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error.log
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source("https://bioconductor.org/biocLite.R")
Bioconductor version 3.5 (BiocInstaller 1.26.1), ?biocLite for help
> biocLite("MSstats")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.5 (BiocInstaller 1.26.1), R 3.4.0 (2017-04-21).
Installing package(s) ‘MSstats’
also installing the dependencies ‘minqa’, ‘nloptr’, ‘caTools’, ‘mzR’, ‘pcaMethods’, ‘lme4’, ‘gplots’, ‘ggrepel’, ‘MSnbase’
trying URL 'https://cran.rstudio.com/src/contrib/minqa_1.2.4.tar.gz'
Content type 'application/x-gzip' length 53548 bytes (52 KB)
==================================================
downloaded 52 KB
trying URL 'https://cran.rstudio.com/src/contrib/nloptr_1.0.4.tar.gz'
Content type 'application/x-gzip' length 353957 bytes (345 KB)
==================================================
downloaded 345 KB
trying URL 'https://cran.rstudio.com/src/contrib/caTools_1.17.1.tar.gz'
Content type 'application/x-gzip' length 63358 bytes (61 KB)
==================================================
downloaded 61 KB
trying URL 'https://bioconductor.org/packages/3.5/bioc/src/contrib/mzR_2.10.0.tar.gz'
Content type 'application/x-gzip' length 5244073 bytes (5.0 MB)
==================================================
downloaded 5.0 MB
trying URL 'https://bioconductor.org/packages/3.5/bioc/src/contrib/pcaMethods_1.68.0.tar.gz'
Content type 'application/x-gzip' length 698177 bytes (681 KB)
==================================================
downloaded 681 KB
trying URL 'https://cran.rstudio.com/src/contrib/lme4_1.1-14.tar.gz'
Content type 'application/x-gzip' length 3601039 bytes (3.4 MB)
==================================================
downloaded 3.4 MB
trying URL 'https://cran.rstudio.com/src/contrib/gplots_3.0.1.tar.gz'
Content type 'application/x-gzip' length 578626 bytes (565 KB)
==================================================
downloaded 565 KB
trying URL 'https://cran.rstudio.com/src/contrib/ggrepel_0.7.0.tar.gz'
Content type 'application/x-gzip' length 613978 bytes (599 KB)
==================================================
downloaded 599 KB
trying URL 'https://bioconductor.org/packages/3.5/bioc/src/contrib/MSnbase_2.2.0.tar.gz'
Content type 'application/x-gzip' length 3748796 bytes (3.6 MB)
==================================================
downloaded 3.6 MB
trying URL 'https://bioconductor.org/packages/3.5/bioc/src/contrib/MSstats_3.8.6.tar.gz'
Content type 'application/x-gzip' length 352315 bytes (344 KB)
==================================================
downloaded 344 KB
* installing *source* package ‘minqa’ ...
** package ‘minqa’ successfully unpacked and MD5 sums checked
** libs
gfortran -fpic -g -O2 -c altmov.f -o altmov.o
gfortran -fpic -g -O2 -c bigden.f -o bigden.o
gfortran -fpic -g -O2 -c biglag.f -o biglag.o
gfortran -fpic -g -O2 -c bobyqa.f -o bobyqa.o
gfortran -fpic -g -O2 -c bobyqb.f -o bobyqb.o
gfortran -fpic -g -O2 -c lagmax.f -o lagmax.o
g++ -I/lustre/scratch115/teams/zeggini/R-3.4.0/include -DNDEBUG -I"/nfs/users/nfs_l/ls11/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include" -I/usr/local/include -fpic -O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function -fpermissive -std=c++11 -c minqa.cpp -o minqa.o
cc1plus: error: unrecognised command line option ‘-std=c++11’
make: *** [minqa.o] Error 1
ERROR: compilation failed for package ‘minqa’
* removing ‘/nfs/users/nfs_l/ls11/R/x86_64-pc-linux-gnu-library/3.4/minqa’
* installing *source* package ‘nloptr’ ...
** package ‘nloptr’ successfully unpacked and MD5 sums checked
checking for g++... g++
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking how to run the C++ preprocessor... g++ -E
checking whether we are using the GNU C++ compiler... (cached) yes
checking whether g++ accepts -g... (cached) yes
checking for pkg-config... yes
configure: Now testing for NLopt header file.
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking nlopt.h usability... yes
checking nlopt.h presence... yes
checking for nlopt.h... yes
configure: Suitable NLopt library found.
configure: creating ./config.status
config.status: creating src/Makevars
** libs
g++ -I/lustre/scratch115/teams/zeggini/R-3.4.0/include -DNDEBUG -I/usr/local/include -fpic -O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function -fpermissive -std=c++11 -c dummy.cpp -o dummy.o
cc1plus: error: unrecognised command line option ‘-std=c++11’
make: *** [dummy.o] Error 1
ERROR: compilation failed for package ‘nloptr’
* removing ‘/nfs/users/nfs_l/ls11/R/x86_64-pc-linux-gnu-library/3.4/nloptr’
* installing *source* package ‘caTools’ ...
** package ‘caTools’ successfully unpacked and MD5 sums checked
** libs
g++ -I/lustre/scratch115/teams/zeggini/R-3.4.0/include -DNDEBUG -I/usr/local/include -fpic -O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function -fpermissive -std=c++11 -c Gif2R.cpp -o Gif2R.o
cc1plus: error: unrecognised command line option ‘-std=c++11’
make: *** [Gif2R.o] Error 1
ERROR: compilation failed for package ‘caTools’
* removing ‘/nfs/users/nfs_l/ls11/R/x86_64-pc-linux-gnu-library/3.4/caTools’
* installing *source* package ‘mzR’ ...
** libs
rm -f cramp.o ramp_base64.o ramp.o RcppRamp.o RcppRampModule.o rnetCDF.o RcppPwiz.o RcppPwizModule.o RcppIdent.o RcppIdentModule.o ./boost/libs/system/src/error_code.o ./boost/libs/regex/src/posix_api.o ./boost/libs/regex/src/fileiter.o ./boost/libs/regex/src/regex_raw_buffer.o ./boost/libs/regex/src/cregex.o ./boost/libs/regex/src/regex_debug.o ./boost/libs/regex/src/instances.o ./boost/libs/regex/src/icu.o ./boost/libs/regex/src/usinstances.o ./boost/libs/regex/src/regex.o ./boost/libs/regex/src/wide_posix_api.o ./boost/libs/regex/src/regex_traits_defaults.o ./boost/libs/regex/src/winstances.o ./boost/libs/regex/src/wc_regex_traits.o ./boost/libs/regex/src/c_regex_traits.o ./boost/libs/regex/src/cpp_regex_traits.o ./boost/libs/regex/src/static_mutex.o ./boost/libs/regex/src/w32_regex_traits.o ./boost/libs/iostreams/src/zlib.o ./boost/libs/iostreams/src/file_descriptor.o ./boost/libs/filesystem/src/operations.o ./boost/libs/filesystem/src/path.o ./boost/libs/filesystem/src/utf8_codecvt_facet.o ./boost/libs/chrono/src/chrono.o ./boost/libs/chrono/src/process_cpu_clocks.o ./boost/libs/chrono/src/thread_clock.o ./pwiz/data/msdata/Version.o ./pwiz/data/identdata/Version.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/common/Unimod.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/MSNumpress.o ./pwiz/data/msdata/SpectrumListCache.o ./pwiz/data/msdata/Index_mzML.o ./pwiz/data/msdata/SpectrumWorkerThreads.o ./pwiz/data/identdata/IdentDataFile.o ./pwiz/data/identdata/IdentData.o ./pwiz/data/identdata/DefaultReaderList.o ./pwiz/data/identdata/Reader.o ./pwiz/data/identdata/Serializer_protXML.o ./pwiz/data/identdata/Serializer_pepXML.o ./pwiz/data/identdata/Serializer_mzid.o ./pwiz/data/identdata/IO.o ./pwiz/data/identdata/References.o ./pwiz/data/identdata/MascotReader.o ./pwiz/data/proteome/Modification.o ./pwiz/data/proteome/Digestion.o ./pwiz/data/proteome/Peptide.o ./pwiz/data/proteome/AminoAcid.o ./pwiz/utility/minimxml/XMLWriter.o ./pwiz/utility/minimxml/SAXParser.o ./pwiz/utility/chemistry/Chemistry.o ./pwiz/utility/chemistry/ChemistryData.o ./pwiz/utility/chemistry/MZTolerance.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 ./RcppExports.o ./boost/libs/thread/src/pthread/once.o ./boost/libs/thread/src/pthread/thread.o rampR.o R_init_mzR.o
find . -name \*~ -exec rm {} \; ## from cleanup
find . -name \*.o -exec rm {} \; ## from cleanup
find . -name "#*#" -exec rm {} \; ## from cleanup
g++ -std=gnu++0x -I/lustre/scratch115/teams/zeggini/R-3.4.0/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/nfs/users/nfs_l/ls11/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include" -I"/lustre/scratch115/realdata/mdt3/teams/zeggini/R-3.4.0/library/zlibbioc/include" -I/usr/local/include -fpic -g -O2 -c cramp.cpp -o cramp.o
/bin/sh: nc-config: command not found
g++ -std=gnu++0x -I/lustre/scratch115/teams/zeggini/R-3.4.0/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/nfs/users/nfs_l/ls11/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include" -I"/lustre/scratch115/realdata/mdt3/teams/zeggini/R-3.4.0/library/zlibbioc/include" -I/usr/local/include -fpic -g -O2 -c ramp_base64.cpp -o ramp_base64.o
/bin/sh: nc-config: command not found
g++ -std=gnu++0x -I/lustre/scratch115/teams/zeggini/R-3.4.0/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/nfs/users/nfs_l/ls11/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include" -I"/lustre/scratch115/realdata/mdt3/teams/zeggini/R-3.4.0/library/zlibbioc/include" -I/usr/local/include -fpic -g -O2 -c ramp.cpp -o ramp.o
/bin/sh: nc-config: command not found
g++ -std=gnu++0x -I/lustre/scratch115/teams/zeggini/R-3.4.0/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/nfs/users/nfs_l/ls11/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include" -I"/lustre/scratch115/realdata/mdt3/teams/zeggini/R-3.4.0/library/zlibbioc/include" -I/usr/local/include -fpic -g -O2 -c RcppRamp.cpp -o RcppRamp.o
/bin/sh: nc-config: command not found
g++ -std=gnu++0x -I/lustre/scratch115/teams/zeggini/R-3.4.0/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/nfs/users/nfs_l/ls11/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include" -I"/lustre/scratch115/realdata/mdt3/teams/zeggini/R-3.4.0/library/zlibbioc/include" -I/usr/local/include -fpic -g -O2 -c RcppRampModule.cpp -o RcppRampModule.o
/bin/sh: nc-config: command not found
gcc -std=gnu99 -I/lustre/scratch115/teams/zeggini/R-3.4.0/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/nfs/users/nfs_l/ls11/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include" -I"/lustre/scratch115/realdata/mdt3/teams/zeggini/R-3.4.0/library/zlibbioc/include" -I/usr/local/include -fpic -I/lustre/scratch115/teams/zeggini/R-3.4.0/zlib-1.2.11 -c rnetCDF.c -o rnetCDF.o
/bin/sh: nc-config: command not found
In file included from rnetCDF.c:2:0:
rnetCDF.h:1:20: fatal error: netcdf.h: No such file or directory
compilation terminated.
make: *** [rnetCDF.o] Error 1
ERROR: compilation failed for package ‘mzR’
* removing ‘/nfs/users/nfs_l/ls11/R/x86_64-pc-linux-gnu-library/3.4/mzR’
* installing *source* package ‘pcaMethods’ ...
** libs
g++ -I/lustre/scratch115/teams/zeggini/R-3.4.0/include -DNDEBUG -I"/nfs/users/nfs_l/ls11/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include" -I/usr/local/include -fpic -O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function -fpermissive -std=c++11 -c RcppExports.cpp -o RcppExports.o
cc1plus: error: unrecognised command line option ‘-std=c++11’
make: *** [RcppExports.o] Error 1
ERROR: compilation failed for package ‘pcaMethods’
* removing ‘/nfs/users/nfs_l/ls11/R/x86_64-pc-linux-gnu-library/3.4/pcaMethods’
* installing *source* package ‘ggrepel’ ...
** package ‘ggrepel’ successfully unpacked and MD5 sums checked
** libs
g++ -I/lustre/scratch115/teams/zeggini/R-3.4.0/include -DNDEBUG -I"/nfs/users/nfs_l/ls11/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include" -I/usr/local/include -fpic -O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function -fpermissive -std=c++11 -c RcppExports.cpp -o RcppExports.o
cc1plus: error: unrecognised command line option ‘-std=c++11’
make: *** [RcppExports.o] Error 1
ERROR: compilation failed for package ‘ggrepel’
* removing ‘/nfs/users/nfs_l/ls11/R/x86_64-pc-linux-gnu-library/3.4/ggrepel’
ERROR: dependencies ‘minqa’, ‘nloptr’ are not available for package ‘lme4’
* removing ‘/nfs/users/nfs_l/ls11/R/x86_64-pc-linux-gnu-library/3.4/lme4’
ERROR: dependency ‘caTools’ is not available for package ‘gplots’
* removing ‘/nfs/users/nfs_l/ls11/R/x86_64-pc-linux-gnu-library/3.4/gplots’
ERROR: dependencies ‘mzR’, ‘pcaMethods’ are not available for package ‘MSnbase’
* removing ‘/nfs/users/nfs_l/ls11/R/x86_64-pc-linux-gnu-library/3.4/MSnbase’
ERROR: dependencies ‘lme4’, ‘gplots’, ‘ggrepel’, ‘MSnbase’ are not available for package ‘MSstats’
* removing ‘/nfs/users/nfs_l/ls11/R/x86_64-pc-linux-gnu-library/3.4/MSstats’
The downloaded source packages are in
‘/lustre/scratch115/realdata/mdt3/teams/zeggini/R-3.4.0/tmp/Rtmp7OjBv6/downloaded_packages’
Old packages: 'dplyr', 'glue', 'IRanges', 'lazyeval', 'Rcpp', 'S4Vectors',
'scales', 'shinystan', 'tibble', 'backports', 'BH', 'checkmate', 'curl',
'data.table', 'DelayedArray', 'GenomeInfoDb', 'GenomicFeatures',
'GenomicRanges', 'gridExtra', 'HDF5Array', 'httr', 'igraph', 'irlba',
'limma', 'openssl', 'RSQLite', 'shiny', 'SummarizedExperiment'
Update all/some/none? [a/s/n]: n
Warning messages:
1: In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘minqa’ had non-zero exit status
2: In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘nloptr’ had non-zero exit status
3: In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘caTools’ had non-zero exit status
4: In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘mzR’ had non-zero exit status
5: In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘pcaMethods’ had non-zero exit status
6: In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘ggrepel’ had non-zero exit status
7: In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘lme4’ had non-zero exit status
8: In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘gplots’ had non-zero exit status
9: In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘MSnbase’ had non-zero exit status
10: In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘MSstats’ had non-zero exit status