Thanks Ista, I will try your procedure next Tuesday. This is going pretty slow because I only work at that machine Tuesday-Thursday.
I will let you know how it goes (lucky you!) by private email as I don't think there is any use in bothering all of r-help. After trying your suggestions next week I will switch over to the r-sig-debian group and start bothering them. Thanks again for everyone that chimed in to help me, Best, KW -- On Jul 31, 2014, at 2:54 PM, Ista Zahn <istaz...@gmail.com> wrote: > 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.
