New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Install error #90

Closed
rsangole opened this Issue Mar 20, 2018 · 12 comments

Comments

Projects
None yet
3 participants
@rsangole
Copy link

rsangole commented Mar 20, 2018

I get an error

> install.packages('fs')
Installing package into ‘/home/hw831/R/x86_64-pc-linux-gnu-library/3.3’
(as ‘lib’ is unspecified)
Warning in install.packages :
package ‘fs’ is not available (for R version 3.3.2)

although the CRAN page specifies that the R dependency is >3.1.

Please advise.

@jimhester

This comment has been minimized.

Copy link
Member

jimhester commented Mar 20, 2018

Try explicitly setting the type of package to source. e.g. install.packages("fs", type = "source")

@rsangole

This comment has been minimized.

Copy link
Author

rsangole commented Mar 20, 2018

Hmm, no luck. Same error.

@rsangole

This comment has been minimized.

Copy link
Author

rsangole commented Mar 20, 2018

install.packages('fs',repos='http://cran.us.r-project.org')
worked though!

@rsangole rsangole closed this Mar 20, 2018

@rsangole rsangole reopened this Mar 20, 2018

@rsangole

This comment has been minimized.

Copy link
Author

rsangole commented Mar 20, 2018

Spoke too soon. I'm trying to install this package on an azure system running R 3.3.2. The install fails in the following way. Any ideas?

version information
image

install & error information

(> install.packages('fs',repos='http://cran.us.r-project.org')
Installing package into ‘/home/hw831/R/x86_64-pc-linux-gnu-library/3.3’
(as ‘lib’ is unspecified)
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0  2  777k    2 19685    0     0  42888      0  0:00:18 --:--:--  0:00:18 42886100  777k  100  777k    0     0   639k      0  0:00:01  0:00:01 --:--:--  639k
* installing *source* package ‘fs’ ...
** package ‘fs’ successfully unpacked and MD5 sums checked
** libs
I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -I./libuv/include -I. -DU_STATIC_IMPLEMENTATION -I"/usr/lib64/microsoft-r/3.3/lib64/R/library/Rcpp/include"      -c id.cc -o id.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:139: recipe for target 'id.o' )failed
make: [id.o] Error 127 (ignored)
I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -I./libuv/include -I. -DU_STATIC_IMPLEMENTATION -I"/usr/lib64/microsoft-r/3.3/lib64/R/library/Rcpp/include"      -c fs.cc -o fs.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:139: recipe for target 'fs.o' failed
make: [fs.o] Error 127 (ignored)
I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -I./libuv/include -I. -DU_STATIC_IMPLEMENTATION -I"/usr/lib64/microsoft-r/3.3/lib64/R/library/Rcpp/include"      -c file.cc -o file.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:139: recipe for target 'file.o' failed
make: [file.o] Error 127 (ignored)
I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -I./libuv/include -I. -DU_STATIC_IMPLEMENTATION -I"/usr/lib64/microsoft-r/3.3/lib64/R/library/Rcpp/include"      -c link.cc -o link.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:139: recipe for target 'link.o' failed
make: [link.o] Error 127 (ignored)
I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -I./libuv/include -I. -DU_STATIC_IMPLEMENTATION -I"/usr/lib64/microsoft-r/3.3/lib64/R/library/Rcpp/include"      -c path.cc -o path.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:139: recipe for target 'path.o' failed
make: [path.o] Error 127 (ignored)
I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -I./libuv/include -I. -DU_STATIC_IMPLEMENTATION -I"/usr/lib64/microsoft-r/3.3/lib64/R/library/Rcpp/include"      -c utils.cc -o utils.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:139: recipe for target 'utils.o' failed
make: [utils.o] Error 127 (ignored)
I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -I./libuv/include -I. -DU_STATIC_IMPLEMENTATION -I"/usr/lib64/microsoft-r/3.3/lib64/R/library/Rcpp/include"      -c dir.cc -o dir.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:139: recipe for target 'dir.o' failed
make: [dir.o] Error 127 (ignored)
I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -I./libuv/include -I. -DU_STATIC_IMPLEMENTATION -I"/usr/lib64/microsoft-r/3.3/lib64/R/library/Rcpp/include"      -c error.cc -o error.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:139: recipe for target 'error.o' failed
make: [error.o] Error 127 (ignored)
I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -I./libuv/include -I. -DU_STATIC_IMPLEMENTATION -I"/usr/lib64/microsoft-r/3.3/lib64/R/library/Rcpp/include"      -c unix/getmode.cc -o unix/getmode.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:139: recipe for target 'unix/getmode.o' failed
make: [unix/getmode.o] Error 127 (ignored)
I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -I./libuv/include -I. -DU_STATIC_IMPLEMENTATION -I"/usr/lib64/microsoft-r/3.3/lib64/R/library/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)
gcc -std=gnu99 -I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -I./libuv/include -I. -DU_STATIC_IMPLEMENTATION -I"/usr/lib64/microsoft-r/3.3/lib64/R/library/Rcpp/include"   -fpic  -DU_STATIC_IMPLEMENTATION -O2 -g  -c bsd/setmode.c -o bsd/setmode.o
gcc -std=gnu99 -I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -I./libuv/include -I. -DU_STATIC_IMPLEMENTATION -I"/usr/lib64/microsoft-r/3.3/lib64/R/library/Rcpp/include"   -fpic  -DU_STATIC_IMPLEMENTATION -O2 -g  -c bsd/strmode.c -o bsd/strmode.o
gcc -std=gnu99 -I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -I./libuv/include -I. -DU_STATIC_IMPLEMENTATION -I"/usr/lib64/microsoft-r/3.3/lib64/R/library/Rcpp/include"   -fpic  -DU_STATIC_IMPLEMENTATION -O2 -g  -c bsd/reallocarray.c -o bsd/reallocarray.o
cp -p -f libuv/m4/lt_obsolete.m4 libuv/m4/lt~obsolete.m4
(cd libuv && CC="gcc -std=gnu99" CFLAGS="-DU_STATIC_IMPLEMENTATION -O2 -g  -fpic -fvisibility=hidden" AR="ar" RANLIB="ranlib" LDFLAGS="" ./configure --quiet)
make --directory=libuv \
	HAVE_DTRACE=0
make[1]: Entering directory '/tmp/RtmpgupyEb/R.INSTALL57b46aa0b777/fs/src/libuv'
  CC       src/libuv_la-fs-poll.lo
  CC       src/libuv_la-inet.lo
  CC       src/libuv_la-threadpool.lo
  CC       src/libuv_la-uv-common.lo
  CC       src/libuv_la-version.lo
  CC       src/unix/libuv_la-async.lo
  CC       src/unix/libuv_la-core.lo
  CC       src/unix/libuv_la-dl.lo
  CC       src/unix/libuv_la-fs.lo
  CC       src/unix/libuv_la-getaddrinfo.lo
  CC       src/unix/libuv_la-getnameinfo.lo
  CC       src/unix/libuv_la-loop-watcher.lo
  CC       src/unix/libuv_la-loop.lo
  CC       src/unix/libuv_la-pipe.lo
  CC       src/unix/libuv_la-poll.lo
  CC       src/unix/libuv_la-process.lo
  CC       src/unix/libuv_la-signal.lo
  CC       src/unix/libuv_la-stream.lo
  CC       src/unix/libuv_la-tcp.lo
  CC       src/unix/libuv_la-thread.lo
  CC       src/unix/libuv_la-timer.lo
  CC       src/unix/libuv_la-tty.lo
  CC       src/unix/libuv_la-udp.lo
  CC       src/unix/libuv_la-linux-core.lo
  CC       src/unix/libuv_la-linux-inotify.lo
  CC       src/unix/libuv_la-linux-syscalls.lo
  CC       src/unix/libuv_la-procfs-exepath.lo
  CC       src/unix/libuv_la-proctitle.lo
  CC       src/unix/libuv_la-sysinfo-loadavg.lo
  CC       src/unix/libuv_la-sysinfo-memory.lo
  CCLD     libuv.la

ar: `u' modifier ignored since `D' is the default (see `U')

make[1]: Leaving directory '/tmp/RtmpgupyEb/R.INSTALL57b46aa0b777/fs/src/libuv'
-shared -L/usr/lib64/microsoft-r/3.3/lib64/R/lib -o fs.so id.o fs.o file.o link.o path.o utils.o dir.o error.o unix/getmode.o RcppExports.o bsd/setmode.o bsd/strmode.o bsd/reallocarray.o ./libuv/.libs/libuv.a -L/usr/lib64/microsoft-r/3.3/lib64/R/lib -lR

sh: line 2: -shared: command not found
/usr/lib64/microsoft-r/3.3/lib64/R/share/make/shlib.mk:6: recipe for target 'fs.so' failed
make: *** [fs.so] Error 127

ERROR: compilation failed for package ‘fs’

* removing ‘/home/hw831/R/x86_64-pc-linux-gnu-library/3.3/fs’

Warning in install.packages :
  installation of package ‘fs’ had non-zero exit status

The downloaded source packages are in
	‘/tmp/Rtmp1040QJ/downloaded_packages’
@jimhester

This comment has been minimized.

Copy link
Member

jimhester commented Mar 20, 2018

Your system seems to be lacking a C++11 compiler, what is the output of R CMD config --all?

@gaborcsardi

This comment has been minimized.

Copy link
Member

gaborcsardi commented Mar 20, 2018

Can you try to compile other packages with C/C++ code from source? E.g. try the testthat package.

@rsangole

This comment has been minimized.

Copy link
Author

rsangole commented Mar 20, 2018

@jimhester where do I run that command? in a shell?

@gaborcsardi Just tried testthat and it installed perfectly fine.

@rsangole

This comment has been minimized.

Copy link
Author

rsangole commented Mar 20, 2018

image

@jimhester

This comment has been minimized.

Copy link
Member

jimhester commented Mar 21, 2018

You will need to set these variables manually in either a user or site Makevars

Likely you need something like

CXX1X=g++
CXX1XSTD=-std=c++0x

@jimhester jimhester closed this in 67cb636 Mar 21, 2018

@jimhester

This comment has been minimized.

Copy link
Member

jimhester commented Mar 21, 2018

I have made changes to allow fs to be compiled on systems with C++11 support, so this should now compile without any changes needed on your system.

@rsangole

This comment has been minimized.

Copy link
Author

rsangole commented Mar 21, 2018

Thanks @jimhester . Intemediate success for sure, but not full success.

I've added:

CXX1X=g++
CXX1XSTD=-std=c++0x

to /home/hw831/.R/ Makevars-x86_64-pc-linux-gnu.

As a result, the myriad of errors after **libs* have disappeared. Refer line 9-line 24: link.

But, I still get a failure, refer line 63 onwards: link

@rsangole

This comment has been minimized.

Copy link
Author

rsangole commented Mar 21, 2018

@jimhester My previous post was made in before you wrote

I have made changes to allow fs to be compiled on systems with C++11 support, so this should now compile without any changes needed on your system.

Will try things out again.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment