I am running into an error while trying to install rjags. I can run JAGS by typing the command jags on the command line. However I dont know where it was installed or how to locate it or what to do next.
(as ‘lib’ is unspecified)
trying URL 'https://cran.rstudio.com/src/contrib/rjags_4-12.tar.gz'
Content type 'application/x-gzip' length 74067 bytes (72 KB)
==================================================
downloaded 72 KB
* installing *source* package ‘rjags’ ...
** package ‘rjags’ successfully unpacked and MD5 sums checked
** using staged installation
checking for pkg-config... /usr/bin/pkg-config
configure: WARNING: pkg-config file for jags 4 unavailable
configure: WARNING: Consider adding the directory containing `jags.pc`
configure: WARNING: to the PKG_CONFIG_PATH environment variable
configure: Attempting legacy configuration of rjags
checking for jags... /usr/bin/jags
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++ -std=gnu++11 accepts -g... yes
checking how to run the C++ preprocessor... g++ -std=gnu++11 -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 Console.h usability... no
checking Console.h presence... no
checking for Console.h... no
configure: error: "cannot find header file /usr/include/JAGS/Console.h. Please use pkg-config to locate the JAGS library. See the INSTALL file for details."
ERROR: configuration failed for package ‘rjags’
Related
I am attempting to learn how to find co-occurrences in R using the openNLP package. However, when I run > install.packages(openNLP) I get the following output:
Installing package into ‘/home/aos11409/R/x86_64-pc-linux-gnu-library/3.5’
(as ‘lib’ is unspecified)
also installing the dependencies ‘openNLPdata’, ‘rJava’
trying URL 'https://cloud.r-project.org/src/contrib/openNLPdata_1.5.3-4.tar.gz'
Content type 'application/x-gzip' length 7318770 bytes (7.0 MB)
==================================================
downloaded 7.0 MB
trying URL 'https://cloud.r-project.org/src/contrib/rJava_0.9-11.tar.gz'
Content type 'application/x-gzip' length 675188 bytes (659 KB)
==================================================
downloaded 659 KB
trying URL 'https://cloud.r-project.org/src/contrib/openNLP_0.2-6.tar.gz'
Content type 'application/x-gzip' length 6656 bytes
==================================================
downloaded 6656 bytes
* 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/lib/jvm/default-java/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 configuInstalling package into ‘/home/aos11409/R/x86_64-pc-linux-gnu-library/3.5’
(as ‘lib’ is unspecified)
also installing the dependencies ‘openNLPdata’, ‘rJava’
trying URL 'https://cloud.r-project.org/src/contrib/openNLPdata_1.5.3-4.tar.gz'
Content type 'application/x-gzip' length 7318770 bytes (7.0 MB)
==================================================
downloaded 7.0 MB
trying URL 'https://cloud.r-project.org/src/contrib/rJava_0.9-11.tar.gz'
Content type 'application/x-gzip' length 675188 bytes (659 KB)
==================================================
downloaded 659 KB
trying URL 'https://cloud.r-project.org/src/contrib/openNLP_0.2-6.tar.gz'
Content type 'application/x-gzip' length 6656 bytes
==================================================
downloaded 6656 bytes
* 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/lib/jvm/default-java/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 ‘/home/aos11409/R/x86_64-pc-linux-gnu-library/3.5/rJava’
Warning in install.packages :
installation of package ‘rJava’ had non-zero exit status
ERROR: dependency ‘rJava’ is not available for package ‘openNLPdata’
* removing ‘/home/aos11409/R/x86_64-pc-linux-gnu-library/3.5/openNLPdata’
Warning in install.packages :
installation of package ‘openNLPdata’ had non-zero exit status
ERROR: dependencies ‘openNLPdata’, ‘rJava’ are not available for package ‘openNLP’
* removing ‘/home/aos11409/R/x86_64-pc-linux-gnu-library/3.5/openNLP’
Warning in install.packages :
installation of package ‘openNLP’ had non-zero exit status
The downloaded source packages are in
‘/tmp/RtmpyeXutE/downloaded_packages’red 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 ‘/home/aos11409/R/x86_64-pc-linux-gnu-library/3.5/rJava’
Warning in install.packages :
installation of package ‘rJava’ had non-zero exit status
ERROR: dependency ‘rJava’ is not available for package ‘openNLPdata’
* removing ‘/home/aos11409/R/x86_64-pc-linux-gnu-library/3.5/openNLPdata’
Warning in install.packages :
installation of package ‘openNLPdata’ had non-zero exit status
ERROR: dependencies ‘openNLPdata’, ‘rJava’ are not available for package ‘openNLP’
* removing ‘/home/aos11409/R/x86_64-pc-linux-gnu-library/3.5/openNLP’
Warning in install.packages :
installation of package ‘openNLP’ had non-zero exit status
The downloaded source packages are in
‘/tmp/RtmpyeXutE/downloaded_packages’
If it's possible to get openNLP running, how do I do so? If not, are there other packages which can do co-occurrences in text strings?
If it helps any, I'm running this from Ubuntu 18.+ and R 3.5.3.
Okay, so, I figured this out myself but I thought it might help someone else. Long story short, read the output carefully. Output says:
configure: error: Java Development Kit (JDK) is missing or not registered in R
Make sure R is configuInstalling package into ‘/home/aos11409/R/x86_64-pc-linux-gnu-library/3.5’
(as ‘lib’ is unspecified)
also installing the dependencies ‘openNLPdata’, ‘rJava’
To solve my dependency problems, I opened terminal and ran the following lines:
1. $ sudo apt-get install -y default-jre to install Java Runtime Environment
2. $ sudo apt-get install -y default-jdk to install Java Development Kit
3. $ sudo R CMD javareconf to tell R where to find things
4. Then in R, > install.packages("rJava")
5. > install.packages("openNLP")
That should work.
This question already has answers here:
Can't install rJava on ubuntu system
(5 answers)
Closed 5 years ago.
Trying to install xlsx package in Rstudio on Ubuntu 14.04 LTS OS type - 64bit but getting errors while installation. Please guide me as how to solve these errors as I am trying to create a script where I can read an Excel file commute some statistics on the column data
install.packages("xlsx")
Installing package into ‘/home/supratech/R/x86_64-pc-linux-gnu-
library/3.3’
(as ‘lib’ is unspecified)
also installing the dependencies ‘rJava’, ‘xlsxjars’
trying URL 'https://cran.rstudio.com/src/contrib/rJava_0.9-8.tar.gz'
Content type 'unknown' length 656615 bytes (641 KB)
==================================================
downloaded 641 KB
trying URL
'https://cran.rstudio.com/src/contrib/xlsxjars_0.6.1.tar.gz'
Content type 'unknown' length 9477071 bytes (9.0 MB)
==================================================
downloaded 9.0 MB
trying URL 'https://cran.rstudio.com/src/contrib/xlsx_0.5.7.tar.gz'
Content type 'unknown' length 312839 bytes (305 KB)
==================================================
downloaded 305 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/lib/jvm/default-java/jre/bin/java'
archiver : '/usr/bin/jar'
compiler : '/usr/bin/javac'
header prep.: '/usr/bin/javah'
cpp flags : ''
java libs : ''
configure: error: One or more Java configuration variables are not
set.
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 ‘/home/supratech/R/x86_64-pc-linux-gnu-library/3.3/rJava’
Warning in install.packages :
installation of package ‘rJava’ had non-zero exit status
ERROR: dependency ‘rJava’ is not available for package ‘xlsxjars’
* removing ‘/home/supratech/R/x86_64-pc-linux-gnu-
library/3.3/xlsxjars’
Warning in install.packages :
installation of package ‘xlsxjars’ had non-zero exit status
ERROR: dependencies ‘rJava’, ‘xlsxjars’ are not available for package
‘xlsx’
* removing ‘/home/supratech/R/x86_64-pc-linux-gnu-library/3.3/xlsx’
Warning in install.packages :
installation of package ‘xlsx’ had non-zero exit status
The downloaded source packages are in
‘/tmp/RtmpH45TY8/downloaded_packages’
The easiest way to get rJava on Ubuntu is to install it from the repositories instead of trying to install it directly from CRAN
sudo apt-get install r-cran-rjava
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
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!
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/