[BioC] A question about GWASTools package

Stephanie M. Gogarten sdmorris at u.washington.edu
Wed Mar 20 19:01:32 CET 2013

Dear Hugo,

This is a problem with installing the dependency "ncdf."  The 
installation info on CRAN might help you:

If that doesn't work, try the ncdf author, whose contact info is on this 

Please copy the Bioconductor mailing list (bioconductor at r-project.org) 
with any follow-up questions.

I also recommend that you upgrade to the latest release of R (2.15) 
before installing, as the version of GWASTools you get when using 
biocLite() on older R versions is out of date.


On 3/20/13 10:46 AM, Hugo Loyola wrote:
> Dear Stephanie
> I am trying to install the GWASTools on my laptop and after run
> biocLite("GWASTools")
> something goes wrong at:
> * installing *source* package ‘ncdf’ ...
> ** package ‘ncdf’ successfully unpacked and MD5 sums checked
> checking for nc-config... no
> checking for gcc... gcc -std=gnu99
> checking whether the C compiler works... yes
> checking for C compiler default output file name... a.out
> checking for suffix of executables...
> checking whether we are cross compiling... no
> checking for suffix of object files... o
> checking whether we are using the GNU C compiler... yes
> checking whether gcc -std=gnu99 accepts -g... yes
> checking for gcc -std=gnu99 option to accept ISO C89... none needed
> checking how to run the C preprocessor... gcc -std=gnu99 -E
> checking for grep that handles long lines and -e... /bin/grep
> checking for egrep... /bin/grep -E
> checking for ANSI C header files... no
> checking for sys/types.h... no
> checking for sys/stat.h... no
> checking for stdlib.h... no
> checking for string.h... no
> checking for memory.h... no
> checking for strings.h... no
> checking for inttypes.h... no
> checking for stdint.h... no
> checking for unistd.h... no
> checking netcdf.h usability... no
> checking netcdf.h presence... no
> checking for netcdf.h... no
> configure: error: netcdf header netcdf.h not found
> ERROR: configuration failed for package ‘ncdf’
> * removing ‘/home/rosa/R/i686-pc-linux-gnu-library/2.14/ncdf’
> ERROR: dependency ‘ncdf’ is not available for package ‘GWASTools’
> * removing ‘/home/rosa/R/i686-pc-linux-gnu-library/2.14/GWASTools’
> Can you please suggest me how to fix this?
> Thank you in advance for your time,
> Hugo

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