[BioC] R package Installation Errors

[Martin Morgan]

Hi Jacob --

It looks like you're using a non-Windows R. You probably need to
re-configure R to build a shared library, and then to re-make R. Do
this with something like

./configure --enable-R-shlib
make

to build R in the source tree (better to build R 'out-of-tree', though
by first making a directory in some convenient location, cd to the
directory, then path/to/R source/configure --enable-R-shlib and make).

See configure --help for more options, and the R installation and
administration manual, section 2, e.g., at

http://cran.fhcrc.org/doc/manuals/R-admin.html

for more information.

Hope that helps,

Martin

"Zhang, Jacob" <Jacob.Zhang at vai.org> writes:

> Hello, everybody:
>
> I just installed the latest version of R and trying to install the
> packages. The eriee thing is: while for some package, it works fine, for
> others, it won't install. Here is one of the similar error messages from
> one   failed installation.  
>
>
> Can anybody take a look and figure out a solution? I sense it is
> something related to the shared library. 
>
> Jacob
>
>
>
> install.packages("aws")
> trying URL
> 'http://www.biometrics.mtu.edu/CRAN/src/contrib/aws_1.3-2.tar.gz'
> Content type 'application/x-gzip' length 52774 bytes
> opened URL
> ==================================================
> downloaded 51Kb
>
> * Installing *source* package 'aws' ...
> ** libs
> g77   -fPIC  -g -O2 -c aws.f -o aws.o
> g77   -fPIC  -g -O2 -c dgemm.f -o dgemm.o
> g77   -fPIC  -g -O2 -c eaws.f -o eaws.o
> g77   -fPIC  -g -O2 -c hawsuni.f -o hawsuni.o
> g77   -fPIC  -g -O2 -c laws.f -o laws.o
> gcc -shared -L/usr/local/lib64 -o aws.so aws.o dgemm.o eaws.o hawsuni.o
> laws.o  -lg2c -lm -lgcc_s -L/usr/home/jacob/R-2.2.1/lib -lR
> /usr/lib64/gcc-lib/x86_64-suse-linux/3.3.3/../../../../x86_64-suse-linux
> /bin/ld: cannot find -lR
> collect2: ld returned 1 exit status
> make: *** [aws.so] Error 1
> ERROR: compilation failed for package 'aws'
> ** Removing '/usr/home/jacob/R-2.2.1/library/aws'
>
> The downloaded packages are in
>         /tmp/Rtmpe25813/downloaded_packages
> Warning message:
> installation of package 'aws' had non-zero exit status in:
> install.packages("aws")
>> sessionInfo()
> R version 2.2.1, 2005-12-20, x86_64-unknown-linux-gnu
>
> attached base packages:
> [1] "tools"     "splines"   "methods"   "stats"     "graphics"
> "grDevices"
> [7] "utils"     "datasets"  "base"
>
> other attached packages:
>     affy  Biobase      ctv survival    xgobi
>  "1.8.1"  "1.8.0"  "0.3-1"   "2.20" "1.2-13"
>
> This email message, including any attachments, is for the so...{{dropped}}
>
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