CODEWITHSUNDEEP
razurerstudiohttpuv
Orhan Yazar
Orhan Yazar

Reputation: 909

httpuv fails to compile on Azure HDI cluster

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’

Upvotes: 3

Views: 198

Answers (0)

Related Questions