[BioC] Installation of XCMS / mzR failed

Mon Jul 30 15:20:24 CEST 2012

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

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