Entering edit mode
Johannes Raffler
▴
20
@johannes-raffler-5428
Last seen 9.6 years ago
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
