another attempt<div><br></div><div><div>> > install.packages("rJava")</div><div>Error: unexpected '>' in ">"</div><div>> Installing package(s) into ‘/home/richard/R/i686-redhat-linux-gnu-library/2.15’</div>
<div>Error: unexpected symbol in "Installing package"</div><div>> (as ‘lib’ is unspecified)</div><div>Error: unexpected input in "(as �"</div><div>> trying URL '<a href="http://cran.stat.sfu.ca/src/contrib/rJava_0.9-3.tar.gz">http://cran.stat.sfu.ca/src/contrib/rJava_0.9-3.tar.gz</a>'</div>
<div>Error: unexpected symbol in "trying URL"</div><div>> Content type 'application/x-gzip' length 537153 bytes (524 Kb)</div><div>Error: unexpected symbol in "Content type"</div><div>> opened URL</div>
<div>Error: unexpected symbol in "opened URL"</div><div>> ==================================================</div><div>Error: unexpected '==' in "=="</div><div>> downloaded 524 Kb</div><div>
Error: unexpected numeric constant in "downloaded 524"</div><div>> </div><div>> * installing *source* package ‘rJava’ ...</div><div>Error: unexpected '*' in "*"</div><div>> ** package ‘rJava’ successfully unpacked and MD5 sums checked</div>
<div>Error: unexpected '^' in "**"</div><div>> checking for gcc... gcc -m32 -std=gnu99</div><div>Error: unexpected 'for' in "checking for"</div><div>> checking for C compiler default output file name... a.out</div>
<div>Error: unexpected 'for' in "checking for"</div><div>> checking whether the C compiler works... yes</div><div>Error: unexpected symbol in "checking whether"</div><div>> checking whether we are cross compiling... no</div>
<div>Error: unexpected symbol in "checking whether"</div><div>> checking for suffix of executables... </div><div>Error: unexpected 'for' in "checking for"</div><div>> checking for suffix of object files... o</div>
<div>Error: unexpected 'for' in "checking for"</div><div>> checking whether we are using the GNU C compiler... yes</div><div>Error: unexpected symbol in "checking whether"</div><div>> checking whether gcc -m32 -std=gnu99 accepts -g... yes</div>
<div>Error: unexpected symbol in "checking whether"</div><div>> checking for gcc -m32 -std=gnu99 option to accept ISO C89... none needed</div><div>Error: unexpected 'for' in "checking for"</div>
<div>> checking how to run the C preprocessor... gcc -m32 -std=gnu99 -E</div><div>Error: unexpected symbol in "checking how"</div><div>> checking for grep that handles long lines and -e... /usr/bin/grep</div>
<div>Error: unexpected 'for' in "checking for"</div><div>> checking for egrep... /usr/bin/grep -E</div><div>Error: unexpected 'for' in "checking for"</div><div>> checking for ANSI C header files... yes</div>
<div>Error: unexpected 'for' in "checking for"</div><div>> checking for sys/wait.h that is POSIX.1 compatible... yes</div><div>Error: unexpected 'for' in "checking for"</div><div>> checking for sys/types.h... yes</div>
<div>Error: unexpected 'for' in "checking for"</div><div>> checking for sys/stat.h... yes</div><div>Error: unexpected 'for' in "checking for"</div><div>> checking for stdlib.h... yes</div>
<div>Error: unexpected 'for' in "checking for"</div><div>> checking for string.h... yes</div><div>Error: unexpected 'for' in "checking for"</div><div>> checking for memory.h... yes</div>
<div>Error: unexpected 'for' in "checking for"</div><div>> checking for strings.h... yes</div><div>Error: unexpected 'for' in "checking for"</div><div>> checking for inttypes.h... yes</div>
<div>Error: unexpected 'for' in "checking for"</div><div>> checking for stdint.h... yes</div><div>Error: unexpected 'for' in "checking for"</div><div>> checking for unistd.h... yes</div>
<div>Error: unexpected 'for' in "checking for"</div><div>> checking for string.h... (cached) yes</div><div>Error: unexpected 'for' in "checking for"</div><div>> checking sys/time.h usability... yes</div>
<div>Error: unexpected symbol in "checking sys"</div><div>> checking sys/time.h presence... yes</div><div>Error: unexpected symbol in "checking sys"</div><div>> checking for sys/time.h... yes</div>
<div>Error: unexpected 'for' in "checking for"</div><div>> checking for unistd.h... (cached) yes</div><div>Error: unexpected 'for' in "checking for"</div><div>> checking for an ANSI C-conforming const... yes</div>
<div>Error: unexpected 'for' in "checking for"</div><div>> checking whether time.h and sys/time.h may both be included... yes</div><div>Error: unexpected symbol in "checking whether"</div><div>
> configure: checking whether gcc -m32 -std=gnu99 supports static inline...</div><div>Error: unexpected symbol in "configure: checking whether"</div><div>> yes</div><div>Error: object 'yes' not found</div>
<div>> checking whether setjmp.h is POSIX.1 compatible... yes</div><div>Error: unexpected symbol in "checking whether"</div><div>> checking whether sigsetjmp is declared... yes</div><div>Error: unexpected symbol in "checking whether"</div>
<div>> checking whether siglongjmp is declared... yes</div><div>Error: unexpected symbol in "checking whether"</div><div>> checking Java support in R... present:</div><div>Error: unexpected symbol in "checking Java"</div>
<div>> interpreter : '/bin/java'</div><div>Error: object 'interpreter' not found</div><div>> archiver : '/bin/jar'</div><div>Error: object 'archiver' not found</div><div>> compiler : '/bin/javac'</div>
<div>Error: object 'compiler' not found</div><div>> header prep.: '/bin/javah'</div><div>Error: unexpected symbol in "header prep."</div><div>> cpp flags : '-I/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.6/jre/../include -I/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.6/jre/../include/linux'</div>
<div>Error: unexpected symbol in "cpp flags"</div><div>> java libs : '-L/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.6/jre/lib/i386 -L/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.6/jre/lib/i386/client -ljvm'</div>
<div>Error: unexpected symbol in "java libs"</div><div>> checking whether JNI programs can be compiled... </div><div>Error: unexpected symbol in "checking whether"</div><div>> configure: error: Cannot compile a simple JNI program. See config.log for details.</div>
<div>Error: unexpected symbol in "configure: error: Cannot compile"</div><div>> </div><div>> Make sure you have Java Development Kit installed and correctly registered in R.</div><div>Error: unexpected symbol in "Make sure"</div>
<div>> If in doubt, re-run "R CMD javareconf" as root.</div><div>Error: unexpected 'in' in "If in"</div><div>> </div><div>> ERROR: configuration failed for package ‘rJava’</div><div>Error: unexpected symbol in "ERROR: configuration failed"</div>
<div>> * removing ‘/home/richard/R/i686-redhat-linux-gnu-library/2.15/rJava’</div><div>Error: unexpected '*' in "*"</div><div>> * restoring previous ‘/home/richard/R/i686-redhat-linux-gnu-library/2.15/rJava’</div>
<div>Error: unexpected '*' in "*"</div><div>> Warning in install.packages :</div><div>Error: unexpected 'in' in "Warning in"</div><div>> installation of package ‘rJava’ had non-zero exit status</div>
<div>Error: unexpected symbol in " installation of"</div><div>> </div><div>> The downloaded source packages are in</div><div>Error: unexpected symbol in "The downloaded"</div><div>> ‘/tmp/Rtmpz86WUb/downloaded_packages’</div>
<div>Error: unexpected input in "�"</div><div>> > library(JGR)</div><div>Error: unexpected '>' in ">"</div><div>> Loading required package: rJava</div><div>Error: unexpected symbol in "Loading required"</div>
<div>> Error : .onLoad failed in loadNamespace() for 'rJava', details:</div><div>Error: unexpected symbol in "Error : .onLoad failed"</div><div>> call: dyn.load(file, DLLpath = DLLpath, ...)</div>
<div>Error: '...' used in an incorrect context</div><div>> error: unable to load shared object '/home/richard/R/i686-redhat-linux-gnu-library/2.15/rJava/libs/rJava.so':</div><div>Error: unexpected symbol in " error: unable to"</div>
<div>> libjvm.so: cannot open shared object file: No such file or directory</div><div>Error: unexpected symbol in " libjvm.so: cannot open"</div><div>> Error: package ‘rJava’ could not be loaded</div><div>
Error: unexpected input in "Error: package �"</div><div>> install.package(rJava)</div><div>Error: could not find function "install.package"</div><div>> install.packages("rJava")</div><div>
Installing package(s) into ‘/home/richard/R/i686-redhat-linux-gnu-library/2.15’</div><div>(as ‘lib’ is unspecified)</div><div>--- Please select a CRAN mirror for use in this session ---</div><div>Loading Tcl/Tk interface ... done</div>
<div>trying URL '<a href="http://cran.stat.sfu.ca/src/contrib/rJava_0.9-3.tar.gz">http://cran.stat.sfu.ca/src/contrib/rJava_0.9-3.tar.gz</a>'</div><div>Content type 'application/x-gzip' length 537153 bytes (524 Kb)</div>
<div>opened URL</div><div>==================================================</div><div>downloaded 524 Kb</div><div><br></div><div>* installing *source* package ‘rJava’ ...</div><div>** package ‘rJava’ successfully unpacked and MD5 sums checked</div>
<div>checking for gcc... gcc -m32 -std=gnu99</div><div>checking for C compiler default output file name... a.out</div><div>checking whether the C compiler works... yes</div><div>checking whether we are cross compiling... no</div>
<div>checking for suffix of executables... </div><div>checking for suffix of object files... o</div><div>checking whether we are using the GNU C compiler... yes</div><div>checking whether gcc -m32 -std=gnu99 accepts -g... yes</div>
<div>checking for gcc -m32 -std=gnu99 option to accept ISO C89... none needed</div><div>checking how to run the C preprocessor... gcc -m32 -std=gnu99 -E</div><div>checking for grep that handles long lines and -e... /usr/bin/grep</div>
<div>checking for egrep... /usr/bin/grep -E</div><div>checking for ANSI C header files... yes</div><div>checking for sys/wait.h that is POSIX.1 compatible... yes</div><div>checking for sys/types.h... yes</div><div>checking for sys/stat.h... yes</div>
<div>checking for stdlib.h... yes</div><div>checking for string.h... yes</div><div>checking for memory.h... yes</div><div>checking for strings.h... yes</div><div>checking for inttypes.h... yes</div><div>checking for stdint.h... yes</div>
<div>checking for unistd.h... yes</div><div>checking for string.h... (cached) yes</div><div>checking sys/time.h usability... yes</div><div>checking sys/time.h presence... yes</div><div>checking for sys/time.h... yes</div>
<div>checking for unistd.h... (cached) yes</div><div>checking for an ANSI C-conforming const... yes</div><div>checking whether time.h and sys/time.h may both be included... yes</div><div>configure: checking whether gcc -m32 -std=gnu99 supports static inline...</div>
<div>yes</div><div>checking whether setjmp.h is POSIX.1 compatible... yes</div><div>checking whether sigsetjmp is declared... yes</div><div>checking whether siglongjmp is declared... yes</div><div>checking Java support in R... present:</div>
<div>interpreter : '/bin/java'</div><div>archiver : '/bin/jar'</div><div>compiler : '/bin/javac'</div><div>header prep.: '/bin/javah'</div><div>cpp flags : '-I/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.6/jre/../include -I/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.6/jre/../include/linux'</div>
<div>java libs : '-L/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.6/jre/lib/i386 -L/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.6/jre/lib/i386/client -ljvm'</div><div>checking whether JNI programs can be compiled... configure: error: Cannot compile a simple JNI program. See config.log for details.</div>
<div><br></div><div>Make sure you have Java Development Kit installed and correctly registered in R.</div><div>If in doubt, re-run "R CMD javareconf" as root.</div><div><br></div><div>ERROR: configuration failed for package ‘rJava’</div>
<div>* removing ‘/home/richard/R/i686-redhat-linux-gnu-library/2.15/rJava’</div><div>* restoring previous ‘/home/richard/R/i686-redhat-linux-gnu-library/2.15/rJava’</div><div><br></div><div>The downloaded source packages are in</div>
<div><span class="Apple-tab-span" style="white-space:pre"> </span>‘/tmp/Rtmp6R1lbj/downloaded_packages’</div><div>Warning message:</div><div>In install.packages("rJava") :</div><div> installation of package ‘rJava’ had non-zero exit status</div>
<br><div class="gmail_quote">On Mon, Oct 22, 2012 at 6:39 PM, Richard Vickery <span dir="ltr"><<a href="mailto:richard.vickeryrv@gmail.com" target="_blank">richard.vickeryrv@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
sorry I mistakenly deleted the R discussion from my inbox. Here is what I get back:<div><br></div><div><span style="border-collapse:separate;font-family:'DejaVu Sans Mono';font-size:13px;line-height:16px;white-space:pre-wrap;border-spacing:0px;background-color:rgb(225,226,229)"><pre style="font-family:'DejaVu Sans Mono';font-size:10pt!important;outline:none;border-style:none;white-space:pre-wrap!important;margin-top:0px;margin-bottom:0px;line-height:1.25">
<span style="white-space:pre-wrap;color:blue">> </span><span style="color:blue">install.packages("rJava")
</span><span>Installing package(s) into ‘/home/richard/R/i686-redhat-linux-gnu-library/2.15’
(as ‘lib’ is unspecified)
</span><span>trying URL '<a href="http://cran.stat.sfu.ca/src/contrib/rJava_0.9-3.tar.gz" target="_blank">http://cran.stat.sfu.ca/src/contrib/rJava_0.9-3.tar.gz</a>'
</span><span>Content type 'application/x-gzip'</span><span> length 537153 bytes (524 Kb)
</span><span>opened URL
</span><span>=</span><span>=</span><span>=</span><span>=</span><span>=</span><span>=</span><span>=</span><span>=</span><span>=</span><span>=</span><span>=</span><span>=</span><span>=</span><span>=</span><span>=</span><span>=</span><span>=</span><span>=</span><span>=</span><span>=</span><span>=</span><span>=</span><span>=</span><span>=</span><span>=</span><span>=</span><span>=</span><span>=</span><span>=</span><span>=</span><span>=</span><span>=</span><span>=</span><span>=</span><span>=</span><span>=</span><span>=</span><span>=</span><span>=</span><span>=</span><span>=</span><span>=</span><span>=</span><span>=</span><span>=</span><span>=</span><span>=</span><span>=</span><span>=</span><span>=</span><span>
</span><span>downloaded 524 Kb
</span><span>* installing *source* package ‘rJava’ ...
</span><span>** package ‘rJava’ successfully unpacked and MD5 sums checked
</span>checking for gcc... gcc -m32 -std=gnu99
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc -m32 -std=gnu99 accepts -g... yes
checking for gcc -m32 -std=gnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -m32 -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 -m32 -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 : '/bin/java'
archiver : '/bin/jar'
compiler : '/bin/javac'
header prep.: '/bin/javah'
cpp flags : '-I/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.6/jre/../include -I/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.6/jre/../include/linux'
java libs : '-L/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.6/jre/lib/i386 -L/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.6/jre/lib/i386/client -ljvm'
checking whether JNI programs can be compiled...
<span>configure: error: Cannot compile a simple JNI program. See config.log for details.
Make sure you have Java Development Kit installed and correctly registered in R.
If in doubt, re-run "R CMD javareconf" as root.
</span><span>ERROR: configuration failed for package ‘rJava’
</span><span>* removing ‘/home/richard/R/i686-redhat-linux-gnu-library/2.15/rJava’
</span><span>* restoring previous ‘/home/richard/R/i686-redhat-linux-gnu-library/2.15/rJava’
</span>Warning in install.packages :
installation of package ‘rJava’ had non-zero exit status
The downloaded source packages are in
‘/tmp/Rtmpz86WUb/downloaded_packages’
<span style="white-space:pre-wrap;color:blue">> </span><span style="color:blue">library(JGR)
</span><span>Loading required package: rJava
</span><span>Error : .onLoad failed in loadNamespace() for 'rJava', details:
call: dyn.load(file, DLLpath = DLLpath, ...)
error: unable to load shared object '/home/richard/R/i686-redhat-linux-gnu-library/2.15/rJava/libs/rJava.so':
libjvm.so: cannot open shared object file: No such file or directory
</span><span>Error: package ‘rJava’ could not be loaded</span></pre></span></div>
</blockquote></div><br></div>