[BioC] GWASTools

[Stephanie M. Gogarten]

Hi Andrzej,

See this posting from the Bioconductor mailing list:
https://stat.ethz.ch/pipermail/bioconductor/2013-March/051597.html

Also, note that upgrading to R 3.0 / Bioconductor 2.12 will get you the 
latest version of GWASTools.

Stephanie

On 8/9/13 11:16 AM, Andrzej Wojtowicz wrote:
> Hello Stephanie,
>
> I have a problem with installing GWASTools package, or more specifically
> ncdf package. Here is an error message that I am getting when I try to
> install it:
>  > biocLite("GWASTools")
> BioC_mirror: http://bioconductor.org
> Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15.
> Installing package(s) 'GWASTools'
> also installing the dependency âncdfâ
>
> trying URL 'http://cran.fhcrc.org/src/contrib/ncdf_1.6.6.tar.gz'
> Content type 'application/x-gzip' length 79403 bytes (77 Kb)
> opened URL
> ==================================================
> downloaded 77 Kb
>
> trying URL
> 'http://bioconductor.org/packages/2.11/bioc/src/contrib/GWASTools_1.4.2.tar.gz'
> Content type 'application/x-gzip' length 1484123 bytes (1.4 Mb)
> opened URL
> ==================================================
> downloaded 1.4 Mb
>
> * installing *source* package âncdfâ ...
> ** package âncdfâ 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 âncdfâ
> * removing â/home/andrzej/R/x86_64-pc-linux-gnu-library/2.15/ncdfâ
> ERROR: dependency âncdfâ is not available for package âGWASToolsâ
> * removing â/home/andrzej/R/x86_64-pc-linux-gnu-library/2.15/GWASToolsâ
>
> The downloaded source packages are in
>          â/tmp/Rtmp4WEzCP/downloaded_packagesâ
> Warning messages:
> 1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
>    installation of package âncdfâ had non-zero exit status
> 2: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
>    installation of package âGWASToolsâ had non-zero exit status
>
> Please let me know how to fix the problem.
>
> Thank you,
> Andrzej Wojtowicz
> Postdoctoral Research Associate
> Department of Animal Sciences
> Washington State University
> Pullman, WA 99164
> 509-339-3540
>