[BioC] problems installing xcms package

[Juliet Hannah]

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


> 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