I am trying to install "rJava" in a linux machine.
Current R-version is : R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
java is already installed and JAVA_HOME variable is set to : /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.101-3.b13.el7_2.x86_64/
should i need to install jdk or something?
It is giving me the following error. Please help me out.
* installing *source* package ‘rJava’ ...
** package ‘rJava’ successfully unpacked and MD5 sums checked
checking for gcc... gcc -std=gnu99
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -std=gnu99 -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/wait.h that is POSIX.1 compatible... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for string.h... (cached) yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking for unistd.h... (cached) yes
checking for an ANSI C-conforming const... yes
checking whether time.h and sys/time.h may both be included... yes
configure: checking whether gcc -std=gnu99 supports static inline...
yes
checking whether setjmp.h is POSIX.1 compatible... yes
checking whether sigsetjmp is declared... yes
checking whether siglongjmp is declared... yes
checking Java support in R... present:
interpreter : '/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.101-3.b13.el7_2.x86_64/jre/bin/java'
archiver : ''
compiler : ''
header prep.: ''
cpp flags : ''
java libs : ''
configure: error: Java Development Kit (JDK) is missing or not registered in R
Make sure R is configured with full Java support (including JDK). Run
R CMD javareconf
as root to add Java support to R.
If you don't have root privileges, run
R CMD javareconf -e
to set all Java-related variables and then install rJava.
ERROR: configuration failed for package ‘rJava’
* removing ‘/root/miniconda2/lib/R/library/rJava’
The downloaded source packages are in
‘/tmp/RtmpeFQ9dA/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning messages:
1: In download.file(url, destfile = f, quiet = TRUE) :
URL 'https://cran.r-project.org/CRAN_mirrors.csv': status was 'SSL connect error'
2: In install.packages("rJava") :
installation of package ‘rJava’ had non-zero exit status
Related
I have some trouble installing Rcplex on linux.
I tried:
R CMD INSTALL --configure-args="
--with-cplex-dir='/opt/ibm/ILOG/CPLEX_Studio129/cplex'" Rcplex_0.3-3.tar.gz
then I get this error:
* installing *source* package ‘Rcplex’ ...
** package ‘Rcplex’ successfully unpacked and MD5 sums checked
checking for gawk... gawk
checking for gcc... gcc -std=gnu99
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ANSI C... none needed
checking how to run the C preprocessor... gcc -std=gnu99 -E
checking for egrep... grep -E
checking for ANSI C header files... no
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking ilcplex/cplex.h usability... yes
checking ilcplex/cplex.h presence... yes
checking for ilcplex/cplex.h... yes
checking for library containing CPXversion... no
configure: error: Could not link CPLEX library using -L/opt/ibm/ILOG/CPLEX_Studio129/cplex/lib/x86-64_linux/static_pic -l$(CPLEXLIB) -lm -lpthread -ldl
ERROR: configuration failed for package ‘Rcplex’
I also tried this:
R CMD INSTALL --configure-args="--with-cplex-include=/opt/ibm/ILOG/CPLEX_Studio129/cplex/include \
--with-cplex-cflags=-fPIC \
--with-cplex-lib=/opt/ibm/ILOG/CPLEX_Studio129/cplex/lib/x86-64_linux/static_pic' \
-lcplex -lm -lpthread'" Rcplex_0.3-3.tar.gz
and get this error:
* installing *source* package ‘Rcplex’ ...
** package ‘Rcplex’ successfully unpacked and MD5 sums checked
checking for gcc... gcc -std=gnu99
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ANSI C... none needed
checking how to run the C preprocessor... gcc -std=gnu99 -E
checking for egrep... grep -E
checking for ANSI C header files... no
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking ilcplex/cplex.h usability... yes
checking ilcplex/cplex.h presence... yes
checking for ilcplex/cplex.h... yes
checking for library containing CPXversion... no
configure: error: Could not link CPLEX library using /opt/ibm/ILOG/CPLEX_Studio129/cplex/lib/x86-64_linux/static_pic -lcplex -lm -lpthread
ERROR: configuration failed for package ‘Rcplex’
I think your best course of action is to look into what exactly the configure script tries to run. Maybe it expects another version of CPLEX?
I experienced the same problem installing the Rcplex 0.3-3 package for R3.6.1 on Ubuntu 18.04 with CPLEX 12.9.
Turns out that the Rcplex package was developed and tested with CPLEX 12.6.3. When I installed this older version of CPLEX on Ubuntu, I was able to install Rcplex 0.3-3 by following the instructions in the INSTALL file.
On my system, this command did the trick:
sudo R CMD INSTALL --configure-args="PKG_CFLAGS=-fPIC PKG_CPPFLAGS=-I/opt/ibm/ILOG/CPLEX_Studio1263/cplex/include PKG_LIBS='-L/opt/ibm/ILOG/CPLEX_Studio1263/cplex/lib/x86-64_linux/static_pic -lcplex -lm -lpthread'" Rcplex_0.3-3.tar.gz
This appears to be an issue with the Linux version of Rcplex only. I was able to install Rcplex with the latest version of CPLEX on my Mac.
I have udunits2 R package installed but units R package still fails even if I use configure.arg containing correct headers and libs:
$ ls /path/apps/udunits/2.2.26/x86_64-linux-2.6-rhel6/include/
converter.h udunits2.h udunits.h
$ ls /path/apps/udunits/2.2.26/x86_64-linux-2.6-rhel6/lib/
libudunits2.a libudunits2.so libudunits2.so.0.1.0
libudunits2.la libudunits2.so.0
Log from package installation:
> library(udunits2)
udunits system database read
configure.args = c(
'--with-udunits2-lib=/path/apps/udunits/2.2.26/x86_64-linux-2.6-rhel6/lib/',
'--with-udunits2-include=/path/apps/udunits/2.2.26/x86_64-linux-2.6-rhel6/include/'
)
> install_packages("units", reps, configure.args = configure.args)
* installing *source* package ‘units’ ...
** package ‘units’ successfully unpacked and MD5 sums checked
configure: units: 0.6-0
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking how to run the C++ preprocessor... g++ -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for stdbool.h that conforms to C99... no
checking for _Bool... no
checking for error_at_line... yes
checking for gcc... gcc
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for XML_ParserCreate in -lexpat... yes
checking udunits2.h usability... no
checking udunits2.h presence... no
checking for udunits2.h... no
checking udunits2/udunits2.h usability... no
checking udunits2/udunits2.h presence... no
checking for udunits2/udunits2.h... no
checking for ut_read_xml in -ludunits2... yes
configure: error: in `/tmp/RtmpPvLQ81/R.INSTALL1c932925e979/units':
configure: error:
--------------------------------------------------------------------------------
udunits2.h not found!
If the udunits2 library is installed in a non-standard location, use:
--configure-args='--with-udunits2-lib=/usr/local/lib'
for example, if the library was not found, and/or
--configure-args='--with-udunits2-include=/usr/include/udunits2'
if the header was not found, replacing paths with appropriate values for your
installation. You can alternatively use the UDUNITS2_INCLUDE and UDUNITS2_LIBS
environment variables.
If udunits2 is not installed, please install it.
It is required for this package.
------------------------------------------
File udunits2.h exists in path:
$ls /path/apps/udunits/2.2.26/x86_64-linux-2.6-rhel6/include/:
converter.h udunits2.h udunits.h
Setting environment variable doesn't help too:
export UDUNITS2_INCLUDE="/path/apps/udunits/2.2.26/x86_64-linux-2.6-rhel6/include"
export UDUNITS2_LIB="/apps/udunits/2.2.26/x86_64-linux-2.6-rhel6/lib"
Any ideas why units fails to install?
I am trying to install a package onto R, namely "BiOps", this package is no longer in the CRAN repository so I have downloaded the tar.gz file to my mac and directed R to it, however once I do, I get the following:
install.packages("~/Documents/R/R Packages/biOps_0.2.2 (3).tar.gz", repos = NULL, type = "source")
* installing *source* package ‘biOps’ ...
** package ‘biOps’ successfully unpacked and MD5 sums checked
checking for gcc... clang
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether clang accepts -g... yes
checking for clang option to accept ISO C89... none needed
checking how to run the C preprocessor... clang -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking fftw3.h usability... no
checking fftw3.h presence... no
checking for fftw3.h... no
configure: WARNING: Can't find fftw3 header
checking jpeglib.h usability... no
checking jpeglib.h presence... no
checking for jpeglib.h... no
configure: WARNING: Can't find libjpeg header
checking tiff.h usability... no
checking tiff.h presence... no
checking for tiff.h... no
configure: WARNING: Can't find libtiff header
checking for jpeg_destroy_compress in -ljpeg... no
checking for TIFFOpen in -ltiff... no
Try static libs needed on OS X
checking for TIFFOpen in -ltiff... no
Error: Could not find libtiff.
ERROR: configuration failed for package ‘biOps’
* removing ‘/Library/Frameworks/R.framework/Versions/3.2/Resources/library/biOps’
Warning in install.packages :
installation of package ‘/Users/justinginger/Documents/R/R
Packages/biOps_0.2.2 (3).tar.gz’ had non-zero exit status
I am at a loose end here. I am studying mathematics with statistics and for my dissertation I want to use this package for image compression. I have been working on this for weeks and am reasonably unfamiliar with code so other similar questions both on here and other websites aren't helping me.I have put in a lot of effort into trying to solve this and really can't get anywhere!
Thank you and Merry Christmas!
Please could you help me, i try to install this packages in R and my OS is linux ubuntu 15.04
devtools
rjava
but i get some error, for example, when i install devtools
Warning in install.packages :
installation of package ‘git2r’ had non-zero exit status
Warning in install.packages :
installation of package ‘devtools’ had non-zero exit status
and when i install rjava
checking for gcc... gcc -std=gnu99
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -std=gnu99 -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/wait.h that is POSIX.1 compatible... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for string.h... (cached) yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking for unistd.h... (cached) yes
checking for an ANSI C-conforming const... yes
checking whether time.h and sys/time.h may both be included... yes
configure: checking whether gcc -std=gnu99 supports static inline...
yes
checking whether setjmp.h is POSIX.1 compatible... yes
checking whether sigsetjmp is declared... yes
checking whether siglongjmp is declared... yes
checking Java support in R... present:
interpreter : '/usr/bin/java'
archiver : '/usr/bin/jar'
compiler : '/usr/bin/javac'
header prep.: '/usr/bin/javah'
cpp flags : '-I/usr/lib/jvm/java-7-openjdk-i386/jre/../include'
java libs : '-L/usr/lib/jvm/java-7-openjdk-i386/jre/lib/i386/client -ljvm'
checking whether Java run-time works...
Picked up JAVA_TOOL_OPTIONS: -javaagent:/usr/share/java/jayatanaag.jar
yes
checking whether -Xrs is supported...
Picked up JAVA_TOOL_OPTIONS: -javaagent:/usr/share/java/jayatanaag.jar
yes
checking whether JNI programs can be compiled...
configure: error: Cannot compile a simple JNI program. See config.log for details.
Make sure you have Java Development Kit installed and correctly registered in R.
If in doubt, re-run "R CMD javareconf" as root.
ERROR: configuration failed for package ‘rJava’
* removing ‘/home/dave/R/i686-pc-linux-gnu-library/3.1/rJava’
Warning in install.packages :
installation of package ‘rJava’ had non-zero exit status
The downloaded source packages are in
‘/tmp/Rtmp86RnJ1/downloaded_packages’
of course before ask this question i found similar questions on this site, but given advices didn't help me
i used this
sudo apt-get build-dep libxml2-dev
sudo apt-get install r-cran-rjava
what i should do to install needed packages. This problem concern and other packages like jgr,deducer,rweka
I am using R on AWS EC2:
AMI ID
RStudio-0.98.501_R-3.0.3_ubuntu-13.10-64bit (ami-f06131a2)
and I cannot install rJava.
As far as I know I do not have access to Ubuntu commandline to run this code:
sudo apt-get install r-cran-rjava
Here is the error. Is there anything I can do inside RStudio?
Installing package into ‘/home/rstudio/R/x86_64-pc-linux-gnu-library/3.0’
(as ‘lib’ is unspecified)
trying URL 'http://cran.rstudio.com/src/contrib/rJava_0.9-6.tar.gz'
Content type 'application/x-gzip' length 567515 bytes (554 Kb)
opened URL
==================================================
downloaded 554 Kb
* installing *source* package ‘rJava’ ...
** package ‘rJava’ successfully unpacked and MD5 sums checked
checking for gcc... gcc -std=gnu99
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -std=gnu99 -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/wait.h that is POSIX.1 compatible... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for string.h... (cached) yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking for unistd.h... (cached) yes
checking for an ANSI C-conforming const... yes
checking whether time.h and sys/time.h may both be included... yes
configure: checking whether gcc -std=gnu99 supports static inline...
yes
checking whether setjmp.h is POSIX.1 compatible... yes
checking whether sigsetjmp is declared... yes
checking whether siglongjmp is declared... yes
checking Java support in R... present:
interpreter : '/usr/bin/java'
archiver : '/usr/bin/jar'
compiler : '/usr/bin/javac'
header prep.: '/usr/bin/javah'
cpp flags : '-I/usr/lib/jvm/java-7-openjdk-amd64/jre/../include'
java libs : '-L/usr/lib/jvm/java-7-openjdk-amd64/jre/lib/amd64/server -ljvm'
checking whether Java run-time works...
./configure: line 3729: /usr/bin/java: No such file or directory
no
configure: error: Java interpreter '/usr/bin/java' does not work
ERROR: configuration failed for package ‘rJava’
* removing ‘/home/rstudio/R/x86_64-pc-linux-gnu-library/3.0/rJava’
Warning in install.packages :
installation of package ‘rJava’ had non-zero exit status
The downloaded source packages are in
‘/tmp/RtmpYSTRK3/downloaded_packages’
Have you tried sudo apt-get install r-cran-rjava ?
Is there a reason you cannot use the distribution's rJava package?
I was having problems installing a package that depended on rJava. Dirk's suggestion worked like a charm on a fresh install of Ubuntu 13.10
I found the answer here. I should use PUTTY terminal to connect to the instance commandline:
http://www.louisaslett.com/RStudio_AMI/