :
  unknown timezone 'zone/tz/2018g.1.0/zoneinfo/America/New_York'
* installing *source* package ‘text2vec’ ...
** package ‘text2vec’ successfully unpacked and MD5 sums checked
** libs
/usr/bin/clang++ -std=gnu++11 -I/Users/user/.local/lib/R/include -DNDEBUG  -I"/Users/user/.R/3.4.2-lib/Rcpp/include" -I"/Users/user/.R/3.4.2-lib/RcppParallel/include" -I"/Users/user/.R/3.4.2-lib/digest/include" -I"/Users/user/.R/3.4.2-lib/sparsepp/include" -I/usr/local/include   -fPIC  -g -O2 -c GloveFitter.cpp -o GloveFitter.o
/usr/bin/clang++ -std=gnu++11 -I/Users/user/.local/lib/R/include -DNDEBUG  -I"/Users/user/.R/3.4.2-lib/Rcpp/include" -I"/Users/user/.R/3.4.2-lib/RcppParallel/include" -I"/Users/user/.R/3.4.2-lib/digest/include" -I"/Users/user/.R/3.4.2-lib/sparsepp/include" -I/usr/local/include   -fPIC  -g -O2 -c HashCorpus.cpp -o HashCorpus.o
/usr/bin/clang++ -std=gnu++11 -I/Users/user/.local/lib/R/include -DNDEBUG  -I"/Users/user/.R/3.4.2-lib/Rcpp/include" -I"/Users/user/.R/3.4.2-lib/RcppParallel/include" -I"/Users/user/.R/3.4.2-lib/digest/include" -I"/Users/user/.R/3.4.2-lib/sparsepp/include" -I/usr/local/include   -fPIC  -g -O2 -c RcppExports.cpp -o RcppExports.o
/usr/bin/clang++ -std=gnu++11 -I/Users/user/.local/lib/R/include -DNDEBUG  -I"/Users/user/.R/3.4.2-lib/Rcpp/include" -I"/Users/user/.R/3.4.2-lib/RcppParallel/include" -I"/Users/user/.R/3.4.2-lib/digest/include" -I"/Users/user/.R/3.4.2-lib/sparsepp/include" -I/usr/local/include   -fPIC  -g -O2 -c VocabCorpus.cpp -o VocabCorpus.o
/usr/bin/clang++ -std=gnu++11 -I/Users/user/.local/lib/R/include -DNDEBUG  -I"/Users/user/.R/3.4.2-lib/Rcpp/include" -I"/Users/user/.R/3.4.2-lib/RcppParallel/include" -I"/Users/user/.R/3.4.2-lib/digest/include" -I"/Users/user/.R/3.4.2-lib/sparsepp/include" -I/usr/local/include   -fPIC  -g -O2 -c Vocabulary.cpp -o Vocabulary.o
/usr/bin/clang++ -std=gnu++11 -I/Users/user/.local/lib/R/include -DNDEBUG  -I"/Users/user/.R/3.4.2-lib/Rcpp/include" -I"/Users/user/.R/3.4.2-lib/RcppParallel/include" -I"/Users/user/.R/3.4.2-lib/digest/include" -I"/Users/user/.R/3.4.2-lib/sparsepp/include" -I/usr/local/include   -fPIC  -g -O2 -c collocations.cpp -o collocations.o
/usr/bin/clang++ -std=gnu++11 -I/Users/user/.local/lib/R/include -DNDEBUG  -I"/Users/user/.R/3.4.2-lib/Rcpp/include" -I"/Users/user/.R/3.4.2-lib/RcppParallel/include" -I"/Users/user/.R/3.4.2-lib/digest/include" -I"/Users/user/.R/3.4.2-lib/sparsepp/include" -I/usr/local/include   -fPIC  -g -O2 -c matrix_utils.cpp -o matrix_utils.o
/usr/bin/clang++ -std=gnu++11 -I/Users/user/.local/lib/R/include -DNDEBUG  -I"/Users/user/.R/3.4.2-lib/Rcpp/include" -I"/Users/user/.R/3.4.2-lib/RcppParallel/include" -I"/Users/user/.R/3.4.2-lib/digest/include" -I"/Users/user/.R/3.4.2-lib/sparsepp/include" -I/usr/local/include   -fPIC  -g -O2 -c memory_tools.cpp -o memory_tools.o
/usr/bin/clang++ -std=gnu++11 -I/Users/user/.local/lib/R/include -DNDEBUG  -I"/Users/user/.R/3.4.2-lib/Rcpp/include" -I"/Users/user/.R/3.4.2-lib/RcppParallel/include" -I"/Users/user/.R/3.4.2-lib/digest/include" -I"/Users/user/.R/3.4.2-lib/sparsepp/include" -I/usr/local/include   -fPIC  -g -O2 -c utils.cpp -o utils.o
/usr/bin/clang++ -std=gnu++11 -I/Users/user/.local/lib/R/include -DNDEBUG  -I"/Users/user/.R/3.4.2-lib/Rcpp/include" -I"/Users/user/.R/3.4.2-lib/RcppParallel/include" -I"/Users/user/.R/3.4.2-lib/digest/include" -I"/Users/user/.R/3.4.2-lib/sparsepp/include" -I/usr/local/include   -fPIC  -g -O2 -c warplda.cpp -o warplda.o
/usr/bin/clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o text2vec.so GloveFitter.o HashCorpus.o RcppExports.o VocabCorpus.o Vocabulary.o collocations.o matrix_utils.o memory_tools.o utils.o warplda.o Looking for libraries in : /Users/user/.R/3.4.2-lib.... Good Bye Tue Dec 25 06:41:13 2018 -Wl,-framework -Wl,CoreFoundation
clang: error: no such file or directory: 'Looking'
clang: error: no such file or directory: 'for'
clang: error: no such file or directory: 'libraries'
clang: error: no such file or directory: 'in'
clang: error: no such file or directory: ':'
clang: error: no such file or directory: '/Users/user/.R/3.4.2-lib....'
clang: error: no such file or directory: 'Good'
clang: error: no such file or directory: 'Bye'
clang: error: no such file or directory: 'Tue'
clang: error: no such file or directory: 'Dec'
clang: error: no such file or directory: '25'
clang: error: no such file or directory: '06:41:14'
clang: error: no such file or directory: '2018'
make: *** [text2vec.so] Error 1
ERROR: compilation failed for package ‘text2vec’
* removing ‘/Users/user/.R/3.4.2-lib/text2vec’

The downloaded source packages are in
    ‘/private/var/folders/0s/qch_8kr55x91vgc08sfvh82w0000gn/T/RtmpDrYNd8/downloaded_packages’
Warning message:
In install.packages("text2vec") :
  installation of package ‘text2vec’ had non-zero exit status

[dselivanov]

Hi. Have no clue why is that. I doubt the issue is in text2vec.

[astrophys]

Looking at the source code, I don't see where compilation occurs (e.g. Makefile). How is compilation done?

[dselivanov]

Installation happens via R CMD install. There are quite a lot things going behind the scenes - you can check https://cran.r-project.org/doc/manuals/r-release/R-exts.html.

I suspect you have some unusual R installation.