[BioC] Installing bioconductor with openSUSE 11.4 and R 2.14

[Dan Tenenbaum]

On Wed, Jan 25, 2012 at 9:42 AM, Bartlett, Thomas
<thomas.bartlett.10 at ucl.ac.uk> wrote:
> Hi,
>
> Thanks for your previous replies about problems I've been having installing Bioconductor when using OpenSUSE 11.4 and R 2.14 I've solved the problem about the C compiler, which has now installed fine. However, I get the following error messages now:
>
> * installing *source* package ‘RSQLite’ ...
> ** package ‘RSQLite’ successfully unpacked and MD5 sums checked
> /usr/lib64/R/bin/config: line 142: make: command not found
> /usr/lib64/R/bin/config: line 143: make: command not found
> /usr/lib64/R/bin/config: line 219: make: command not found
> /usr/lib64/R/bin/config: line 142: make: command not found
> /usr/lib64/R/bin/config: line 143: make: command not found
> /usr/lib64/R/bin/config: line 219: make: command not found
> checking for gcc... gcc
> 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 accepts -g... yes
> checking for gcc option to accept ISO C89... none needed
> checking how to run the C preprocessor... gcc -E
> checking for gcc... (cached) gcc
> checking whether we are using the GNU C compiler... (cached) yes
> checking whether gcc accepts -g... (cached) yes
> checking for gcc option to accept ISO C89... (cached) none needed
> checking for library containing fdatasync... none required
> configure: creating ./config.status
> config.status: creating src/Makevars
> ** libs
> sh: make: command not found
> ERROR: compilation failed for package ‘RSQLite’
> * removing ‘/usr/lib64/R/library/RSQLite’
> * installing *source* package ‘Biobase’ ...
> ** libs
> sh: make: command not found
> ERROR: compilation failed for package ‘Biobase’
> * removing ‘/usr/lib64/R/library/Biobase’
> * installing *source* package ‘IRanges’ ...
> ** libs
> sh: make: command not found
> ERROR: compilation failed for package ‘IRanges’
> * removing ‘/usr/lib64/R/library/IRanges’
> ERROR: dependencies ‘Biobase’, ‘RSQLite’, ‘IRanges’ are not available for package ‘AnnotationDbi’
> * removing ‘/usr/lib64/R/library/AnnotationDbi’
>

Use
sudo rpm -q make
to find out what package "make" is in.
Then use
sudo zypper install PKGNAME
where PKGNAME is the package name from the previous step.
Dan



>
> any help would be very much appreciated!
>
> Tom Bartlett
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