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[Bioc-devel] problem of RMAGEML installation

2 messages · Xinan Yang, Vincent Carey

Original
Xinan Yang
# 
I tryed to install RMAGEMLpackage on my linux machine with R version 2.3.1.
BUt failed to do so.
The error message are as below:

 > biocLite("RMAGEML")
Running getBioC version 0.1.6 with R version 2.3.1
Running biocinstall version 1.8.4 with R version 2.3.1
Your version of R requires version 1.8 of Bioconductor.
trying URL 
'http://bioconductor.org/packages/1.8/bioc/src/contrib/RMAGEML_2.6.0.tar.gz'
Content type 'application/x-gzip' length 4918370 bytes
opened URL
==================================================
downloaded 4803Kb

* Installing *source* package 'RMAGEML' ...
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -I/usr/local/lib/R/include -I/usr/local/lib/R/include -I/include 
-I/include/linux  -I/usr/local/include   -fpic  -g -O2 -std=gnu99 -c 
rmageml.c -o rmageml.o
gcc -shared -L/usr/local/lib -o RMAGEML.so rmageml.o -L/jre/lib/amd64 
-L/jre/lib/i386 -ljava -L/jre/lib/amd64/server -L/jre/lib/i386/client -ljvm
/usr/bin/ld: cannot find -ljava
collect2: ld returned 1 exit status
make: *** [RMAGEML.so] Error 1
chmod: failed to get attributes of 
`/usr/local/lib/R/library/RMAGEML/libs/*': No such file or directory
ERROR: compilation failed for package 'RMAGEML'
** Removing '/usr/local/lib/R/library/RMAGEML'

The downloaded packages are in
        /tmp/RtmptjeQhj/downloaded_packages
Warning message:
installation of package 'RMAGEML' had non-zero exit status in: 
install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies,



as I guess it requires some jave enviroment or  .....?
what should I do firstly?
Please give me instrument step by step in details.


tnaks,

xinan
Vincent Carey
# 
Hi, before writing to bioc-devel, you should try to learn
about the package and contact the package author.

In this case, you can download a source version of the package, uncompress
it and read the INSTALL and README files.
if questions remain, contact the package author.  you
can determine that from the DESCRIPTION file.

---
Vince Carey, PhD
Assoc. Prof Med (Biostatistics)
Harvard Medical School
Channing Laboratory - ph 6175252265 fa 6177311541
181 Longwood Ave Boston MA 02115 USA
stvjc at channing.harvard.edu
On Thu, 3 Aug 2006, xinan yang wrote: