Question: GWASTools depends on the ncdf CRAN package, but this package has been removed
0
gravatar for jeremy37
3.3 years ago by
jeremy370
jeremy370 wrote:

> biocLite("GWASTools")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.1 (BiocInstaller 1.18.5), R version 3.2.2.
Installing package(s) ‘GWASTools’
Warning: dependency ‘ncdf’ is not available
...[lots of other installation happens]...
ERROR: dependency ‘ncdf’ is not available for package ‘GWASTools’
* removing ‘/nfs/users/nfs_j/js29/R-3.2.2/library/GWASTools’

 

 

I have tried to install ncdf myself by finding an archived version, but that also fails on my system due to lacking netcdf.h.

Anyone have tips on how to get this installed?

 

package installation • 977 views
ADD COMMENTlink written 3.3 years ago by jeremy370

Hitting the same roadblock here too... :/

Thanks in advance for any tip!

ADD REPLYlink written 3.2 years ago by kevin.rue220

If you use the current release version of Bioconductor (3.2), a binary version (no compilation needed) of ncdf is available via biocLite(), so all you should need to do is:

biocLite("GWASTools")

If you are on Linux then you need to install netcdf to get the netcdf.h header.

For more information about building from source, download the ncdf tarball and untar it and read the INSTALL file.

If you are using an older version of Bioconductor, then upgrade.

 

 

ADD REPLYlink written 3.2 years ago by Dan Tenenbaum8.2k
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