[BioC] Installation of XCMS / mzR failed

Mon Jul 30 21:52:51 CEST 2012

On Mon, Jul 30, 2012 at 12:50 PM, James W. MacDonald <jmacdon at uw.edu> wrote:
> 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.
>

Installing netcdf with apt-get *should* do the right thing:

sudo apt-get install netcdf libnetcdf-dev

Dan

>
> 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
>>
>>
>> Helmholtz Zentrum München
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>>
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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
>
>
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