[BioC] GWASTools

[Stephanie M. Gogarten]

Upgrading to R 3.0 won't solve your problem, it only affects the version 
of GWASTools (and other Bioconductor packages) that you get.

On Linux, you need to install the NetCDF library before you can install 
the "ncdf" package.  It is available here:
ftp://ftp.unidata.ucar.edu/pub/netcdf/

If you already have NetCDF and you are still having problems, try 
setting the environment variable NETCDF_INCLUDE as described here:
http://cran.r-project.org/web/packages/ncdf/INSTALL

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

Stephanie

On 8/9/13 1:21 PM, Andrzej Wojtowicz wrote:
> Thank you Stephanie. It seems that upgrading to R 3.0 and Bioconductor
> 2.12 should be an easier option because tips in the link you sent are a
> little bit unclear for me. However, standard 'apt-get upgrade R' takes
> me only to R 2.15 not 3.0. So, maybe I'll try later upgrade R in some
> other way.
>
> Andrzej
>
> On 8/9/2013 11:45 AM, Stephanie M. Gogarten wrote:
>> 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
>>>
>