[BioC] problems installing xcms package

[Dan Tenenbaum]

Hi Juliet,

On Sat, Mar 24, 2012 at 12:43 PM, Juliet Hannah <juliet.hannah at gmail.com> wrote:
> All,
>
> Can anyone confirm the following problem installing the xcms package? Thanks.
>
>  biocLite("xcms")
>
> ends with:
>
>
> netCDF.c:2:20: error: netcdf.h: No such file or directory
> netCDF.c: In function âNetCDFStrErrorâ:
> netCDF.c:8: warning: implicit declaration of function ânc_strerrorâ
> netCDF.c:8: warning: passing argument 2 of â__builtin_strncpyâ makes
> pointer from integer without a cast
> netCDF.c: In function âNetCDFOpenâ:
> netCDF.c:13: warning: implicit declaration of function ânc_openâ
> netCDF.c:13: error: âNC_NOWRITEâ undeclared (first use in this function)
> netCDF.c:13: error: (Each undeclared identifier is reported only once
> netCDF.c:13: error: for each function it appears in.)
> netCDF.c: In function âNetCDFCloseâ:
> netCDF.c:18: warning: implicit declaration of function ânc_closeâ
> netCDF.c: In function âNetCDFVarIDâ:
> netCDF.c:23: warning: implicit declaration of function ânc_inq_varidâ
> netCDF.c: In function âNetCDFVarLenâ:
> netCDF.c:28: error: âNC_MAX_VAR_DIMSâ undeclared (first use in this function)
> netCDF.c:31: warning: implicit declaration of function ânc_inq_varndimsâ
> netCDF.c:34: warning: implicit declaration of function ânc_inq_vardimidâ
> netCDF.c:39: warning: implicit declaration of function ânc_inq_dimlenâ
> netCDF.c: In function âNetCDFVarDoubleâ:
> netCDF.c:55: warning: implicit declaration of function ânc_get_var_doubleâ
> netCDF.c:58: warning: implicit declaration of function ânc_inq_attâ
> netCDF.c:59: warning: implicit declaration of function ânc_get_att_doubleâ
> netCDF.c: In function âNetCDFVarIntâ:
> netCDF.c:77: warning: implicit declaration of function ânc_get_var_intâ
> make: *** [netCDF.o] Error 1
> ERROR: compilation failed for package âxcmsâ
> * removing â/nfs/jh/R-2.14.2/library/xcmsâ
>
> The downloaded packages are in
>        â/tmp/RtmpJG8Uee/downloaded_packagesâ
> Updating HTML index of packages in '.Library'
> Making packages.html  ... done
> Warning message:
> In install.packages(pkgs = pkgs, repos = repos, ...) :
>  installation of package âxcmsâ had non-zero exit status
>
>

Looks like you need netcdf on your computer. I don't know which linux
distribution you are running, bit if it's Ubuntu, the following
command should do it:

sudo apt-get install netcdf libnetcdf-dev

Dan


>> sessionInfo()
> R version 2.14.2 (2012-02-29)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>  [7] LC_PAPER=C                 LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] affy_1.32.1         Biobase_2.14.0      BiocInstaller_1.2.1
>
> loaded via a namespace (and not attached):
> [1] affyio_1.22.0         preprocessCore_1.16.0 tools_2.14.2
> [4] zlibbioc_1.0.1
>
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