httpuv fails to compile on Azure HDI cluster

httpuv fails to compile on Azure HDI cluster - r

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
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 13 2637k 13 360k 0 0 2422k 0 0:00:01 --:--:-- 0:00:01 2417k100 2637k 100 2637k 0 0 12.1M 0 --:--:-- --:--:-- --:--:-- 12.0M
* 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’

Related

Cannot install rJava on R 4.2.2 arm64: ld: library not found for -lpcre2-8

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

R data.table compiled installation failing: Error: shared object ‘datatable.so’ not found

I'm installing R on a new laptop (no migration from a previous laptop or OS version).
R 4.0.1 installed fine.
> sessionInfo()
R version 4.0.1 (2020-06-06)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.5
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_4.0.1 tools_4.0.1
Then I move on to install data.table:
> install.packages("data.table")
trying URL 'https://cran.revolutionanalytics.com/bin/macosx/contrib/4.0/data.table_1.12.8.tgz'
Content type 'application/octet-stream' length 2070859 bytes (2.0 MB)
==================================================
downloaded 2.0 MB
The downloaded binary packages are in
/var/folders/tg/5sw17w2n28g_2n1c_cs0ydlw0000gn/T//RtmpU0QnBY/downloaded_packages
Seems fine. But when I load it:
> library(data.table)
data.table 1.12.8 using 1 threads (see ?getDTthreads). Latest news: r-datatable.com
**********
This installation of data.table has not detected OpenMP support. It should still work but in single-threaded mode. If this is a Mac, please ensure you are using R>=3.4.0 and have followed our Mac instructions here: https://github.com/Rdatatable/data.table/wiki/Installation. This warning message should not occur on Windows or Linux. If it does, please file a GitHub issue.
**********
I want to use multiple cores so I go to the suggested web page above and follow instructions there. I do all three steps and they all seem to work (no error messages).
install command line tools with "xcode-select --install"
install Brew and then "brew update && brew install llvm"
finally create and edit "~/.R/Makevars" as suggested.
At this point I go back and try installing data.table and compiling it with:
> install.packages("data.table", type = "source",
+ repos = "https://Rdatatable.gitlab.io/data.table")
trying URL 'https://Rdatatable.gitlab.io/data.table/src/contrib/data.table_1.12.9.tar.gz'
Content type 'application/gzip' length 5207555 bytes (5.0 MB)
==================================================
downloaded 5.0 MB
* installing *source* package ‘data.table’ ...
** using staged installation
*** pkg-config is not installed.
*** Compilation will now be attempted and if it works you can ignore this message. However,
*** if compilation fails, try 'locate zlib.h zconf.h' and ensure the zlib development library
*** is installed :
*** deb: zlib1g-dev (Debian, Ubuntu, ...)
*** rpm: zlib-devel (Fedora, EPEL, ...)
*** brew: zlib (OSX)
*** Note that zlib is required to compile R itself so you may find the advice in the R-admin
*** guide helpful regarding zlib. On Debian/Ubuntu, zlib1g-dev is a dependency of r-base as
*** shown by 'apt-cache showsrc r-base | grep ^Build-Depends | grep zlib', and therefore
*** 'sudo apt-get build-dep r-base' should be sufficient too.
*** To silence this message, please ensure that :
*** 1) 'pkg-config --exists zlib' succeeds (i.e. $? -eq 0)
*** 2) 'pkg-config --libs zlib' contains -lz
*** Compilation will now be attempted ...
** libs
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c assign.c -o assign.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c between.c -o between.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c bmerge.c -o bmerge.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c chmatch.c -o chmatch.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c cj.c -o cj.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c coalesce.c -o coalesce.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c dogroups.c -o dogroups.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fastmean.c -o fastmean.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fcast.c -o fcast.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fifelse.c -o fifelse.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fmelt.c -o fmelt.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c forder.c -o forder.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c frank.c -o frank.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fread.c -o fread.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c freadR.c -o freadR.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c froll.c -o froll.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c frollR.c -o frollR.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c frolladaptive.c -o frolladaptive.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fsort.c -o fsort.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fwrite.c -o fwrite.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fwriteR.c -o fwriteR.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c gsumm.c -o gsumm.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c ijoin.c -o ijoin.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c init.c -o init.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c inrange.c -o inrange.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c nafill.c -o nafill.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c nqrecreateindices.c -o nqrecreateindices.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c openmp-utils.c -o openmp-utils.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c quickselect.c -o quickselect.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c rbindlist.c -o rbindlist.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c reorder.c -o reorder.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c shift.c -o shift.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c snprintf.c -o snprintf.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c subset.c -o subset.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c transpose.c -o transpose.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c types.c -o types.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c uniqlist.c -o uniqlist.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c utils.c -o utils.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c vecseq.c -o vecseq.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c wrappers.c -o wrappers.o
/usr/local/opt/llvm/bin/clang -fopenmp -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/opt/gettext/lib -L/usr/local/opt/llvm/lib -Wl,-rpath,/usr/local/opt/llvm/lib -o data.table.so assign.o between.o bmerge.o chmatch.o cj.o coalesce.o dogroups.o fastmean.o fcast.o fifelse.o fmelt.o forder.o frank.o fread.o freadR.o froll.o frollR.o frolladaptive.o fsort.o fwrite.o fwriteR.o gsumm.o ijoin.o init.o inrange.o nafill.o nqrecreateindices.o openmp-utils.o quickselect.o rbindlist.o reorder.o shift.o snprintf.o subset.o transpose.o types.o uniqlist.o utils.o vecseq.o wrappers.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-data.table/00new/data.table/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for ‘data.table’ in library.dynam(lib, package, package.lib):
shared object ‘datatable.so’ not found
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/data.table’
The downloaded source packages are in
‘/private/var/folders/tg/5sw17w2n28g_2n1c_cs0ydlw0000gn/T/RtmpU0QnBY/downloaded_packages’
Warning message:
In install.packages("data.table", type = "source", repos = "https://Rdatatable.gitlab.io/data.table") :
installation of package ‘data.table’ had non-zero exit status
Didn't work.
What does the error message mean "Error: package or namespace load failed for ‘data.table’ in library.dynam(lib, package, package.lib):
shared object ‘datatable.so’ not found" ???

Error: package or namespace load failed for ‘data.table’ in library.dynam(lib, package, package.lib): shared object ‘datatable.so’ not found

install.packages("data.table")
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.5/data.table_1.12.8.tgz'
Content type 'application/x-gzip' length 2117137 bytes (2.0 MB)
downloaded 2.0 MB
The downloaded binary packages are in
/var/folders/r1/1rsn2y0j78v907qgv0btm_fm0000gn/T//RtmppBu3UK/downloaded_packages
updating to the latest development version using provided code:
data.table::update.dev.pkg()
The printed console:
Warning: unable to access index for repository https://Rdatatable.gitlab.io/data.table/bin/macosx/el-capitan/contrib/3.5:
cannot open URL 'https://Rdatatable.gitlab.io/data.table/bin/macosx/el-capitan/contrib/3.5/PACKAGES'
Package which is only available in source form, and may need compilation of C/C++/Fortran: ‘data.table’
Do you want to attempt to install these from sources? (Yes/no/cancel) Yes
installing the source package ‘data.table’
trying URL 'https://Rdatatable.gitlab.io/data.table/src/contrib/data.table_1.12.9.tar.gz'
Content type 'application/gzip' length 5189945 bytes (4.9 MB)
==================================================
downloaded 4.9 MB
* installing *source* package ‘data.table’ ...
*** pkg-config is not installed.
*** Compilation will now be attempted and if it works you can ignore this message. However,
*** if compilation fails, try 'locate zlib.h zconf.h' and ensure the zlib development library
*** is installed :
*** deb: zlib1g-dev (Debian, Ubuntu, ...)
*** rpm: zlib-devel (Fedora, EPEL, ...)
*** brew: zlib (OSX)
*** Note that zlib is required to compile R itself so you may find the advice in the R-admin
*** guide helpful regarding zlib. On Debian/Ubuntu, zlib1g-dev is a dependency of r-base as
*** shown by 'apt-cache showsrc r-base | grep ^Build-Depends | grep zlib', and therefore
*** 'sudo apt-get build-dep r-base' should be sufficient too.
*** To silence this message, please ensure that :
*** 1) 'pkg-config --exists zlib' succeeds (i.e. $? -eq 0)
*** 2) 'pkg-config --libs zlib' contains -lz
*** Compilation will now be attempted ...
** libs
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c assign.c -o assign.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c between.c -o between.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c bmerge.c -o bmerge.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c chmatch.c -o chmatch.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c cj.c -o cj.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c coalesce.c -o coalesce.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c dogroups.c -o dogroups.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fastmean.c -o fastmean.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fcast.c -o fcast.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fifelse.c -o fifelse.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fmelt.c -o fmelt.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c forder.c -o forder.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c frank.c -o frank.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fread.c -o fread.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c freadR.c -o freadR.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c froll.c -o froll.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c frollR.c -o frollR.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c frolladaptive.c -o frolladaptive.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fsort.c -o fsort.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fwrite.c -o fwrite.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fwriteR.c -o fwriteR.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c gsumm.c -o gsumm.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c ijoin.c -o ijoin.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c init.c -o init.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c inrange.c -o inrange.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c nafill.c -o nafill.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c nqrecreateindices.c -o nqrecreateindices.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c openmp-utils.c -o openmp-utils.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c quickselect.c -o quickselect.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c rbindlist.c -o rbindlist.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c reorder.c -o reorder.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c shift.c -o shift.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c subset.c -o subset.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c transpose.c -o transpose.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c types.c -o types.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c uniqlist.c -o uniqlist.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c utils.c -o utils.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c vecseq.c -o vecseq.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c wrappers.c -o wrappers.o
/usr/local/opt/llvm/bin/clang -fopenmp -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/opt/gettext/lib -L/usr/local/opt/llvm/lib -Wl,-rpath,/usr/local/opt/llvm/lib -o data.table.so assign.o between.o bmerge.o chmatch.o cj.o coalesce.o dogroups.o fastmean.o fcast.o fifelse.o fmelt.o forder.o frank.o fread.o freadR.o froll.o frollR.o frolladaptive.o fsort.o fwrite.o fwriteR.o gsumm.o ijoin.o init.o inrange.o nafill.o nqrecreateindices.o openmp-utils.o quickselect.o rbindlist.o reorder.o shift.o subset.o transpose.o types.o uniqlist.o utils.o vecseq.o wrappers.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/data.table/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Error: package or namespace load failed for ‘data.table’ in library.dynam(lib, package, package.lib):
shared object ‘datatable.so’ not found
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/data.table’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/data.table’
The downloaded source packages are in
‘/private/var/folders/r1/1rsn2y0j78v907qgv0btm_fm0000gn/T/RtmppBu3UK/downloaded_packages’
R data.table package has been updated to NA (1.12.8)
Warning message:
In utils::install.packages(pkg, repos = repo, type = type, lib = lib, :
installation of package ‘data.table’ had non-zero exit status
What is wrong with this ‘datatable.so’ not found? And I didn't find any posting related to datatable.so so far.
FYI: I've followed all instruction here when first problem (the gettext issue) solved, the datatable.so did not. I've went through all related/possible post and followed all the instruction including brewing, clang, gfortan etc. But nothing seems to be working.
I'm trying to use 'fcase' as provided in the answer to my previous question here.

The problem you are facing is compilation package from source on macOS. It is known to be causing much more troubles than on other platforms. We have a dedicated wiki page:
https://github.com/Rdatatable/data.table/wiki/Installation
As you mentioned you followed those instructions. If they were not sufficient to solve your configuration, please do submit issue in github repository describing your current setup, Makevars, compiler, version.

Unable to Install openxlsx library in R

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

R 3.5.1 - Building data.table from source fails on Travis CI

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)

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