Question: Installation of XCMS / mzR failed
0
gravatar for Johannes Raffler
6.5 years ago by
Johannes Raffler20 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 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 M?nchen Deutsches Forschungszentrum f?r Gesundheit und Umwelt (GmbH) Ingolst?dter Landstr. 1 85764 Neuherberg www.helmholtz-muenchen.de Aufsichtsratsvorsitzende: MinDir?in B?rbel Brumme-Bothe Gesch?ftsf?hrer: Prof. Dr. G?nther Wess und Dr. Nikolaus Blum Registergericht: Amtsgericht M?nchen HRB 6466 USt-IdNr: DE 129521671
xcms biocinstaller cdf • 1.9k views
ADD COMMENTlink modified 6.5 years ago by James W. MacDonald49k • written 6.5 years ago by Johannes Raffler20
Answer: Installation of XCMS / mzR failed
0
gravatar for James W. MacDonald
6.5 years ago by
United States
James W. MacDonald49k 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_1.3 2.0.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 > > > Helmholtz Zentrum M?nchen > Deutsches Forschungszentrum f?r Gesundheit und Umwelt (GmbH) > Ingolst?dter Landstr. 1 > 85764 Neuherberg > www.helmholtz-muenchen.de > Aufsichtsratsvorsitzende: MinDir?in B?rbel Brumme-Bothe > Gesch?ftsf?hrer: Prof. Dr. G?nther Wess und Dr. Nikolaus Blum > Registergericht: Amtsgericht M?nchen HRB 6466 > USt-IdNr: DE 129521671 > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
ADD COMMENTlink written 6.5 years ago by James W. MacDonald49k
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 M?nchen >> Deutsches Forschungszentrum f?r Gesundheit und Umwelt (GmbH) >> Ingolst?dter Landstr. 1 >> 85764 Neuherberg >> www.helmholtz-muenchen.de >> Aufsichtsratsvorsitzende: MinDir?in B?rbel Brumme-Bothe >> Gesch?ftsf?hrer: Prof. Dr. G?nther Wess und Dr. Nikolaus Blum >> Registergericht: Amtsgericht M?nchen HRB 6466 >> USt-IdNr: DE 129521671 >> >> _______________________________________________ >> 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 > > > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 > > > _______________________________________________ > 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 REPLYlink written 6.5 years ago by Dan Tenenbaum8.2k
>> >> 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 > Thank you very much, Dan and Jim! It works fine now. Johannes Helmholtz Zentrum M?nchen Deutsches Forschungszentrum f?r Gesundheit und Umwelt (GmbH) Ingolst?dter Landstr. 1 85764 Neuherberg www.helmholtz-muenchen.de Aufsichtsratsvorsitzende: MinDir?in B?rbel Brumme-Bothe Gesch?ftsf?hrer: Prof. Dr. G?nther Wess und Dr. Nikolaus Blum Registergericht: Amtsgericht M?nchen HRB 6466 USt-IdNr: DE 129521671
ADD REPLYlink written 6.5 years ago by Johannes Raffler20
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