[BioC] Regarding MotIv and PICS package install

[Dan Tenenbaum]

On Thu, Apr 19, 2012 at 9:41 AM, Swaroopa Muppiri <swaroopa at appistry.com> wrote:
> Hello
>
> Iam trying to install bioconductor 2.10 on my machine .Ruby script was written to call all the packages that are required for me .
>
> When I tried to execute I got the following error :
>

What command is being executed here?


> checking whether gcc -std=gnu99 accepts -g... yes
> checking for gcc -std=gnu99 option to accept ISO C89... none needed
> checking for gsl-config... /opt/users/swaroopa/LSBUILDBOX/trunk/dependencies/bioconductor210/build/srcLibs/../../../gsl-1_13/gsl/bin/gsl-config
> checking for GSL - version >= 1.6... yes
> configure: creating ./config.status
> config.status: creating src/Makevars
> ** libs
> gcc -std=gnu99 -shared -L/usr/local/lib64 -o PICS.so background.o pics.o segment.o -lgsl -lgslcblas -lm
> /usr/bin/ld: cannot find -lgsl
> collect2: ld returned 1 exit status
> make: *** [PICS.so] Error 1
> ERROR: compilation failed for package 'PICS'
>
> As part of troubleshooting I executed the highlighted command on the command prompt .It gave the same error .So I changed the highlighted statement and found that its working fine .

The mailing list strips off HTML versions of emails, so we can't see
what you highlighted.


> Here is the command :
>
> gcc -std=gnu99 -shared -L/opt/users/swaroopa/LSBUILDBOX/trunk/dependencies/gsl-1_13/gsl/lib -o PICS.so src/background.o src/pics.o src/segment.o -lgsl -lgslcblas -lm
>
> This worked fine and able to get the PICS.so
>
> But the question in my mind is where exactly these values are modified .
>

You could edit PICS/src/Makevars or (a better alternative) pass the
appropriate values by passing the configure.args argument to
install.packages(), biocLite(), or whatever you are using to install
PICS (if you are using R CMD INSTALL, you can add the --configure-vars
argument).

Dan



> Thanks for your time
>
>
> Thanks,
> Swaroopa
>
>
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>
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