[BioC] Installation of XCMS / mzR failed

Mon Jul 30 21:50:53 CEST 2012

Hi Johannes,

On 7/30/2012 9:20 AM, Johannes Raffler wrote:
> Hi everybody,
>
> I have a problem installing xcms. When it comes to the compilation mzR,
> the installation fails due to some error with "rnetCDF" (see below). I'm
> using R 2.15.1 under Ubuntu 10.04 x64. I also tried older versions of R
> / Bioconductor and a previous version of Rcpp, since I found a posting
> where there was an issue with Rcpp under Windows, but it didn't help.
>
> Any hints?
>
> Cheers,
>
> Johannes
>
>
>
> > sessionInfo()
> R version 2.15.1 (2012-06-22)
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> locale:
> [1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C
> [3] LC_TIME=en_US.utf8 LC_COLLATE=en_US.utf8
> [5] LC_MONETARY=en_US.utf8 LC_MESSAGES=en_US.utf8
> [7] LC_PAPER=C LC_NAME=C
> [9] LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] BiocInstaller_1.4.7
>
> loaded via a namespace (and not attached):
> [1] tools_2.15.1
>
>
> > biocLite("xcms")
> BioC_mirror: http://bioconductor.org
> Using R version 2.15, BiocInstaller version 1.4.7.
> Installing package(s) 'xcms'
> also installing the dependency ‘mzR’
>
> trying URL
> 'http://www.bioconductor.org/packages/2.10/bioc/src/contrib/mzR_1.2.2.tar.gz' 
>
> Content type 'application/x-gzip' length 4893343 bytes (4.7 Mb)
> opened URL
> ==================================================
> downloaded 4.7 Mb
>
> trying URL
> 'http://www.bioconductor.org/packages/2.10/bioc/src/contrib/xcms_1.32.0.tar.gz' 
>
> Content type 'application/x-gzip' length 1320111 bytes (1.3 Mb)
> opened URL
> ==================================================
> downloaded 1.3 Mb
>
> * installing *source* package ‘mzR’ ...
> ** libs
> rm -f cramp.o ramp_base64.o ramp.o RcppRamp.o RcppRampModule.o rnetCDF.o
> ./boost/system/src/error_code.o ./boost/regex/src/posix_api.o
> ./boost/regex/src/fileiter.o ./boost/regex/src/regex_raw_buffer.o
> ./boost/regex/src/cregex.o ./boost/regex/src/regex_debug.o
> ./boost/regex/src/instances.o ./boost/regex/src/icu.o
> ./boost/regex/src/usinstances.o ./boost/regex/src/regex.o
> ./boost/regex/src/wide_posix_api.o
> ./boost/regex/src/regex_traits_defaults.o ./boost/regex/src/winstances.o
> ./boost/regex/src/wc_regex_traits.o ./boost/regex/src/c_regex_traits.o
> ./boost/regex/src/cpp_regex_traits.o ./boost/regex/src/static_mutex.o
> ./boost/regex/src/w32_regex_traits.o ./pwiz/data/msdata/Version.o
> ./pwiz/utility/minimxml/XMLWriter.o ./pwiz/utility/minimxml/SAXParser.o
> ./boost/iostreams/src/zlib.o ./boost/thread/src/pthread/once.o
> ./boost/filesystem/src/operations.o ./pwiz/data/common/MemoryIndex.o
> ./pwiz/data/common/CVTranslator.o ./pwiz/data/common/cv.o
> ./pwiz/data/common/ParamTypes.o ./pwiz/data/common/BinaryIndexStream.o
> ./pwiz/data/common/diff_std.o ./pwiz/data/msdata/SpectrumList_MGF.o
> ./pwiz/data/msdata/DefaultReaderList.o
> ./pwiz/data/msdata/ChromatogramList_mzML.o ./pwiz/data/msdata/examples.o
> ./pwiz/data/msdata/Serializer_mzML.o ./pwiz/data/msdata/Serializer_MSn.o
> ./pwiz/data/msdata/Reader.o ./pwiz/data/msdata/Serializer_MGF.o
> ./pwiz/data/msdata/Serializer_mzXML.o
> ./pwiz/data/msdata/SpectrumList_mzML.o
> ./pwiz/data/msdata/SpectrumList_MSn.o
> ./pwiz/data/msdata/BinaryDataEncoder.o ./pwiz/data/msdata/Diff.o
> ./pwiz/data/msdata/MSData.o ./pwiz/data/msdata/References.o
> ./pwiz/data/msdata/SpectrumList_mzXML.o ./pwiz/data/msdata/IO.o
> ./pwiz/data/msdata/SpectrumList_BTDX.o ./pwiz/data/msdata/SpectrumInfo.o
> ./pwiz/data/msdata/RAMPAdapter.o ./pwiz/data/msdata/LegacyAdapter.o
> ./pwiz/data/msdata/SpectrumIterator.o ./pwiz/data/msdata/MSDataFile.o
> ./pwiz/data/msdata/SpectrumListCache.o ./pwiz/utility/misc/IntegerSet.o
> ./pwiz/utility/misc/Base64.o ./pwiz/utility/misc/IterationListener.o
> ./pwiz/utility/misc/MSIHandler.o ./pwiz/utility/misc/Filesystem.o
> ./pwiz/utility/misc/TabReader.o
> ./pwiz/utility/misc/random_access_compressed_ifstream.o
> ./pwiz/utility/misc/SHA1.o ./pwiz/utility/misc/SHA1Calculator.o
> ./pwiz/utility/misc/sha1calc.o ./random_access_gzFile.o rampR.o
> g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/
> -I. -DHAVE_PWIZ_MZML_LIB -I"/usr/local/lib/R/site-library/Rcpp/include"
> -fpic -O3 -pipe -g -c cramp.cpp -o cramp.o
> g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/
> -I. -DHAVE_PWIZ_MZML_LIB -I"/usr/local/lib/R/site-library/Rcpp/include"
> -fpic -O3 -pipe -g -c ramp_base64.cpp -o ramp_base64.o
> g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/
> -I. -DHAVE_PWIZ_MZML_LIB -I"/usr/local/lib/R/site-library/Rcpp/include"
> -fpic -O3 -pipe -g -c ramp.cpp -o ramp.o
> g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/
> -I. -DHAVE_PWIZ_MZML_LIB -I"/usr/local/lib/R/site-library/Rcpp/include"
> -fpic -O3 -pipe -g -c RcppRamp.cpp -o RcppRamp.o
> g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/
> -I. -DHAVE_PWIZ_MZML_LIB -I"/usr/local/lib/R/site-library/Rcpp/include"
> -fpic -O3 -pipe -g -c RcppRampModule.cpp -o RcppRampModule.o
> gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE
> -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB
> -I"/usr/local/lib/R/site-library/Rcpp/include" -fpic -O3 -pipe -g -c
> rnetCDF.c -o rnetCDF.o
> rnetCDF.c:2:20: error: netcdf.h: No such file or directory

That is your hint ^^^^^^^^^^^^^^^^^^^

You need to have the netcdf headers available and in your path. Looking 
at the dependencies for xcms and then following the links to ncdf 
brought me to this page:

http://cran.fhcrc.org/web/packages/ncdf/INSTALL

Which may be helpful.

Best,

Jim

> rnetCDF.c: In function ‘NetCDFStrError’:
> rnetCDF.c:8: warning: implicit declaration of function ‘nc_strerror’
> rnetCDF.c:8: warning: passing argument 2 of ‘strncpy’ makes pointer from
> integer without a cast
> /usr/include/bits/string3.h:120: note: expected ‘const char * restrict’
> but argument is of type ‘int’
> rnetCDF.c: In function ‘NetCDFOpen’:
> rnetCDF.c:13: warning: implicit declaration of function ‘nc_open’
> rnetCDF.c:13: error: ‘NC_NOWRITE’ undeclared (first use in this function)
> rnetCDF.c:13: error: (Each undeclared identifier is reported only once
> rnetCDF.c:13: error: for each function it appears in.)
> rnetCDF.c: In function ‘NetCDFClose’:
> rnetCDF.c:18: warning: implicit declaration of function ‘nc_close’
> rnetCDF.c: In function ‘NetCDFVarID’:
> rnetCDF.c:23: warning: implicit declaration of function ‘nc_inq_varid’
> rnetCDF.c: In function ‘NetCDFVarLen’:
> rnetCDF.c:28: error: ‘NC_MAX_VAR_DIMS’ undeclared (first use in this
> function)
> rnetCDF.c:31: warning: implicit declaration of function ‘nc_inq_varndims’
> rnetCDF.c:34: warning: implicit declaration of function ‘nc_inq_vardimid’
> rnetCDF.c:39: warning: implicit declaration of function ‘nc_inq_dimlen’
> rnetCDF.c: In function ‘NetCDFVarDouble’:
> rnetCDF.c:55: warning: implicit declaration of function 
> ‘nc_get_var_double’
> rnetCDF.c:58: warning: implicit declaration of function ‘nc_inq_att’
> rnetCDF.c:59: warning: implicit declaration of function 
> ‘nc_get_att_double’
> rnetCDF.c: In function ‘NetCDFVarInt’:
> rnetCDF.c:77: warning: implicit declaration of function ‘nc_get_var_int’
> make: *** [rnetCDF.o] Error 1
> ERROR: compilation failed for package ‘mzR’
> * removing ‘/usr/local/lib/R/site-library/mzR’
> ERROR: dependency ‘mzR’ is not available for package ‘xcms’
> * removing ‘/usr/local/lib/R/site-library/xcms’
>
> The downloaded source packages are in
> ‘/tmp/RtmpiiDwPY/downloaded_packages’
> Warning messages:
> 1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
> installation of package ‘mzR’ had non-zero exit status
> 2: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
> installation of package ‘xcms’ had non-zero exit status
>
>
> -- 
> Johannes Raffler
> Metabolomics Group
> Institute of Bioinformatics and Systems Biology
>
> Phone: +49-89-3187-3640
> Fax: +49-89-3187-3585
> Mail: johannes.raffler at helmholtz-muenchen.de
>
>
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099