[R-sig-Fedora] building R, rJava, & Rserve on Centos without admin privileges (or support)

[Mike Landis]

I am trying to build R on a Centos server without admin privileges (or 
support), so I can call R functions from NetLogo models (via the NetLogo 
R extension or possibly Rserve), but I'm getting stuck near the end of 
make.  Any suggestions?

Here's the setup...
$ R_SHELL=/bin/sh
$ R_HOME=~/R-devel
$ cd $R_HOME; ./configure; make
       returns
...
begin installing recommended package MASS
Error in untar2(tarfile, files, list, exdir, restore_times) :
   incomplete block on file
make[2]: *** [MASS.ts] Error 1
make[2]: Leaving directory `/home1/optimal1/R-devel/src/library/Recommended'
make[1]: *** [recommended-packages] Error 2
make[1]: Leaving directory `/home1/optimal1/R-devel/src/library/Recommended'
make: *** [stamp-recommended] Error 2

$ cd ../R-packages; R CMD INSTALL MASS
      succeeds, though

$ make
      still fails on MASS, as above

$ cd $R_HOME; ./configure --enable-R-shlib
      returns
...
gcc -std=gnu99 -shared -fopenmp -L/usr/local/lib64  -o libR.so 
CommandLineArgs.o Rdynload.o Renviron.o RNG.o agrep.o apply.o 
arithmetic.o array.o attrib.o bind.o builtin.o character.o coerce.o 
colors.o complex.o connections.o context.o cum.o dcf.o datetime.o 
debug.o deparse.o devices.o dotcode.o dounzip.o dstruct.o duplicate.o 
edit.o engine.o envir.o errors.o eval.o format.o gevents.o gram.o 
gram-ex.o graphics.o grep.o identical.o inlined.o inspect.o internet.o 
iosupport.o lapack.o list.o localecharset.o logic.o main.o mapply.o 
match.o memory.o names.o objects.o options.o paste.o platform.o plot.o 
plot3d.o plotmath.o print.o printarray.o printvector.o printutils.o 
qsort.o random.o raw.o registration.o relop.o rlocale.o saveload.o 
scan.o seq.o serialize.o sort.o source.o split.o sprintf.o startup.o 
subassign.o subscript.o subset.o summary.o sysutils.o unique.o util.o 
version.o vfonts.o xxxpr.o   `ls ../unix/*.o ../appl/*.o ../nmath/*.o` 
../extra/zlib/libz.a ../extra/bzip2/libbz2.a ../extra/pcre/libpcre.a 
../extra/tre/libtre.a  ../extra/xz/liblzma.a  -L../../lib -lRblas 
-lgfortran -lm   -lreadline  -lrt -ldl -lm -licuuc -licui18n
/usr/bin/ld: CommandLineArgs.o: relocation R_X86_64_32 against 
`.rodata.str1.1' can not be used when making a shared object; recompile 
with -fPIC
CommandLineArgs.o: could not read symbols: Bad value
collect2: ld returned 1 exit status
make[3]: *** [libR.so] Error 1
make[3]: Leaving directory `/home1/optimal1/R-devel/src/main'
make[2]: *** [R] Error 2
make[2]: Leaving directory `/home1/optimal1/R-devel/src/main'
make[1]: *** [R] Error 1
make[1]: Leaving directory `/home1/optimal1/R-devel/src'
make: *** [R] Error 1
-----------------------------
$ cd ../R-packages; R CMD INSTALL Rserve
      returns
...
** libs
gcc -std=gnu99 -shared -L/usr/local/lib64 -o Rserve.so RSserver.o 
Rserv.o base64.o http.o md5.o oc.o qap_decode.o qap_encode.o rsio.o 
session.o sha1.o standalone.o tls.o websockets.o winembed.o -lssl 
-lcrypto -ldl -lcrypt -L/home1/optimal1/R-devel/lib -lR
/usr/bin/ld: cannot find -lR
collect2: ld returned 1 exit status
make: *** [Rserve.so] Error 1
ERROR: compilation failed for package 'Rserve'
* removing '/home1/optimal1/R-devel/library/Rserve'
-----------------------------
$ $JAVA_HOME=~/jdk1.7.0_40
# $PATH includes $JAVA_HOME/bin & $R_HOME/bin
$ R CMD INSTALL rJava
     returns
...
interpreter : ''
archiver    : ''
compiler    : ''
header prep.: ''
cpp flags   : ''
java libs   : ''
configure: error: Java Development Kit (JDK) is missing or not 
registered in R
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 '/home1/optimal1/R-devel/library/rJava'
------------------------
$ R CMD javareconf -e
      returns
Java interpreter : /home1/optimal1/jdk1.7.0_40/jre/bin/java 
(surprisingly, not $JAVA_HOME/bin/java)
Error: Could not create the Java Virtual Machine.
Error: A fatal exception has occurred. Program will exit.
Error occurred during initialization of VM
Could not reserve enough space for object heap
*** Java interpreter doesn't work properly.
-----------------------
$ java -version
      complains
Error occurred during initialization of VM
Could not reserve enough space for object heap
Error: Could not create the Java Virtual Machine.
Error: A fatal exception has occurred. Program will exit.
      but
$ alias java $JAVA_HOME/bin/java -Xmx668m -XX:MaxPermSize=128m
$ java -version
    works, though javareconf still fails as above

Any ideas?

-- 
Mike Landis
Computational Ingelligence <http://3c58.com>
Las Vegas, NV
702-763-1957