Entering edit mode
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 ?NetCDFStrError?:
netCDF.c:8: warning: implicit declaration of function ?nc_strerror?
netCDF.c:8: warning: passing argument 2 of ?__builtin_strncpy? makes
pointer from integer without a cast
netCDF.c: In function ?NetCDFOpen?:
netCDF.c:13: warning: implicit declaration of function ?nc_open?
netCDF.c:13: error: ?NC_NOWRITE? 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 ?NetCDFClose?:
netCDF.c:18: warning: implicit declaration of function ?nc_close?
netCDF.c: In function ?NetCDFVarID?:
netCDF.c:23: warning: implicit declaration of function ?nc_inq_varid?
netCDF.c: In function ?NetCDFVarLen?:
netCDF.c:28: error: ?NC_MAX_VAR_DIMS? undeclared (first use in this
function)
netCDF.c:31: warning: implicit declaration of function
?nc_inq_varndims?
netCDF.c:34: warning: implicit declaration of function
?nc_inq_vardimid?
netCDF.c:39: warning: implicit declaration of function ?nc_inq_dimlen?
netCDF.c: In function ?NetCDFVarDouble?:
netCDF.c:55: warning: implicit declaration of function
?nc_get_var_double?
netCDF.c:58: warning: implicit declaration of function ?nc_inq_att?
netCDF.c:59: warning: implicit declaration of function
?nc_get_att_double?
netCDF.c: In function ?NetCDFVarInt?:
netCDF.c:77: warning: implicit declaration of function
?nc_get_var_int?
make: *** [netCDF.o] Error 1
ERROR: compilation failed for package ?xcms?
* removing ?/nfs/jh/R-2.14.2/library/xcms?
The downloaded packages are in
?/tmp/RtmpJG8Uee/downloaded_packages?
Updating HTML index of packages in '.Library'
Making packages.html ... done
Warning message:
In install.packages(pkgs = pkgs, repos = repos, ...) :
installation of package ?xcms? 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
