[Bioc-devel] problem of RMAGEML installation

Vincent Carey 525-2265 stvjc at channing.harvard.edu
Thu Aug 3 05:30:59 CEST 2006


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:

> 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
>
> _______________________________________________
> Bioc-devel at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>



More information about the Bioc-devel mailing list