Question: problems installing xcms package
0
gravatar for Juliet Hannah
7.6 years ago by
Juliet Hannah360
United States
Juliet Hannah360 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 ?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
cdf xcms • 1.2k views
ADD COMMENTlink modified 7.6 years ago by Dan Tenenbaum8.2k • written 7.6 years ago by Juliet Hannah360
Answer: problems installing xcms package
0
gravatar for Dan Tenenbaum
7.6 years ago by
Dan Tenenbaum8.2k
United States
Dan Tenenbaum8.2k wrote:
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 ?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 > > 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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD COMMENTlink written 7.6 years ago by Dan Tenenbaum8.2k
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