Your post does not have the requested session information that will tell us your computing environment, nor the version of R.
However, I'm experiencing at least a related problem, as this morning I updated R (in Linux Mind Rafaela 17.2, so I get an operating system notice to update via the package manager). Afterwards I ran update.packages() but could not get rJava to carry out the update, though other packages did complete. Possibly there is some mismatch between rJava and R 3.2.3 and/or gcj. I'm a bit surprised this hasn't surfaced before, as I'm a "slow updater" and 3.2.3 is over a month old now. Below is the output from the update -- AFTER I ran "R CMD javareconf" as root -- along with the session information, which shows Ubuntu rather than the derivative Linux Mint. Cheers, JN > update.packages() rJava : Version 0.9-6 installed in /usr/lib/R/site-library Version 0.9-8 available at https://rweb.crmda.ku.edu/cran Update (y/N/c)? y trying URL 'https://rweb.crmda.ku.edu/cran/src/contrib/rJava_0.9-8.tar.gz' Content type 'application/x-gzip' length 656615 bytes (641 KB) ================================================== downloaded 641 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 : '-L/usr/lib/jvm/java-7-openjdk-amd64/jre/lib/amd64/server -ljvm' 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 ‘/usr/lib/R/site-library/rJava’ * restoring previous ‘/usr/lib/R/site-library/rJava’ The downloaded source packages are in ‘/tmp/RtmpXCs91E/downloaded_packages’ Warning message: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, : installation of package ‘rJava’ had non-zero exit status > > sessionInfo() R version 3.2.3 (2015-12-10) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 14.04.3 LTS locale: [1] LC_CTYPE=en_CA.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_CA.UTF-8 LC_COLLATE=en_CA.UTF-8 [5] LC_MONETARY=en_CA.UTF-8 LC_MESSAGES=en_CA.UTF-8 [7] LC_PAPER=en_CA.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] tools_3.2.3 tcltk_3.2.3 > On 16-01-14 05:45 PM, AASHISH JAIN wrote: > Hello, > > I am using an R package called Rknots, which uses rJava (and others like > rSymPy, rjson, rJython) and I am getting some error due to rJava. When I run > my R code, the execution gets halted with the following error: > > Error in .jcheck() : No running JVM detected. Maybe .jinit() would help. > (found this line in rjava.c) > Calls: computeInvariant ... sympy -> $ -> $ -> hasField -> .jcall -> .jcheck > -> .Call (this line comes from Rknots package when the function > computeInvariant is called) > Execution halted > > Note that since I could not install these packages on root level, I installed > them locally on unix OS. Since the other Java and R software appears to be > working, it seems like the error is specific to the rJava package. Possibly > rJava makes some assumptions about the Java installation (perhaps its > location) that cause it to be confused. I would like to know if a non-root > Java installation would cause problems. > > FYI, here are the versions of different packages that I currently have: > 1. rSymPy_0.2-1.1.tar > 2. rJava_0.9-8.tar > 3. rjson_0.2.15.tar.gz > 4. rJython_0.0-4.tar > 5. Rknots_1.2.1.tar > > I would really appreciate any help. > > I want to apologize if this forum is not a right place to discuss about rJava. > > Thanks! > Aashish Jain > Postdoctoral Associate > Department of Chemical Engineering and Material Science > 151 Amundson Hall > 421 Washington Ave SE > Minneapolis, MN 55455 USA > Ph: +1 612-806-7154 > > ______________________________________________ > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
