This is happening to me with R 2.9 and 2.8 on jaunty. whit at spartan:~$ R CMD config JAVA_CPPFLAGS ~autodetect~ whit at spartan:~$ I can see the "~autodetect~" strings here: https://svn.r-project.org/R/trunk/m4/java.m4 but JAVA_LIBS ends up being the correct value in my installation: whit at spartan:~/dvl/R.packages$ R CMD config JAVA_LIBS -L/usr/lib/jvm/java-6-openjdk/jre/lib/amd64/server -L/usr/lib/jvm/java-6-openjdk/jre/lib/amd64 -L/usr/lib/jvm/java-6-openjdk/jre/../lib/amd64 -L/usr/local/lib64 -L/usr/java/packages/lib/amd64 -L/usr/lib64 -L/lib64 -L/lib -L/usr/lib -ljvm whit at spartan:~/dvl/R.packages$ R CMD config JAVA_CPPFLAGS ~autodetect~ whit at spartan:~/dvl/R.packages$ -Whit
Whit, I ran the same command on my Jaunty system and got the following: mrutter at yorick ~/D/R_Stuff> R CMD config JAVA_CPPFLAGS -I/usr/lib/jvm/java-6-openjdk/jre/../include A quick check of my java related packages: ca-certificates-java install java-common install libaccess-bridge-java install sun-java6-bin install sun-java6-jre install tzdata-java install Maybe this will help. Micheal On Sun, May 3, 2009 at 7:52 PM, Whit Armstrong <armstrong.whit at gmail.com> wrote:> This is happening to me with R 2.9 and 2.8 on jaunty. > > whit at spartan:~$ R CMD config JAVA_CPPFLAGS > ~autodetect~ > whit at spartan:~$ > > > I can see the "~autodetect~" strings here: > https://svn.r-project.org/R/trunk/m4/java.m4 > > but JAVA_LIBS ends up being the correct value in my installation: > > whit at spartan:~/dvl/R.packages$ R CMD config JAVA_LIBS > -L/usr/lib/jvm/java-6-openjdk/jre/lib/amd64/server > -L/usr/lib/jvm/java-6-openjdk/jre/lib/amd64 > -L/usr/lib/jvm/java-6-openjdk/jre/../lib/amd64 -L/usr/local/lib64 > -L/usr/java/packages/lib/amd64 -L/usr/lib64 -L/lib64 -L/lib -L/usr/lib > -ljvm > whit at spartan:~/dvl/R.packages$ R CMD config JAVA_CPPFLAGS > ~autodetect~ > whit at spartan:~/dvl/R.packages$ > > -Whit > > _______________________________________________ > R-SIG-Debian mailing list > R-SIG-Debian at r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-debian >-- Dr. Michael A. Rutter School of Science Penn State Erie, The Behrend College Station Road Erie, PA 16563 http://math.bd.psu.edu/faculty/rutter
Thanks, Michael. Is that after compiling form source? or a version of R from ubnutu/apt-get? My issues were from R 2.9 and 2.8 compiled from source. However, this has never been a problem before. -Whit On Mon, May 4, 2009 at 5:53 PM, Michael Rutter <mar36 at psu.edu> wrote:> Whit, > > I ran the same command on my Jaunty system and got the following: > > mrutter at yorick ~/D/R_Stuff> R CMD config JAVA_CPPFLAGS > -I/usr/lib/jvm/java-6-openjdk/jre/../include > > A quick check of my java related packages: > > ca-certificates-java ? ? ? ? ? ? ? ? ? ? ? ? ? ?install > java-common ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? install > libaccess-bridge-java ? ? ? ? ? ? ? ? ? ? ? ? ? install > sun-java6-bin ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? install > sun-java6-jre ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? install > tzdata-java ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? install > > Maybe this will help. > > Micheal > > On Sun, May 3, 2009 at 7:52 PM, Whit Armstrong <armstrong.whit at gmail.com> wrote: >> This is happening to me with R 2.9 and 2.8 on jaunty. >> >> whit at spartan:~$ R CMD config JAVA_CPPFLAGS >> ~autodetect~ >> whit at spartan:~$ >> >> >> I can see the "~autodetect~" strings here: >> https://svn.r-project.org/R/trunk/m4/java.m4 >> >> but JAVA_LIBS ends up being the correct value in my installation: >> >> whit at spartan:~/dvl/R.packages$ R CMD config JAVA_LIBS >> -L/usr/lib/jvm/java-6-openjdk/jre/lib/amd64/server >> -L/usr/lib/jvm/java-6-openjdk/jre/lib/amd64 >> -L/usr/lib/jvm/java-6-openjdk/jre/../lib/amd64 -L/usr/local/lib64 >> -L/usr/java/packages/lib/amd64 -L/usr/lib64 -L/lib64 -L/lib -L/usr/lib >> -ljvm >> whit at spartan:~/dvl/R.packages$ R CMD config JAVA_CPPFLAGS >> ~autodetect~ >> whit at spartan:~/dvl/R.packages$ >> >> -Whit >> >> _______________________________________________ >> R-SIG-Debian mailing list >> R-SIG-Debian at r-project.org >> https://stat.ethz.ch/mailman/listinfo/r-sig-debian >> > > > > -- > Dr. Michael A. Rutter > School of Science > Penn State Erie, The Behrend College > Station Road > Erie, PA 16563 > http://math.bd.psu.edu/faculty/rutter >
Whit, Those results came for the apt-get binaries available on CRAN. I would recommend those, as we update them very quickly and there are fewer issues like the one you are having. Michael On Mon, May 4, 2009 at 9:29 PM, Whit Armstrong <armstrong.whit at gmail.com> wrote:> Thanks, Michael. > > Is that after compiling form source? or a version of R from ubnutu/apt-get? > > My issues were from R 2.9 and 2.8 compiled from source. ?However, this > has never been a problem before. > > -Whit > > On Mon, May 4, 2009 at 5:53 PM, Michael Rutter <mar36 at psu.edu> wrote: >> Whit, >> >> I ran the same command on my Jaunty system and got the following: >> >> mrutter at yorick ~/D/R_Stuff> R CMD config JAVA_CPPFLAGS >> -I/usr/lib/jvm/java-6-openjdk/jre/../include >> >> A quick check of my java related packages: >> >> ca-certificates-java ? ? ? ? ? ? ? ? ? ? ? ? ? ?install >> java-common ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? install >> libaccess-bridge-java ? ? ? ? ? ? ? ? ? ? ? ? ? install >> sun-java6-bin ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? install >> sun-java6-jre ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? install >> tzdata-java ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? install >> >> Maybe this will help. >> >> Micheal >> >> On Sun, May 3, 2009 at 7:52 PM, Whit Armstrong <armstrong.whit at gmail.com> wrote: >>> This is happening to me with R 2.9 and 2.8 on jaunty. >>> >>> whit at spartan:~$ R CMD config JAVA_CPPFLAGS >>> ~autodetect~ >>> whit at spartan:~$ >>> >>> >>> I can see the "~autodetect~" strings here: >>> https://svn.r-project.org/R/trunk/m4/java.m4 >>> >>> but JAVA_LIBS ends up being the correct value in my installation: >>> >>> whit at spartan:~/dvl/R.packages$ R CMD config JAVA_LIBS >>> -L/usr/lib/jvm/java-6-openjdk/jre/lib/amd64/server >>> -L/usr/lib/jvm/java-6-openjdk/jre/lib/amd64 >>> -L/usr/lib/jvm/java-6-openjdk/jre/../lib/amd64 -L/usr/local/lib64 >>> -L/usr/java/packages/lib/amd64 -L/usr/lib64 -L/lib64 -L/lib -L/usr/lib >>> -ljvm >>> whit at spartan:~/dvl/R.packages$ R CMD config JAVA_CPPFLAGS >>> ~autodetect~ >>> whit at spartan:~/dvl/R.packages$ >>> >>> -Whit >>> >>> _______________________________________________ >>> R-SIG-Debian mailing list >>> R-SIG-Debian at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/r-sig-debian >>> >> >> >> >> -- >> Dr. Michael A. Rutter >> School of Science >> Penn State Erie, The Behrend College >> Station Road >> Erie, PA 16563 >> http://math.bd.psu.edu/faculty/rutter >> >-- Dr. Michael A. Rutter School of Science Penn State Erie, The Behrend College Station Road Erie, PA 16563 http://math.bd.psu.edu/faculty/rutter