Hi Keith, So the plot thickens. How is it that you have R 3.1.1 but apt-get install rJava gives you an old version of the package? This may be potentially difficult to figure out, but you can try some easy things first. If I were you I would start with
sudo apt-get remove r-base r-devel sudo apt-get update sudo apt-get dist-upgrade sudo apt-get install r-base r-devel r-cran-rjava sudo R CM D javareconf Then restart the computer. Or something like that. Finally, note that there is a specific mailing list for those running R on debian (of which mint is a (n indirect) derivative): see https://stat.ethz.ch/mailman/listinfo/r-sig-debian. You may have better luck asking your question there. Best, Ista On Thu, Jul 31, 2014 at 8:46 AM, Keith S Weintraub <kw1...@gmail.com> wrote: > Ista Et Al, > Unfortunately your suggestion to use remove.packages did exactly the reverse > of what you thought would happen. > > I have cleaned up my installation but still have trouble getting rJava to > install properly and of course that means that XLConnect cannot install > either. > > ------------------------------------- > I think this shows that the java-7-openjdk is working. > ------------------------------------- > /home/refserv $ sudo R CMD javareconf > Java interpreter : /usr/bin/java > Java version : 1.7.0_55 > Java home path : /usr/lib/jvm/java-7-openjdk-i386/jre > Java compiler : /usr/bin/javac > Java headers gen.: /usr/bin/javah > Java archive tool: /usr/bin/jar > > trying to compile and link a JNI progam > detected JNI cpp flags : -I$(JAVA_HOME)/../include > detected JNI linker flags : -L$(JAVA_HOME)/lib/i386/client -ljvm > gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG > -I/usr/lib/jvm/java-7-openjdk-i386/jre/../include -fpic -g -O2 > -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security > -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c conftest.c -o conftest.o > gcc -std=gnu99 -shared -Wl,-Bsymbolic-functions -Wl,-z,relro -o conftest.so > conftest.o -L/usr/lib/jvm/java-7-openjdk-i386/jre/lib/i386/client -ljvm > -L/usr/lib/R/lib -lR > > > JAVA_HOME : /usr/lib/jvm/java-7-openjdk-i386/jre > Java library path: $(JAVA_HOME)/lib/i386/client > JNI cpp flags : -I$(JAVA_HOME)/../include > JNI linker flags : -L$(JAVA_HOME)/lib/i386/client -ljvm > Updating Java configuration in /usr/lib/R > Done. > ___________________________________ > > > ------------------------------------- > Purge and re-install rjava > ------------------------------------- > /home/refserv $ sudo apt-get --purge remove r-cran-rjava > Reading package lists... Done > Building dependency tree > Reading state information... Done > The following packages will be REMOVED: > r-cran-rjava* > 0 upgraded, 0 newly installed, 1 to remove and 3 not upgraded. > After this operation, 1,651 kB disk space will be freed. > Do you want to continue [Y/n]? y > (Reading database ... 173764 files and directories currently installed.) > Removing r-cran-rjava ... > > /home/refserv $ sudo apt-get install r-cran-rjava > Reading package lists... Done > Building dependency tree > Reading state information... Done > The following NEW packages will be installed: > r-cran-rjava > 0 upgraded, 1 newly installed, 0 to remove and 3 not upgraded. > Need to get 0 B/557 kB of archives. > After this operation, 1,651 kB of additional disk space will be used. > Selecting previously unselected package r-cran-rjava. > (Reading database ... 173625 files and directories currently installed.) > Unpacking r-cran-rjava (from .../r-cran-rjava_0.9-3-1_i386.deb) ... > Setting up r-cran-rjava (0.9-3-1) ... > ------------------------------------- > ------------------------------------- > > > > ------------------------------------- > Here I try to install rJava in R > but it looks like there is a version problem. > > Given I am using openjdk above I am not sure why R is looking at the oracle > Java > ------------------------------------- > > home/refserv $ R > > R version 3.1.1 (2014-07-10) -- "Sock it to Me" > Copyright (C) 2014 The R Foundation for Statistical Computing > Platform: i686-pc-linux-gnu (32-bit) > > ........................................ (just cutting down on the output) > >> require(rJava) > Loading required package: rJava > Failed with error: ‘package ‘rJava’ was built before R 3.0.0: please > re-install it’ >> install.packages("rJava") > Installing package into ‘/home/refserv/R/i686-pc-linux-gnu-library/3.1’ > (as ‘lib’ is unspecified) > --- Please select a CRAN mirror for use in this session --- > trying URL 'http://cran.mirrors.hoobly.com/src/contrib/rJava_0.9-6.tar.gz' > Content type 'application/x-gzip' length 567515 bytes (554 Kb) > opened URL > ================================================== > downloaded 554 Kb > > > ........................................ (just cutting down on the output) > > > checking Java support in R... present: > interpreter : '/usr/lib/jvm/java-7-oracle/jre/bin/java' > archiver : '/usr/lib/jvm/java-7-oracle/bin/jar' > compiler : '/usr/lib/jvm/java-7-oracle/bin/javac' > header prep.: '/usr/lib/jvm/java-7-oracle/bin/javah' > cpp flags : '-I/usr/lib/jvm/java-7-oracle/include > -I/usr/lib/jvm/java-7-oracle/include/linux' > java libs : '-L/usr/lib/jvm/java-7-oracle/jre/lib/i386/client -ljvm' > checking whether Java run-time works... ./configure: line 3729: > /usr/lib/jvm/java-7-oracle/jre/bin/java: No such file or directory > no > configure: error: Java interpreter '/usr/lib/jvm/java-7-oracle/jre/bin/java' > does not work > ERROR: configuration failed for package ‘rJava’ > * removing ‘/home/refserv/R/i686-pc-linux-gnu-library/3.1/rJava’ > > The downloaded source packages are in > ‘/tmp/RtmpwvY4Md/downloaded_packages’ > Warning message: > In install.packages("rJava") : > installation of package ‘rJava’ had non-zero exit status > > ------------------------------------- > ------------------------------------- > > Thanks again for your time, > Best, > KW > > > -- > > On Jul 29, 2014, at 2:22 PM, Ista Zahn <istaz...@gmail.com> wrote: > >> On Tue, Jul 29, 2014 at 12:54 PM, Jeff Newmiller >> <jdnew...@dcn.davis.ca.us> wrote: >>> Sounds to me like a problem outside of R (off topic here). >> >> Possibly, but I suspect that the OP now has two versions of XLConnect >> installed, one in the user R library and one in the system-wide R >> library. >> >> Keith, try >> >> remove.packages("XLConnect") >> remove.packages("rJava") >> >> WITHOUT sudo. Then restart R; you should now get the (working) >> system-wide versions of rJava and XLConnect. >> >> HTH, >> Ista >> >> In particular, it doesn't sound like you are using the appropriate >> tools (apt-get package manager for R and a JDK; R install.package() >> for your R packages) to admin your machine. The only thing you should >> need sudo for is to run apt-get... everything else should be done as a >> normal user unless you really know what you are doing. I had no >> problem installing it just now on my Ubuntu machine with OpenJDK. I >> have no experience with Mint but Google tells me you should be able to >> use the instructions for Ubuntu... I would expect Google to tell you >> the same thing if you ask nicely... your most challenging task at this >> point should be cleaning up the mess you have made by excessive use of >> sudo ... most likely running R with it (only update your personal R >> library directories so you are not tempted to go rogue) but you don't >> say how you installed the jdk so that could also be messed up. >>> --------------------------------------------------------------------------- >>> Jeff Newmiller The ..... ..... Go Live... >>> DCN:<jdnew...@dcn.davis.ca.us> Basics: ##.#. ##.#. Live Go... >>> Live: OO#.. Dead: OO#.. Playing >>> Research Engineer (Solar/Batteries O.O#. #.O#. with >>> /Software/Embedded Controllers) .OO#. .OO#. rocks...1k >>> --------------------------------------------------------------------------- >>> Sent from my phone. Please excuse my brevity. >>> >>> On July 29, 2014 8:19:33 AM PDT, Keith S Weintraub <kw1...@gmail.com> wrote: >>>> John Et Al. >>>> >>>> I can get rJava and XLConnect to work only if I run as super user. >>>> >>>> Note that I have built rJava and XLConnect as super user (otherwise >>>> neither package works). >>>> >>>> >>>> ____________________________________________ >>>> Without sudo >>>> >>>>> require(XLConnect) >>>> Loading required package: XLConnect >>>> Error : .onLoad failed in loadNamespace() for 'rJava', details: >>>> call: dyn.load(file, DLLpath = DLLpath, ...) >>>> error: unable to load shared object >>>> '/home/refserv/R/i686-pc-linux-gnu-library/3.1/rJava/libs/rJava.so': >>>> libjvm.so: cannot open shared object file: No such file or directory >>>> _____________________________________________ >>>> With sudo >>>> >>>>> require(XLConnect) >>>> Loading required package: XLConnect >>>> XLConnect 0.2-7 by Mirai Solutions GmbH >>>> http://www.mirai-solutions.com , >>>> http://miraisolutions.wordpress.com >>>> >>>> ______________________________________________ >>>> Note that I have changed the ownership (recursively) for rJava and >>>> XLConnect because they were previously owned by root. Also note that >>>> ggplot2 (included for comparison) was installed the usual way with no >>>> problem. >>>> >>>> drwxr-xr-x 11 refserv refserv 4096 Jul 24 14:07 ggplot2/ >>>> drwxr-xr-x 10 refserv refserv 4096 Jul 29 08:28 rJava/ >>>> drwxr-xr-x 11 refserv refserv 4096 Jul 29 10:09 XLConnect/ >>>> >>>> ________________________________________________ >>>> >>>> Despite "no such file or directory" above: >>>> >>>> /home/refserv/R/i686-pc-linux-gnu-library/3.1/rJava $ ls -altr >>>> /home/refserv/> >>>> -rwxr-xr-x 1 refserv refserv 273489 Jul 29 08:28 >>>> /home/refserv/R/i686-pc-linux-gnu-library/3.1/rJava/libs/rJava.so >>>> >>>> The file rJava.so exists. >>>> >>>> Thanks so much for your time and help, >>>> Best, >>>> KW >>>> >>>> -- >>>> >>>> On Jul 24, 2014, at 11:16 PM, John McKown >>>> <john.archie.mck...@gmail.com> wrote: >>>> >>>>> On Thu, Jul 24, 2014 at 8:36 PM, Keith S Weintraub <kw1...@gmail.com> >>>> wrote: >>>>>> Folks, >>>>>> >>>>>> I have been trying to get XLConnect to work on my Linux Mint Maya >>>> machine. >>>>>> >>>>>> R works fine but this package doesn't seem to want to build. Here is >>>> the message I get after supposedly building XLConnect and rJava: >>>>>> >>>>>> >>>>>>>> require(XLConnect) >>>>>>> Loading required package: XLConnect >>>>>>> Error : .onLoad failed in loadNamespace() for 'rJava', details: >>>>>>> call: dyn.load(file, DLLpath = DLLpath, ...) >>>>>>> error: unable to load shared object >>>> '/home/refserv/R/i686-pc-linux-gnu-library/3.1/rJava/libs/rJava.so': >>>>>>> libjvm.so: cannot open shared object file: No such file or >>>> directory >>>>>> >>>>>> >>>>>> I purged the openJDK and downloaded the 1.7.0_65 JDK form Oracle. >>>>>> >>>>>> The build and the compile seemed to work ok as there were no errors. >>>> For example I can generate ggplot2 graphs. >>>>>> >>>>>> I know this is probably the wrong forum but if someone could gently >>>> point me in the right direction I would be very appreciative. >>>>>> >>>>>> Thanks so much for your time, >>>>>> KW >>>>> >>>>> It works fine for me on Fedora 20 (and 19 before it). When I >>>> installed >>>>> R, it installed into /usr/lib64/R. There exists a file: >>>>> /usr/lib64/R/etc/ldpaths which is executed by the R executable >>>> script. >>>>> This sets up the LD_LIBRARY_PATH to point to the Java installation on >>>>> my machine. In the /usr/lib64/R/bin directory, there is a program >>>>> called "javareconf". I would suggest that you run this with the -n >>>>> switch, like: >>>>> >>>>> R CMD /usr/lib64/R/bin/javareconf -n >>>>> >>>>> This will show you what it _would_ do if you left off the "-n". Make >>>>> sure it looks reasonable. If it does, then run the same command, >>>>> without the "-n", as the "root" superuser. In my case, that would be: >>>>> >>>>> sudo R CMD /usr/lib64/R/bin/javareconf >>>>> >>>>> You need to be "root" because it update the file >>>>> /usr/lib64/R/etc/ldpaths . I am fairly sure this will fix your >>>>> problem. >>>>> >>>>> === >>>>> >>>>> As a possible alternative to XLConnect, have you looked at openxlsx? >>>>> It appears to have the same abilities, just some different syntax. It >>>>> says that it is written in C and so should be faster than XLConnect. >>>> I >>>>> have tested both packages, a little, and they both seem to work well. >>>>> >>>>> Well, it's 22:14 hours here and I wish that I could fall asleep. >>>> We're >>>>> having problems at work and I know that the "big boss" will blame us >>>>> peons if the hardware isn't fixed promptly Despite the fact that we >>>>> are only software people and aren't allowed to touch the hardware. >>>> Our >>>>> management's minds are not using the same logic as mine does. >>>>> Frustrating. >>>>> >>>>> -- >>>>> There is nothing more pleasant than traveling and meeting new people! >>>>> Genghis Khan >>>>> >>>>> Maranatha! <>< >>>>> John McKown >>>> >>>> ______________________________________________ >>>> R-help@r-project.org mailing list >>>> 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 >>> 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 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.
