XCMS installation problem

[bevans-danforth]

Steffen,

After wiping the system again and then installinr r-base by "sudo apt-get install r-base", then following the instructions here: https://github.com/Bioconductor/bioc_docker/blob/master/out/release_protmetcore/Dockerfile, I got an error at "install.R/tmp", "No such directory". I procedded to try and install both xcms alone or just mzR, which seems to be the problem. The log for the mzR installation is below.

`` R version 3.2.3 (2015-12-10) -- "Wooden Christmas-Tree" Copyright (C) 2015 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details.

Natural language support but running in an English locale

R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R.

source("http://bioconductor.org/biocLite.R") # downloads the latest bioconductor script/repos Bioconductor version 3.2 (BiocInstaller 1.20.3), ?biocLite for help A new version of Bioconductor is available after installing the most recent version of R; see http://bioconductor.org/install

biocLite("mzR") BioC_mirror: https://bioconductor.org Using Bioconductor 3.2 (BiocInstaller 1.20.3), R 3.2.3 (2015-12-10). Installing package(s) ‘mzR’ --2017-05-04 11:02:26-- https://bioconductor.org/packages/3.2/bioc/src/contrib/mzR_2.4.1.tar.gz Resolving bioconductor.org (bioconductor.org)... 52.84.0.54, 52.84.0.118, 52.84.0.10, ... Connecting to bioconductor.org (bioconductor.org)|52.84.0.54|:443... connected. HTTP request sent, awaiting response... 200 OK Length: 14656607 (14M) [application/x-gzip] Saving to: ‘/tmp/Rtmpskg3Y4/downloaded_packages/mzR_2.4.1.tar.gz’

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2017-05-04 11:02:31 (3.11 MB/s) - ‘/tmp/Rtmpskg3Y4/downloaded_packages/mzR_2.4.1.tar.gz’ saved [14656607/14656607]

• 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/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 ./boost/iostreams/src/zlib.o ./boost/iostreams/src/file_descriptor.o ./boost/thread/src/pthread/once.o ./boost/thread/src/pthread/thread.o ./boost/filesystem/src/operations.o ./boost/filesystem/src/path.o ./boost/filesystem/src/utf8_codecvt_facet.o ./pwiz/data/msdata/Version.o ./pwiz... find . -name *~ -exec rm {} \; ## from cleanup find . -name *.o -exec rm {} \; ## from cleanup find . -name "#*#" -exec rm {} \; ## from cleanup g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost nc-config --cflags || /bin/true -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include" -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/zlibbioc/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 -D_NODEBUG -DWITHOUT_MZ5 -I./boost nc-config --cflags || /bin/true -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include" -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/zlibbioc/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 -D_NODEBUG -DWITHOUT_MZ5 -I./boost nc-config --cflags || /bin/true -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include" -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/zlibbioc/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 -D_NODEBUG -DWITHOUT_MZ5 -I./boost nc-config --cflags || /bin/true -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include" -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/zlibbioc/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 -D_NODEBUG -DWITHOUT_MZ5 -I./boost nc-config --cflags || /bin/true -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include" -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/zlibbioc/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 -D_NODEBUG -DWITHOUT_MZ5 -I./boost nc-config --cflags || /bin/true -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include" -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/zlibbioc/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rnetCDF.c -o rnetCDF.o g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost nc-config --cflags || /bin/true -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include" -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/zlibbioc/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c RcppPwiz.cpp -o RcppPwiz.o In file included from ./boost/format/alt_sstream.hpp:20:0, from ./boost/format/internals.hpp:23, from ./boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from pwiz/utility/misc/Std.hpp:31, from RcppPwiz.h:19, from RcppPwiz.cpp:1: ./boost/utility/base_from_member.hpp:100:19: warning: variadic templates only available with -std=c++11 or -std=gnu++11 template<typename ...T> ^ ./boost/utility/base_from_member.hpp:105:43: warning: variadic templates only available with -std=c++11 or -std=gnu++11 template<typename T, typename U, typename ...U2> ^ g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost nc-config --cflags || /bin/true -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include" -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/zlibbioc/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c RcppPwizModule.cpp -o RcppPwizModule.o In file included from ./boost/format/alt_sstream.hpp:20:0, from ./boost/format/internals.hpp:23, from ./boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from pwiz/utility/misc/Std.hpp:31, from RcppPwiz.h:19, from RcppPwizModule.cpp:2: ./boost/utility/base_from_member.hpp:100:19: warning: variadic templates only available with -std=c++11 or -std=gnu++11 template<typename ...T> ^ ./boost/utility/base_from_member.hpp:105:43: warning: variadic templates only available with -std=c++11 or -std=gnu++11 template<typename T, typename U, typename ...U2> ^ g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost nc-config --cflags || /bin/true -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include" -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/zlibbioc/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c RcppIdent.cpp -o RcppIdent.o In file included from ./boost/format/alt_sstream.hpp:20:0, from ./boost/format/internals.hpp:23, from ./boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from pwiz/utility/misc/Std.hpp:31, from RcppIdent.h:14, from RcppIdent.cpp:1: ./boost/utility/base_from_member.hpp:100:19: warning: variadic templates only available with -std=c++11 or -std=gnu++11 template<typename ...T> ^ ./boost/utility/base_from_member.hpp:105:43: warning: variadic templates only available with -std=c++11 or -std=gnu++11 template<typename T, typename U, typename ...U2> ^ g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost nc-config --cflags || /bin/true -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include" -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/zlibbioc/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c RcppIdentModule.cpp -o RcppIdentModule.o In file included from ./boost/format/alt_sstream.hpp:20:0, from ./boost/format/internals.hpp:23, from ./boost/format.hpp:38, from ./pwiz/utility/misc/String.hpp:30, from pwiz/utility/misc/Std.hpp:31, from RcppIdent.h:14, from RcppIdentModule.cpp:2: ./boost/utility/base_from_member.hpp:100:19: warning: variadic templates only available with -std=c++11 or -std=gnu++11 template<typename ...T> ^ ./boost/utility/base_from_member.hpp:105:43: warning: variadic templates only available with -std=c++11 or -std=gnu++11 template<typename T, typename U, typename ...U2> ^ g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost nc-config --cflags || /bin/true -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include" -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/zlibbioc/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c boost/system/src/error_code.cpp -o boost/system/src/error_code.o g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost nc-config --cflags || /bin/true -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include" -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/zlibbioc/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c boost/regex/src/posix_api.cpp -o boost/regex/src/posix_api.o g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost nc-config --cflags || /bin/true -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include" -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/zlibbioc/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c boost/regex/src/fileiter.cpp -o boost/regex/src/fileiter.o g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost nc-config --cflags || /bin/true -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include" -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/zlibbioc/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c boost/regex/src/regex_raw_buffer.cpp -o boost/regex/src/regex_raw_buffer.o g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost nc-config --cflags || /bin/true -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include" -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/zlibbioc/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c boost/regex/src/cregex.cpp -o boost/regex/src/cregex.o g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost nc-config --cflags || /bin/true -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include" -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/zlibbioc/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c boost/regex/src/regex_debug.cpp -o boost/regex/src/regex_debug.o g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost nc-config --cflags || /bin/true -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include" -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/zlibbioc/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c boost/regex/src/instances.cpp -o boost/regex/src/instances.o g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost nc-config --cflags || /bin/true -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include" -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/zlibbioc/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c boost/regex/src/icu.cpp -o boost/regex/src/icu.o g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost nc-config --cflags || /bin/true -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include" -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/zlibbioc/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c boost/regex/src/usinstances.cpp -o boost/regex/src/usinstances.o g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost nc-config --cflags || /bin/true -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include" -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/zlibbioc/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c boost/regex/src/regex.cpp -o boost/regex/src/regex.o g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost nc-config --cflags || /bin/true -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include" -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/zlibbioc/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c boost/regex/src/wide_posix_api.cpp -o boost/regex/src/wide_posix_api.o g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost nc-config --cflags || /bin/true -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include" -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/zlibbioc/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c boost/regex/src/regex_traits_defaults.cpp -o boost/regex/src/regex_traits_defaults.o g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost nc-config --cflags || /bin/true -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include" -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/zlibbioc/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c boost/regex/src/winstances.cpp -o boost/regex/src/winstances.o g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost nc-config --cflags || /bin/true -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include" -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/zlibbioc/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c boost/regex/src/wc_regex_traits.cpp -o boost/regex/src/wc_regex_traits.o g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost nc-config --cflags || /bin/true -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include" -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/zlibbioc/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c boost/regex/src/c_regex_traits.cpp -o boost/regex/src/c_regex_traits.o g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost nc-config --cflags || /bin/true -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include" -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/zlibbioc/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c boost/regex/src/cpp_regex_traits.cpp -o boost/regex/src/cpp_regex_traits.o g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost nc-config --cflags || /bin/true -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include" -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/zlibbioc/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c boost/regex/src/static_mutex.cpp -o boost/regex/src/static_mutex.o g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost nc-config --cflags || /bin/true -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include" -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/zlibbioc/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c boost/regex/src/w32_regex_traits.cpp -o boost/regex/src/w32_regex_traits.o g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost nc-config --cflags || /bin/true -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include" -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/zlibbioc/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c boost/iostreams/src/zlib.cpp -o boost/iostreams/src/zlib.o g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost nc-config --cflags || /bin/true -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include" -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/zlibbioc/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c boost/iostreams/src/file_descriptor.cpp -o boost/iostreams/src/file_descriptor.o g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost nc-config --cflags || /bin/true -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include" -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/zlibbioc/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c boost/thread/src/pthread/once.cpp -o boost/thread/src/pthread/once.o In file included from ./boost/thread/pthread/once_atomic.hpp:17:0, from ./boost/thread/once.hpp:20, from boost/thread/src/pthread/./once_atomic.cpp:9, from boost/thread/src/pthread/once.cpp:8: ./boost/thread/detail/invoke.hpp:242:51: warning: variadic templates only available with -std=c++11 or -std=gnu++11 template <class Ret, class A, class A0, class ...Args> ^ ./boost/thread/detail/invoke.hpp:249:28: warning: variadic templates only available with -std=c++11 or -std=gnu++11 invoke(Ret (A::f)(Args...), BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args) ^ ./boost/thread/detail/invoke.hpp:249:91: warning: variadic templates only available with -std=c++11 or -std=gnu++11 invoke(Ret (A::f)(Args...), BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args) ^ ./boost/thread/detail/invoke.hpp:254:51: warning: variadic templates only available with -std=c++11 or -std=gnu++11 template <class Ret, class A, class A0, class ...Args> ^ ./boost/thread/detail/invoke.hpp:261:28: warning: variadic templates only available with -std=c++11 or -std=gnu++11 invoke(Ret (A::f)(Args...) const, BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args) ^ ./boost/thread/detail/invoke.hpp:261:97: warning: variadic templates only available with -std=c++11 or -std=gnu++11 invoke(Ret (A::f)(Args...) const, BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args) ^ ./boost/thread/detail/invoke.hpp:266:51: warning: variadic templates only available with -std=c++11 or -std=gnu++11 template <class Ret, class A, class A0, class ...Args> ^ ./boost/thread/detail/invoke.hpp:273:28: warning: variadic templates only available with -std=c++11 or -std=gnu++11 invoke(Ret (A::f)(Args...) volatile, BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args) ^ ./boost/thread/detail/invoke.hpp:273:100: warning: variadic templates only available with -std=c++11 or -std=gnu++11 invoke(Ret (A::f)(Args...) volatile, BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args) ^ ./boost/thread/detail/invoke.hpp:278:51: warning: variadic templates only available with -std=c++11 or -std=gnu++11 template <class Ret, class A, class A0, class ...Args> ^ ./boost/thread/detail/invoke.hpp:285:28: warning: variadic templates only available with -std=c++11 or -std=gnu++11 invoke(Ret (A::f)(Args...) const volatile, BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args) ^ ./boost/thread/detail/invoke.hpp:285:106: warning: variadic templates only available with -std=c++11 or -std=gnu++11 invoke(Ret (A::f)(Args...) const volatile, BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args) ^ ./boost/thread/detail/invoke.hpp:293:51: warning: variadic templates only available with -std=c++11 or -std=gnu++11 template <class Ret, class A, class A0, class ...Args> ^ ./boost/thread/detail/invoke.hpp:300:28: warning: variadic templates only available with -std=c++11 or -std=gnu++11 invoke(Ret (A::f)(Args...), BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args) ^ ./boost/thread/detail/invoke.hpp:300:91: warning: variadic templates only available with -std=c++11 or -std=gnu++11 invoke(Ret (A::f)(Args...), BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args) ^ ./boost/thread/detail/invoke.hpp:305:51: warning: variadic templates only available with -std=c++11 or -std=gnu++11 template <class Ret, class A, class A0, class ...Args> ^ ./boost/thread/detail/invoke.hpp:312:28: warning: variadic templates only available with -std=c++11 or -std=gnu++11 invoke(Ret (A::f)(Args...) const, BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args) ^ ./boost/thread/detail/invoke.hpp:312:97: warning: variadic templates only available with -std=c++11 or -std=gnu++11 invoke(Ret (A::f)(Args...) const, BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args) ^ ./boost/thread/detail/invoke.hpp:317:51: warning: variadic templates only available with -std=c++11 or -std=gnu++11 template <class Ret, class A, class A0, class ...Args> ^ ./boost/thread/detail/invoke.hpp:324:28: warning: variadic templates only available with -std=c++11 or -std=gnu++11 invoke(Ret (A::f)(Args...) volatile, BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args) ^ ./boost/thread/detail/invoke.hpp:324:100: warning: variadic templates only available with -std=c++11 or -std=gnu++11 invoke(Ret (A::f)(Args...) volatile, BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args) ^ ./boost/thread/detail/invoke.hpp:329:51: warning: variadic templates only available with -std=c++11 or -std=gnu++11 template <class Ret, class A, class A0, class ...Args> ^ ./boost/thread/detail/invoke.hpp:336:28: warning: variadic templates only available with -std=c++11 or -std=gnu++11 invoke(Ret (A::f)(Args...) const volatile, BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args) ^ ./boost/thread/detail/invoke.hpp:336:106: warning: variadic templates only available with -std=c++11 or -std=gnu++11 invoke(Ret (A::f)(Args...) const volatile, BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args) ^ ./boost/thread/detail/invoke.hpp:398:42: warning: variadic templates only available with -std=c++11 or -std=gnu++11 template <class Ret, class Fp, class ...Args> ^ ./boost/thread/detail/invoke.hpp:405:68: warning: variadic templates only available with -std=c++11 or -std=gnu++11 invoke(BOOST_THREAD_RV_REF(Fp) f, BOOST_THREAD_RV_REF(Args) ...args) ^ ./boost/thread/detail/invoke.hpp:409:32: warning: variadic templates only available with -std=c++11 or -std=gnu++11 template <class Ret, class ...Args> ^ ./boost/thread/detail/invoke.hpp:411:24: warning: variadic templates only available with -std=c++11 or -std=gnu++11 invoke(Ret(f)(Args... ), BOOST_THREAD_RV_REF(Args) ...args) ^ ./boost/thread/detail/invoke.hpp:411:60: warning: variadic templates only available with -std=c++11 or -std=gnu++11 invoke(Ret(f)(Args... ), BOOST_THREAD_RV_REF(Args) ...args) ^ In file included from ./boost/thread/once.hpp:20:0, from boost/thread/src/pthread/./once_atomic.cpp:9, from boost/thread/src/pthread/once.cpp:8: ./boost/thread/pthread/once_atomic.hpp:120:37: warning: variadic templates only available with -std=c++11 or -std=gnu++11 template<typename Function, class ...ArgTypes> ^ ./boost/thread/pthread/once_atomic.hpp:121:108: warning: variadic templates only available with -std=c++11 or -std=gnu++11 inline void call_once(once_flag& flag, BOOST_THREAD_RV_REF(Function) f, BOOST_THREAD_RV_REF(ArgTypes)... args) ^ g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost nc-config --cflags || /bin/true -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include" -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/zlibbioc/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c boost/thread/src/pthread/thread.cpp -o boost/thread/src/pthread/thread.o In file included from ./boost/chrono/duration.hpp:42:0, from ./boost/chrono/time_point.hpp:33, from ./boost/thread/lock_types.hpp:22, from ./boost/thread/pthread/thread_data.hpp:12, from ./boost/thread/thread_only.hpp:17, from boost/thread/src/pthread/thread.cpp:11: ./boost/type_traits/common_type.hpp:69:22: warning: variadic templates only available with -std=c++11 or -std=gnu++11 template ^ ./boost/type_traits/common_type.hpp:149:46: warning: variadic templates only available with -std=c++11 or -std=gnu++11 template<typename T, typename U, typename... V> ^ In file included from ./boost/thread/detail/thread.hpp:21:0, from ./boost/thread/thread_only.hpp:22, from boost/thread/src/pthread/thread.cpp:11: ./boost/thread/detail/make_tuple_indices.hpp:35:26: warning: variadic templates only available with -std=c++11 or -std=gnu++11 template struct tuple_indices ^ ./boost/thread/detail/make_tuple_indices.hpp:41:46: warning: variadic templates only available with -std=c++11 or -std=gnu++11 template <std::size_t Sp, std::size_t ...Indices, std::size_t Ep> ^ ./boost/thread/detail/make_tuple_indices.hpp:47:46: warning: variadic templates only available with -std=c++11 or -std=gnu++11 template <std::size_t Ep, std::size_t ...Indices> ^ In file included from ./boost/thread/detail/thread.hpp:22:0, from ./boost/thread/thread_only.hpp:22, from boost/thread/src/pthread/thread.cpp:11: ./boost/thread/detail/invoke.hpp:242:51: warning: variadic templates only available with -std=c++11 or -std=gnu++11 template <class Ret, class A, class A0, class ...Args> ^ ./boost/thread/detail/invoke.hpp:249:28: warning: variadic templates only available with -std=c++11 or -std=gnu++11 invoke(Ret (A::f)(Args...), BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args) ^ ./boost/thread/detail/invoke.hpp:249:91: warning: variadic templates only available with -std=c++11 or -std=gnu++11 invoke(Ret (A::f)(Args...), BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args) ^ ./boost/thread/detail/invoke.hpp:254:51: warning: variadic templates only available with -std=c++11 or -std=gnu++11 template <class Ret, class A, class A0, class ...Args> ^ ./boost/thread/detail/invoke.hpp:261:28: warning: variadic templates only available with -std=c++11 or -std=gnu++11 invoke(Ret (A::f)(Args...) const, BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args) ^ ./boost/thread/detail/invoke.hpp:261:97: warning: variadic templates only available with -std=c++11 or -std=gnu++11 invoke(Ret (A::f)(Args...) const, BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args) ^ ./boost/thread/detail/invoke.hpp:266:51: warning: variadic templates only available with -std=c++11 or -std=gnu++11 template <class Ret, class A, class A0, class ...Args> ^ ./boost/thread/detail/invoke.hpp:273:28: warning: variadic templates only available with -std=c++11 or -std=gnu++11 invoke(Ret (A::f)(Args...) volatile, BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args) ^ ./boost/thread/detail/invoke.hpp:273:100: warning: variadic templates only available with -std=c++11 or -std=gnu++11 invoke(Ret (A::f)(Args...) volatile, BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args) ^ ./boost/thread/detail/invoke.hpp:278:51: warning: variadic templates only available with -std=c++11 or -std=gnu++11 template <class Ret, class A, class A0, class ...Args> ^ ./boost/thread/detail/invoke.hpp:285:28: warning: variadic templates only available with -std=c++11 or -std=gnu++11 invoke(Ret (A::f)(Args...) const volatile, BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args) ^ ./boost/thread/detail/invoke.hpp:285:106: warning: variadic templates only available with -std=c++11 or -std=gnu++11 invoke(Ret (A::f)(Args...) const volatile, BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args) ^ ./boost/thread/detail/invoke.hpp:293:51: warning: variadic templates only available with -std=c++11 or -std=gnu++11 template <class Ret, class A, class A0, class ...Args> ^ ./boost/thread/detail/invoke.hpp:300:28: warning: variadic templates only available with -std=c++11 or -std=gnu++11 invoke(Ret (A::f)(Args...), BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args) ^ ./boost/thread/detail/invoke.hpp:300:91: warning: variadic templates only available with -std=c++11 or -std=gnu++11 invoke(Ret (A::f)(Args...), BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args) ^ ./boost/thread/detail/invoke.hpp:305:51: warning: variadic templates only available with -std=c++11 or -std=gnu++11 template <class Ret, class A, class A0, class ...Args> ^ ./boost/thread/detail/invoke.hpp:312:28: warning: variadic templates only available with -std=c++11 or -std=gnu++11 invoke(Ret (A::f)(Args...) const, BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args) ^ ./boost/thread/detail/invoke.hpp:312:97: warning: variadic templates only available with -std=c++11 or -std=gnu++11 invoke(Ret (A::f)(Args...) const, BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args) ^ ./boost/thread/detail/invoke.hpp:317:51: warning: variadic templates only available with -std=c++11 or -std=gnu++11 template <class Ret, class A, class A0, class ...Args> ^ ./boost/thread/detail/invoke.hpp:324:28: warning: variadic templates only available with -std=c++11 or -std=gnu++11 invoke(Ret (A::f)(Args...) volatile, BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args) ^ ./boost/thread/detail/invoke.hpp:324:100: warning: variadic templates only available with -std=c++11 or -std=gnu++11 invoke(Ret (A::f)(Args...) volatile, BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args) ^ ./boost/thread/detail/invoke.hpp:329:51: warning: variadic templates only available with -std=c++11 or -std=gnu++11 template <class Ret, class A, class A0, class ...Args> ^ ./boost/thread/detail/invoke.hpp:336:28: warning: variadic templates only available with -std=c++11 or -std=gnu++11 invoke(Ret (A::f)(Args...) const volatile, BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args) ^ ./boost/thread/detail/invoke.hpp:336:106: warning: variadic templates only available with -std=c++11 or -std=gnu++11 invoke(Ret (A::f)(Args...) const volatile, BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args) ^ ./boost/thread/detail/invoke.hpp:398:42: warning: variadic templates only available with -std=c++11 or -std=gnu++11 template <class Ret, class Fp, class ...Args> ^ ./boost/thread/detail/invoke.hpp:405:68: warning: variadic templates only available with -std=c++11 or -std=gnu++11 invoke(BOOST_THREAD_RV_REF(Fp) f, BOOST_THREAD_RV_REF(Args) ...args) ^ ./boost/thread/detail/invoke.hpp:409:32: warning: variadic templates only available with -std=c++11 or -std=gnu++11 template <class Ret, class ...Args> ^ ./boost/thread/detail/invoke.hpp:411:24: warning: variadic templates only available with -std=c++11 or -std=gnu++11 invoke(Ret(f)(Args... ), BOOST_THREAD_RV_REF(Args) ...args) ^ ./boost/thread/detail/invoke.hpp:411:60: warning: variadic templates only available with -std=c++11 or -std=gnu++11 invoke(Ret(f)(Args... ), BOOST_THREAD_RV_REF(Args) ...args) ^ In file included from ./boost/thread/once.hpp:20:0, from boost/thread/src/pthread/thread.cpp:17: ./boost/thread/pthread/once_atomic.hpp:120:37: warning: variadic templates only available with -std=c++11 or -std=gnu++11 template<typename Function, class ...ArgTypes> ^ ./boost/thread/pthread/once_atomic.hpp:121:108: warning: variadic templates only available with -std=c++11 or -std=gnu++11 inline void call_once(once_flag& flag, BOOST_THREAD_RV_REF(Function) f, BOOST_THREAD_RV_REF(ArgTypes)... args) ^ boost/thread/src/pthread/thread.cpp: In function ‘boost::detail::thread_data_base boost::detail::get_current_thread_data()’: boost/thread/src/pthread/thread.cpp:140:88: error: no matching function for call to ‘call_once(boost::once_flag&, void (&)())’ boost::call_once(current_thread_tls_init_flag,create_current_thread_tls_key); ^ In file included from ./boost/thread/once.hpp:20:0, from boost/thread/src/pthread/thread.cpp:17: ./boost/thread/pthread/once_atomic.hpp:121:15: note: candidate: template<class Function, class ... ArgTypes> void boost::call_once(boost::once_flag&, boost::detail::thread_move_t, boost::detail::thread_move_t...) inline void call_once(once_flag& flag, BOOST_THREAD_RV_REF(Function) f, BOOST_THREAD_RV_REF(ArgTypes)... args) ^ ./boost/thread/pthread/once_atomic.hpp:121:15: note: template argument deduction/substitution failed: boost/thread/src/pthread/thread.cpp:140:88: note: mismatched types ‘boost::detail::thread_move_t’ and ‘void ()()’ boost::call_once(current_thread_tls_init_flag,create_current_thread_tls_key); ^ In file included from boost/thread/src/pthread/thread.cpp:17:0: ./boost/thread/once.hpp:35:13: note: candidate: template void boost::call_once(Function, boost::once_flag&) inline void call_once(Function func,once_flag& flag) ^ ./boost/thread/once.hpp:35:13: note: template argument deduction/substitution failed: boost/thread/src/pthread/thread.cpp:140:88: note: cannot convert ‘boost::detail::{anonymous}::create_current_thread_tls_key’ (type ‘void()’) to type ‘boost::once_flag&’ boost::call_once(current_thread_tls_init_flag,create_current_thread_tls_key); ^ boost/thread/src/pthread/thread.cpp: In function ‘void boost::detail::set_current_thread_data(boost::detail::thread_data_base)’: boost/thread/src/pthread/thread.cpp:146:88: error: no matching function for call to ‘call_once(boost::once_flag&, void (&)())’ boost::call_once(current_thread_tls_init_flag,create_current_thread_tls_key); ^ In file included from ./boost/thread/once.hpp:20:0, from boost/thread/src/pthread/thread.cpp:17: ./boost/thread/pthread/once_atomic.hpp:121:15: note: candidate: template<class Function, class ... ArgTypes> void boost::call_once(boost::once_flag&, boost::detail::thread_move_t, boost::detail::thread_move_t...) inline void call_once(once_flag& flag, BOOST_THREAD_RV_REF(Function) f, BOOST_THREAD_RV_REF(ArgTypes)... args) ^ ./boost/thread/pthread/once_atomic.hpp:121:15: note: template argument deduction/substitution failed: boost/thread/src/pthread/thread.cpp:146:88: note: mismatched types ‘boost::detail::thread_move_t’ and ‘void ()()’ boost::call_once(current_thread_tls_init_flag,create_current_thread_tls_key); ^ In file included from boost/thread/src/pthread/thread.cpp:17:0: ./boost/thread/once.hpp:35:13: note: candidate: template void boost::call_once(Function, boost::once_flag&) inline void call_once(Function func,once_flag& flag) ^ ./boost/thread/once.hpp:35:13: note: template argument deduction/substitution failed: boost/thread/src/pthread/thread.cpp:146:88: note: cannot convert ‘boost::detail::{anonymous}::create_current_thread_tls_key’ (type ‘void()’) to type ‘boost::once_flag&’ boost::call_once(current_thread_tls_init_flag,create_current_thread_tls_key); ^ /usr/lib/R/etc/Makeconf:143: recipe for target 'boost/thread/src/pthread/thread.o' failed make: * [boost/thread/src/pthread/thread.o] Error 1 ERROR: compilation failed for package ‘mzR’
• removing ‘/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/mzR’

The downloaded source packages are in ‘/tmp/Rtmpskg3Y4/downloaded_packages’ Old packages: 'boot', 'cluster', 'codetools', 'foreign', 'lattice', 'MASS', 'Matrix', 'mgcv', 'nlme', 'rpart', 'survival' Update all/some/none? [a/s/n]:

[sneumann]

Hi, so you seem to be on Ubuntu or Debian. Please apt-get install libnetcdf-dev and then retry biocLite("mzR") Yours, Steffen

[bevans-danforth]

Steffen,

I just tried that, same result. In the log above, and just now, there is this warning:

./boost/thread/detail/invoke.hpp:324:100: warning: variadic templates only available with -std=c++11 or -std=gnu++11 invoke(Ret (A::*f)(Args...) volatile, BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args)

Does this mean something relevant to the failure?

Thanks,

Brad

[sneumann]

Ah, since you have R-3.2.3 biocLite() is pulling the mzR_2.4.1 (see http://bioconductor.org/packages/3.2/bioc/html/mzR.html) which is pretty old and won't compile on recent distributions. Similarly you will get pretty old xcms-1.46.0 (http://bioconductor.org/packages/3.2/bioc/html/xcms.html) and other bioc packages.

I recommend to manually download recent packages from e.g. http://bioconductor.org/packages/release/bioc/html/mzR.html and manually R CMD INSTALL mzR_2.10.0.tar.gz.

If you use biocLite(xcms) this will then get you the xcms-1.46.0 on top of the current mzR-2.10.0.

Getting current BioC packages on a 18 month old R is going to be tedious, and may or not may work (will break if one of the underlying packages depends on some R-3.3 or R-3.4 feature).

Yours, Steffen

[bevans-danforth]

Steffen,

Using the mzR version you suggested did resolve the problem I had above, but a new one arose. I tried installing the newest version of R, but because I need to configure R with "--enable-R-shlib", R fails to make. This happens on R-3.4.0 down to R-3.2.5. I tried R-3.2.5 then used the instructions for getting the xcms dependencies then manually installed mzR as specified above, but I still get an error. the output of the console is below (what was maintained through the process).

from ./boost/boost/algorithm/string/trim.hpp:23, from ./boost/boost/algorithm/string.hpp:19, from pwiz/utility/misc/String.hpp:29, from pwiz/utility/misc/Filesystem.hpp:29, from pwiz/utility/misc/Filesystem.cpp:26: /usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here template<typename> class auto_ptr; ^ In file included from ./boost/boost/shared_ptr.hpp:17:0, from ./boost/boost/format/alt_sstream.hpp:21, from ./boost/boost/format/internals.hpp:23, from ./boost/boost/format.hpp:38, from pwiz/utility/misc/String.hpp:30, from pwiz/utility/misc/Filesystem.hpp:29, from pwiz/utility/misc/Filesystem.cpp:26: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’: ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this ); ^ In file included from /usr/include/c++/5/bits/locale_conv.h:41:0, from /usr/include/c++/5/locale:43, from ./boost/boost/algorithm/string/classification.hpp:15, from ./boost/boost/algorithm/string/trim.hpp:23, from ./boost/boost/algorithm/string.hpp:19, from pwiz/utility/misc/String.hpp:29, from pwiz/utility/misc/Filesystem.hpp:29, from pwiz/utility/misc/Filesystem.cpp:26: /usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here template<typename> class auto_ptr; ^ g++ -std=c++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5nc-config --cflags || /bin/true-I/usr/local/include -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include" -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/zlibbioc/include" -fpic -g -O2 -c pwiz/utility/misc/TabReader.cpp -o pwiz/utility/misc/TabReader.o In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28:0, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/TabReader.hpp:29, from pwiz/utility/misc/TabReader.cpp:24: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) ) ^ In file included from /usr/include/c++/5/memory:81:0, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/TabReader.hpp:29, from pwiz/utility/misc/TabReader.cpp:24: /usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here template<typename> class auto_ptr; ^ In file included from ./boost/boost/shared_ptr.hpp:17:0, from pwiz/utility/misc/TabReader.hpp:29, from pwiz/utility/misc/TabReader.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^ In file included from /usr/include/c++/5/memory:81:0, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/TabReader.hpp:29, from pwiz/utility/misc/TabReader.cpp:24: /usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here template<typename> class auto_ptr; ^ In file included from ./boost/boost/shared_ptr.hpp:17:0, from pwiz/utility/misc/TabReader.hpp:29, from pwiz/utility/misc/TabReader.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn() ^ In file included from /usr/include/c++/5/memory:81:0, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/TabReader.hpp:29, from pwiz/utility/misc/TabReader.cpp:24: /usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here template<typename> class auto_ptr; ^ In file included from ./boost/boost/shared_ptr.hpp:17:0, from pwiz/utility/misc/TabReader.hpp:29, from pwiz/utility/misc/TabReader.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn() ^ In file included from /usr/include/c++/5/memory:81:0, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/TabReader.hpp:29, from pwiz/utility/misc/TabReader.cpp:24: /usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here template<typename> class auto_ptr; ^ In file included from ./boost/boost/shared_ptr.hpp:17:0, from pwiz/utility/misc/TabReader.hpp:29, from pwiz/utility/misc/TabReader.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr<Y> & r ) ^ In file included from /usr/include/c++/5/memory:81:0, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/TabReader.hpp:29, from pwiz/utility/misc/TabReader.cpp:24: /usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here template<typename> class auto_ptr; ^ In file included from ./boost/boost/shared_ptr.hpp:17:0, from pwiz/utility/misc/TabReader.hpp:29, from pwiz/utility/misc/TabReader.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr<Y> && r ) ^ In file included from /usr/include/c++/5/memory:81:0, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/TabReader.hpp:29, from pwiz/utility/misc/TabReader.cpp:24: /usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here template<typename> class auto_ptr; ^ In file included from ./boost/boost/shared_ptr.hpp:17:0, from pwiz/utility/misc/TabReader.hpp:29, from pwiz/utility/misc/TabReader.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’: ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this ); ^ In file included from /usr/include/c++/5/memory:81:0, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/TabReader.hpp:29, from pwiz/utility/misc/TabReader.cpp:24: /usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here template<typename> class auto_ptr; ^ In file included from ./boost/boost/bind/mem_fn.hpp:25:0, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/utility/misc/TabReader.cpp:25: ./boost/boost/get_pointer.hpp: At global scope: ./boost/boost/get_pointer.hpp:27:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] template<class T> T * get_pointer(std::auto_ptr<T> const& p) ^ In file included from /usr/include/c++/5/memory:81:0, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/TabReader.hpp:29, from pwiz/utility/misc/TabReader.cpp:24: /usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here template<typename> class auto_ptr; ^ In file included from ./boost/boost/scoped_ptr.hpp:14:0, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/utility/misc/TabReader.cpp:25: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() ) ^ In file included from /usr/include/c++/5/memory:81:0, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/TabReader.hpp:29, from pwiz/utility/misc/TabReader.cpp:24: /usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here template<typename> class auto_ptr; ^ g++ -std=c++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5nc-config --cflags || /bin/true-I/usr/local/include -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include" -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/zlibbioc/include" -fpic -g -O2 -c pwiz/utility/misc/random_access_compressed_ifstream.cpp -o pwiz/utility/misc/random_access_compressed_ifstream.o In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28:0, from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/iostreams/device/file_descriptor.hpp:28, from pwiz/utility/misc/random_access_compressed_ifstream.cpp:75: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) ) ^ In file included from /usr/include/c++/5/bits/locale_conv.h:41:0, from /usr/include/c++/5/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from pwiz/utility/misc/random_access_compressed_ifstream.hpp:71, from pwiz/utility/misc/random_access_compressed_ifstream.cpp:67: /usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here template<typename> class auto_ptr; ^ In file included from ./boost/boost/shared_ptr.hpp:17:0, from ./boost/boost/iostreams/device/file_descriptor.hpp:28, from pwiz/utility/misc/random_access_compressed_ifstream.cpp:75: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^ In file included from /usr/include/c++/5/bits/locale_conv.h:41:0, from /usr/include/c++/5/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from pwiz/utility/misc/random_access_compressed_ifstream.hpp:71, from pwiz/utility/misc/random_access_compressed_ifstream.cpp:67: /usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here template<typename> class auto_ptr; ^ In file included from ./boost/boost/shared_ptr.hpp:17:0, from ./boost/boost/iostreams/device/file_descriptor.hpp:28, from pwiz/utility/misc/random_access_compressed_ifstream.cpp:75: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn() ^ In file included from /usr/include/c++/5/bits/locale_conv.h:41:0, from /usr/include/c++/5/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from pwiz/utility/misc/random_access_compressed_ifstream.hpp:71, from pwiz/utility/misc/random_access_compressed_ifstream.cpp:67: /usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here template<typename> class auto_ptr; ^ In file included from ./boost/boost/shared_ptr.hpp:17:0, from ./boost/boost/iostreams/device/file_descriptor.hpp:28, from pwiz/utility/misc/random_access_compressed_ifstream.cpp:75: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn() ^ In file included from /usr/include/c++/5/bits/locale_conv.h:41:0, from /usr/include/c++/5/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from pwiz/utility/misc/random_access_compressed_ifstream.hpp:71, from pwiz/utility/misc/random_access_compressed_ifstream.cpp:67: /usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here template<typename> class auto_ptr; ^ In file included from ./boost/boost/shared_ptr.hpp:17:0, from ./boost/boost/iostreams/device/file_descriptor.hpp:28, from pwiz/utility/misc/random_access_compressed_ifstream.cpp:75: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr<Y> & r ) ^ In file included from /usr/include/c++/5/bits/locale_conv.h:41:0, from /usr/include/c++/5/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from pwiz/utility/misc/random_access_compressed_ifstream.hpp:71, from pwiz/utility/misc/random_access_compressed_ifstream.cpp:67: /usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here template<typename> class auto_ptr; ^ In file included from ./boost/boost/shared_ptr.hpp:17:0, from ./boost/boost/iostreams/device/file_descriptor.hpp:28, from pwiz/utility/misc/random_access_compressed_ifstream.cpp:75: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr<Y> && r ) ^ In file included from /usr/include/c++/5/bits/locale_conv.h:41:0, from /usr/include/c++/5/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from pwiz/utility/misc/random_access_compressed_ifstream.hpp:71, from pwiz/utility/misc/random_access_compressed_ifstream.cpp:67: /usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here template<typename> class auto_ptr; ^ In file included from ./boost/boost/shared_ptr.hpp:17:0, from ./boost/boost/iostreams/device/file_descriptor.hpp:28, from pwiz/utility/misc/random_access_compressed_ifstream.cpp:75: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’: ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this ); ^ In file included from /usr/include/c++/5/bits/locale_conv.h:41:0, from /usr/include/c++/5/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from pwiz/utility/misc/random_access_compressed_ifstream.hpp:71, from pwiz/utility/misc/random_access_compressed_ifstream.cpp:67: /usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here template<typename> class auto_ptr; ^ In file included from ./boost/boost/bind/mem_fn.hpp:25:0, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/utility/misc/random_access_compressed_ifstream.cpp:82: ./boost/boost/get_pointer.hpp: At global scope: ./boost/boost/get_pointer.hpp:27:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] template<class T> T * get_pointer(std::auto_ptr<T> const& p) ^ In file included from /usr/include/c++/5/bits/locale_conv.h:41:0, from /usr/include/c++/5/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from pwiz/utility/misc/random_access_compressed_ifstream.hpp:71, from pwiz/utility/misc/random_access_compressed_ifstream.cpp:67: /usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here template<typename> class auto_ptr; ^ In file included from ./boost/boost/scoped_ptr.hpp:14:0, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/utility/misc/random_access_compressed_ifstream.cpp:82: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() ) ^ In file included from /usr/include/c++/5/bits/locale_conv.h:41:0, from /usr/include/c++/5/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from pwiz/utility/misc/random_access_compressed_ifstream.hpp:71, from pwiz/utility/misc/random_access_compressed_ifstream.cpp:67: /usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here template<typename> class auto_ptr; ^ In file included from ./boost/boost/thread/thread.hpp:13:0, from ./boost/boost/thread.hpp:13, from pwiz/utility/misc/random_access_compressed_ifstream.cpp:83: ./boost/boost/thread/detail/thread_group.hpp: In member function ‘boost::thread* boost::thread_group::create_thread(F)’: ./boost/boost/thread/detail/thread_group.hpp:78:18: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr<thread> new_thread(new thread(threadfunc)); ^ In file included from /usr/include/c++/5/bits/locale_conv.h:41:0, from /usr/include/c++/5/locale:43, from ./boost/boost/iostreams/detail/config/codecvt.hpp:62, from ./boost/boost/iostreams/positioning.hpp:21, from pwiz/utility/misc/random_access_compressed_ifstream.hpp:71, from pwiz/utility/misc/random_access_compressed_ifstream.cpp:67: /usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here template<typename> class auto_ptr; ^ g++ -std=c++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5nc-config --cflags || /bin/true-I/usr/local/include -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include" -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/zlibbioc/include" -fpic -g -O2 -c pwiz/utility/misc/SHA1.cpp -o pwiz/utility/misc/SHA1.o In file included from ./boost/boost/scoped_ptr.hpp:14:0, from ./boost_aux/boost/nowide/fstream.hpp:14, from pwiz/utility/misc/SHA1.cpp:17: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() ) ^ In file included from /usr/include/c++/5/memory:81:0, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from pwiz/utility/misc/SHA1.cpp:17: /usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here template<typename> class auto_ptr; ^ In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28:0, from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/filesystem/path.hpp:29, from ./boost/boost/filesystem/operations.hpp:25, from pwiz/utility/misc/SHA1.cpp:18: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) ) ^ In file included from /usr/include/c++/5/memory:81:0, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from pwiz/utility/misc/SHA1.cpp:17: /usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here template<typename> class auto_ptr; ^ In file included from ./boost/boost/shared_ptr.hpp:17:0, from ./boost/boost/filesystem/path.hpp:29, from ./boost/boost/filesystem/operations.hpp:25, from pwiz/utility/misc/SHA1.cpp:18: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^ In file included from /usr/include/c++/5/memory:81:0, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from pwiz/utility/misc/SHA1.cpp:17: /usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here template<typename> class auto_ptr; ^ In file included from ./boost/boost/shared_ptr.hpp:17:0, from ./boost/boost/filesystem/path.hpp:29, from ./boost/boost/filesystem/operations.hpp:25, from pwiz/utility/misc/SHA1.cpp:18: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn() ^ In file included from /usr/include/c++/5/memory:81:0, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from pwiz/utility/misc/SHA1.cpp:17: /usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here template<typename> class auto_ptr; ^ In file included from ./boost/boost/shared_ptr.hpp:17:0, from ./boost/boost/filesystem/path.hpp:29, from ./boost/boost/filesystem/operations.hpp:25, from pwiz/utility/misc/SHA1.cpp:18: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn() ^ In file included from /usr/include/c++/5/memory:81:0, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from pwiz/utility/misc/SHA1.cpp:17: /usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here template<typename> class auto_ptr; ^ In file included from ./boost/boost/shared_ptr.hpp:17:0, from ./boost/boost/filesystem/path.hpp:29, from ./boost/boost/filesystem/operations.hpp:25, from pwiz/utility/misc/SHA1.cpp:18: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr<Y> & r ) ^ In file included from /usr/include/c++/5/memory:81:0, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from pwiz/utility/misc/SHA1.cpp:17: /usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here template<typename> class auto_ptr; ^ In file included from ./boost/boost/shared_ptr.hpp:17:0, from ./boost/boost/filesystem/path.hpp:29, from ./boost/boost/filesystem/operations.hpp:25, from pwiz/utility/misc/SHA1.cpp:18: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr<Y> && r ) ^ In file included from /usr/include/c++/5/memory:81:0, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from pwiz/utility/misc/SHA1.cpp:17: /usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here template<typename> class auto_ptr; ^ In file included from ./boost/boost/shared_ptr.hpp:17:0, from ./boost/boost/filesystem/path.hpp:29, from ./boost/boost/filesystem/operations.hpp:25, from pwiz/utility/misc/SHA1.cpp:18: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’: ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this ); ^ In file included from /usr/include/c++/5/memory:81:0, from ./boost/boost/smart_ptr/scoped_ptr.hpp:21, from ./boost/boost/scoped_ptr.hpp:14, from ./boost_aux/boost/nowide/fstream.hpp:14, from pwiz/utility/misc/SHA1.cpp:17: /usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here template<typename> class auto_ptr; ^ g++ -std=c++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5nc-config --cflags || /bin/true-I/usr/local/include -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include" -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/zlibbioc/include" -fpic -g -O2 -c pwiz/utility/misc/SHA1Calculator.cpp -o pwiz/utility/misc/SHA1Calculator.o In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28:0, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/SHA1Calculator.cpp:32: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) ) ^ In file included from /usr/include/c++/5/memory:81:0, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/SHA1Calculator.cpp:32: /usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here template<typename> class auto_ptr; ^ In file included from ./boost/boost/shared_ptr.hpp:17:0, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/SHA1Calculator.cpp:32: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^ In file included from /usr/include/c++/5/memory:81:0, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/SHA1Calculator.cpp:32: /usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here template<typename> class auto_ptr; ^ In file included from ./boost/boost/shared_ptr.hpp:17:0, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/SHA1Calculator.cpp:32: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn() ^ In file included from /usr/include/c++/5/memory:81:0, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/SHA1Calculator.cpp:32: /usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here template<typename> class auto_ptr; ^ In file included from ./boost/boost/shared_ptr.hpp:17:0, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/SHA1Calculator.cpp:32: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn() ^ In file included from /usr/include/c++/5/memory:81:0, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/SHA1Calculator.cpp:32: /usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here template<typename> class auto_ptr; ^ In file included from ./boost/boost/shared_ptr.hpp:17:0, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/SHA1Calculator.cpp:32: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr<Y> & r ) ^ In file included from /usr/include/c++/5/memory:81:0, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/SHA1Calculator.cpp:32: /usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here template<typename> class auto_ptr; ^ In file included from ./boost/boost/shared_ptr.hpp:17:0, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/SHA1Calculator.cpp:32: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr<Y> && r ) ^ In file included from /usr/include/c++/5/memory:81:0, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/SHA1Calculator.cpp:32: /usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here template<typename> class auto_ptr; ^ In file included from ./boost/boost/shared_ptr.hpp:17:0, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/SHA1Calculator.cpp:32: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’: ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this ); ^ In file included from /usr/include/c++/5/memory:81:0, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/SHA1Calculator.cpp:32: /usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here template<typename> class auto_ptr; ^ In file included from ./boost/boost/bind/mem_fn.hpp:25:0, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from ./pwiz/utility/misc/String.hpp:29, from ./pwiz/utility/misc/Std.hpp:31, from pwiz/utility/misc/SHA1Calculator.cpp:33: ./boost/boost/get_pointer.hpp: At global scope: ./boost/boost/get_pointer.hpp:27:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] template<class T> T * get_pointer(std::auto_ptr<T> const& p) ^ In file included from /usr/include/c++/5/memory:81:0, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/SHA1Calculator.cpp:32: /usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here template<typename> class auto_ptr; ^ In file included from ./boost/boost/scoped_ptr.hpp:14:0, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/utility/misc/SHA1Calculator.cpp:33: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() ) ^ In file included from /usr/include/c++/5/memory:81:0, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/SHA1Calculator.cpp:32: /usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here template<typename> class auto_ptr; ^ g++ -std=c++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5nc-config --cflags || /bin/true-I/usr/local/include -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include" -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/zlibbioc/include" -fpic -g -O2 -c pwiz/utility/misc/sha1calc.cpp -o pwiz/utility/misc/sha1calc.o In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28:0, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/sha1calc.cpp:24: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) ) ^ In file included from /usr/include/c++/5/memory:81:0, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/sha1calc.cpp:24: /usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here template<typename> class auto_ptr; ^ In file included from ./boost/boost/shared_ptr.hpp:17:0, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/sha1calc.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^ In file included from /usr/include/c++/5/memory:81:0, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/sha1calc.cpp:24: /usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here template<typename> class auto_ptr; ^ In file included from ./boost/boost/shared_ptr.hpp:17:0, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/sha1calc.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn() ^ In file included from /usr/include/c++/5/memory:81:0, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/sha1calc.cpp:24: /usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here template<typename> class auto_ptr; ^ In file included from ./boost/boost/shared_ptr.hpp:17:0, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/sha1calc.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn() ^ In file included from /usr/include/c++/5/memory:81:0, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/sha1calc.cpp:24: /usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here template<typename> class auto_ptr; ^ In file included from ./boost/boost/shared_ptr.hpp:17:0, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/sha1calc.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr<Y> & r ) ^ In file included from /usr/include/c++/5/memory:81:0, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/sha1calc.cpp:24: /usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here template<typename> class auto_ptr; ^ In file included from ./boost/boost/shared_ptr.hpp:17:0, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/sha1calc.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr<Y> && r ) ^ In file included from /usr/include/c++/5/memory:81:0, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/sha1calc.cpp:24: /usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here template<typename> class auto_ptr; ^ In file included from ./boost/boost/shared_ptr.hpp:17:0, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/sha1calc.cpp:24: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’: ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this ); ^ In file included from /usr/include/c++/5/memory:81:0, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/sha1calc.cpp:24: /usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here template<typename> class auto_ptr; ^ In file included from ./boost/boost/bind/mem_fn.hpp:25:0, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/function/detail/prologue.hpp:18, from ./boost/boost/function.hpp:24, from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18, from ./boost/boost/algorithm/string/find_iterator.hpp:24, from ./boost/boost/algorithm/string/iter_find.hpp:27, from ./boost/boost/algorithm/string/split.hpp:16, from ./boost/boost/algorithm/string.hpp:23, from pwiz/utility/misc/String.hpp:29, from pwiz/utility/misc/Filesystem.hpp:29, from pwiz/utility/misc/unit.hpp:30, from pwiz/utility/misc/sha1calc.cpp:25: ./boost/boost/get_pointer.hpp: At global scope: ./boost/boost/get_pointer.hpp:27:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] template<class T> T * get_pointer(std::auto_ptr<T> const& p) ^ In file included from /usr/include/c++/5/memory:81:0, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/sha1calc.cpp:24: /usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here template<typename> class auto_ptr; ^ In file included from ./boost/boost/scoped_ptr.hpp:14:0, from ./boost_aux/boost/nowide/fstream.hpp:14, from ./pwiz/utility/misc/Stream.hpp:30, from ./pwiz/utility/misc/Std.hpp:32, from pwiz/utility/misc/sha1calc.cpp:26: ./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() ) ^ In file included from /usr/include/c++/5/memory:81:0, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from pwiz/utility/misc/SHA1Calculator.hpp:28, from pwiz/utility/misc/sha1calc.cpp:24: /usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here template<typename> class auto_ptr; ^ g++ -std=c++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5nc-config --cflags || /bin/true-I/usr/local/include -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include" -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/zlibbioc/include" -fpic -g -O2 -c random_access_gzFile.cpp -o random_access_gzFile.o g++ -std=c++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5nc-config --cflags || /bin/true-I/usr/local/include -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include" -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/zlibbioc/include" -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o g++ -std=c++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5nc-config --cflags || /bin/true-I/usr/local/include -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include" -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/zlibbioc/include" -fpic -g -O2 -c boost/libs/thread/src/pthread/once.cpp -o boost/libs/thread/src/pthread/once.o In file included from ./boost/boost/bind/mem_fn.hpp:25:0, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/bind/bind.hpp:26, from ./boost/boost/bind.hpp:22, from ./boost/boost/thread/pthread/once_atomic.hpp:19, from ./boost/boost/thread/once.hpp:20, from boost/libs/thread/src/pthread/./once_atomic.cpp:9, from boost/libs/thread/src/pthread/once.cpp:8: ./boost/boost/get_pointer.hpp:27:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] template<class T> T * get_pointer(std::auto_ptr<T> const& p) ^ In file included from /usr/include/c++/5/memory:81:0, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/get_pointer.hpp:14, from ./boost/boost/bind/mem_fn.hpp:25, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/bind/bind.hpp:26, from ./boost/boost/bind.hpp:22, from ./boost/boost/thread/pthread/once_atomic.hpp:19, from ./boost/boost/thread/once.hpp:20, from boost/libs/thread/src/pthread/./once_atomic.cpp:9, from boost/libs/thread/src/pthread/once.cpp:8: /usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here template<typename> class auto_ptr; ^ g++ -std=c++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5nc-config --cflags || /bin/true-I/usr/local/include -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include" -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/zlibbioc/include" -fpic -g -O2 -c boost/libs/thread/src/pthread/thread.cpp -o boost/libs/thread/src/pthread/thread.o In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28:0, from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/date_time/time_clock.hpp:17, from ./boost/boost/thread/thread_time.hpp:9, from ./boost/boost/thread/lock_types.hpp:18, from ./boost/boost/thread/pthread/thread_data.hpp:12, from ./boost/boost/thread/thread_only.hpp:17, from boost/libs/thread/src/pthread/thread.cpp:11: ./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) ) ^ In file included from /usr/include/c++/5/memory:81:0, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/date_time/time_clock.hpp:17, from ./boost/boost/thread/thread_time.hpp:9, from ./boost/boost/thread/lock_types.hpp:18, from ./boost/boost/thread/pthread/thread_data.hpp:12, from ./boost/boost/thread/thread_only.hpp:17, from boost/libs/thread/src/pthread/thread.cpp:11: /usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here template<typename> class auto_ptr; ^ In file included from ./boost/boost/shared_ptr.hpp:17:0, from ./boost/boost/date_time/time_clock.hpp:17, from ./boost/boost/thread/thread_time.hpp:9, from ./boost/boost/thread/lock_types.hpp:18, from ./boost/boost/thread/pthread/thread_data.hpp:12, from ./boost/boost/thread/thread_only.hpp:17, from boost/libs/thread/src/pthread/thread.cpp:11: ./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^ In file included from /usr/include/c++/5/memory:81:0, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/date_time/time_clock.hpp:17, from ./boost/boost/thread/thread_time.hpp:9, from ./boost/boost/thread/lock_types.hpp:18, from ./boost/boost/thread/pthread/thread_data.hpp:12, from ./boost/boost/thread/thread_only.hpp:17, from boost/libs/thread/src/pthread/thread.cpp:11: /usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here template<typename> class auto_ptr; ^ In file included from ./boost/boost/shared_ptr.hpp:17:0, from ./boost/boost/date_time/time_clock.hpp:17, from ./boost/boost/thread/thread_time.hpp:9, from ./boost/boost/thread/lock_types.hpp:18, from ./boost/boost/thread/pthread/thread_data.hpp:12, from ./boost/boost/thread/thread_only.hpp:17, from boost/libs/thread/src/pthread/thread.cpp:11: ./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn() ^ In file included from /usr/include/c++/5/memory:81:0, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/date_time/time_clock.hpp:17, from ./boost/boost/thread/thread_time.hpp:9, from ./boost/boost/thread/lock_types.hpp:18, from ./boost/boost/thread/pthread/thread_data.hpp:12, from ./boost/boost/thread/thread_only.hpp:17, from boost/libs/thread/src/pthread/thread.cpp:11: /usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here template<typename> class auto_ptr; ^ In file included from ./boost/boost/shared_ptr.hpp:17:0, from ./boost/boost/date_time/time_clock.hpp:17, from ./boost/boost/thread/thread_time.hpp:9, from ./boost/boost/thread/lock_types.hpp:18, from ./boost/boost/thread/pthread/thread_data.hpp:12, from ./boost/boost/thread/thread_only.hpp:17, from boost/libs/thread/src/pthread/thread.cpp:11: ./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn() ^ In file included from /usr/include/c++/5/memory:81:0, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/date_time/time_clock.hpp:17, from ./boost/boost/thread/thread_time.hpp:9, from ./boost/boost/thread/lock_types.hpp:18, from ./boost/boost/thread/pthread/thread_data.hpp:12, from ./boost/boost/thread/thread_only.hpp:17, from boost/libs/thread/src/pthread/thread.cpp:11: /usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here template<typename> class auto_ptr; ^ In file included from ./boost/boost/shared_ptr.hpp:17:0, from ./boost/boost/date_time/time_clock.hpp:17, from ./boost/boost/thread/thread_time.hpp:9, from ./boost/boost/thread/lock_types.hpp:18, from ./boost/boost/thread/pthread/thread_data.hpp:12, from ./boost/boost/thread/thread_only.hpp:17, from boost/libs/thread/src/pthread/thread.cpp:11: ./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr<Y> & r ) ^ In file included from /usr/include/c++/5/memory:81:0, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/date_time/time_clock.hpp:17, from ./boost/boost/thread/thread_time.hpp:9, from ./boost/boost/thread/lock_types.hpp:18, from ./boost/boost/thread/pthread/thread_data.hpp:12, from ./boost/boost/thread/thread_only.hpp:17, from boost/libs/thread/src/pthread/thread.cpp:11: /usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here template<typename> class auto_ptr; ^ In file included from ./boost/boost/shared_ptr.hpp:17:0, from ./boost/boost/date_time/time_clock.hpp:17, from ./boost/boost/thread/thread_time.hpp:9, from ./boost/boost/thread/lock_types.hpp:18, from ./boost/boost/thread/pthread/thread_data.hpp:12, from ./boost/boost/thread/thread_only.hpp:17, from boost/libs/thread/src/pthread/thread.cpp:11: ./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr<Y> && r ) ^ In file included from /usr/include/c++/5/memory:81:0, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/date_time/time_clock.hpp:17, from ./boost/boost/thread/thread_time.hpp:9, from ./boost/boost/thread/lock_types.hpp:18, from ./boost/boost/thread/pthread/thread_data.hpp:12, from ./boost/boost/thread/thread_only.hpp:17, from boost/libs/thread/src/pthread/thread.cpp:11: /usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here template<typename> class auto_ptr; ^ In file included from ./boost/boost/shared_ptr.hpp:17:0, from ./boost/boost/date_time/time_clock.hpp:17, from ./boost/boost/thread/thread_time.hpp:9, from ./boost/boost/thread/lock_types.hpp:18, from ./boost/boost/thread/pthread/thread_data.hpp:12, from ./boost/boost/thread/thread_only.hpp:17, from boost/libs/thread/src/pthread/thread.cpp:11: ./boost/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’: ./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this ); ^ In file included from /usr/include/c++/5/memory:81:0, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/date_time/time_clock.hpp:17, from ./boost/boost/thread/thread_time.hpp:9, from ./boost/boost/thread/lock_types.hpp:18, from ./boost/boost/thread/pthread/thread_data.hpp:12, from ./boost/boost/thread/thread_only.hpp:17, from boost/libs/thread/src/pthread/thread.cpp:11: /usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here template<typename> class auto_ptr; ^ In file included from ./boost/boost/bind/mem_fn.hpp:25:0, from ./boost/boost/mem_fn.hpp:22, from ./boost/boost/bind/bind.hpp:26, from ./boost/boost/bind.hpp:22, from ./boost/boost/thread/detail/thread.hpp:30, from ./boost/boost/thread/thread_only.hpp:22, from boost/libs/thread/src/pthread/thread.cpp:11: ./boost/boost/get_pointer.hpp: At global scope: ./boost/boost/get_pointer.hpp:27:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] template<class T> T * get_pointer(std::auto_ptr<T> const& p) ^ In file included from /usr/include/c++/5/memory:81:0, from ./boost/boost/config/no_tr1/memory.hpp:21, from ./boost/boost/smart_ptr/shared_ptr.hpp:23, from ./boost/boost/shared_ptr.hpp:17, from ./boost/boost/date_time/time_clock.hpp:17, from ./boost/boost/thread/thread_time.hpp:9, from ./boost/boost/thread/lock_types.hpp:18, from ./boost/boost/thread/pthread/thread_data.hpp:12, from ./boost/boost/thread/thread_only.hpp:17, from boost/libs/thread/src/pthread/thread.cpp:11: /usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here template<typename> class auto_ptr; ^ g++ -std=c++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5nc-config --cflags || /bin/true-I/usr/local/include -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include" -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/zlibbioc/include" -fpic -g -O2 -c rampR.cpp -o rampR.o gcc -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5nc-config --cflags || /bin/true` -I/usr/local/include -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include" -I"/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/zlibbioc/include" -fpic -g -O2 -c R_init_mzR.c -o R_init_mzR.o g++ -std=c++11 -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o mzR.so 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... installing to /home/massspec/R/x86_64-pc-linux-gnu-library/3.2/mzR/libs R inst ** preparing package for lazy loading Creating a generic function for ‘close’ from package ‘base’ in package ‘mzR’ Error in setMethod("chromatogram", "mzRpwiz", function(object, chrom) { : no existing definition for function ‘chromatogram’ Error : unable to load R code in package ‘mzR’ ERROR: lazy loading failed for package ‘mzR’

• removing ‘/home/massspec/R/x86_64-pc-linux-gnu-library/3.2/mzR’ Warning in install.packages : installation of package ‘/home/massspec/Desktop/Installed Packages for MetaboAnalyst/mzR_2.10.0.tar.gz’ had non-zero exit status`

It seems now the problem is with "chomatogram" and "mzRpwiz". Do you have a suggestion? Maybe a list of older xcms packages that will work on an older R version such as 3.2.5?

Thanks,

Brad

[sneumann]

Maybe I still need more context: what OS exactly are you running ? WHich gcc is used ? apt-get install r-base on Ubuntu should give you /usr/lib/R/lib/libR.so which is in r-base-core . so I don't understand the need for manual R compilation. WIth a current R, biocLite() should get you an mzR that is recent enough for the gcc in your OS. Or what exactly are your special version requirements ?

[bevans-danforth]

Steffen,

We are using Ubuntu 16.04, not sure about the gcc, it is what came with the OS. The reason we need to compile R is that we need to configure it with shared libraries enabled. In any case we were able to finally put things together and get xcms to work. Thanks fo your help and isntrucitons.

Best,

Brad

Bradley S. Evans, Ph.D Director, Proteomics & Mass Spectrometry Facility Donald Danforth Plant Science Center 975 North Warson Road Saint Louis, MO 63132 bevans@danforthcenter.orgmailto:bevans@danforthcenter.org pmsf pagehttp://www.danforthcenter.org/scientists-research/core-technologies/proteomics-mass-spectrometry

From: sneumann [mailto:notifications@github.com] Sent: Friday, May 05, 2017 3:43 AM To: Bioconductor/bioc_docker Cc: Evans, Bradley; Author Subject: Re: [Bioconductor/bioc_docker] XCMS installation problem (#20)

Maybe I still need more context: what OS exactly are you running ? WHich gcc is used ? apt-get install r-base on Ubuntu should give you /usr/lib/R/lib/libR.so which is in r-base-core . so I don't understand the need for manual R compilation. WIth a current R, biocLite() should get you an mzR that is recent enough for the gcc in your OS. Or what exactly are your special version requirements ?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/Bioconductor/bioc_docker/issues/20#issuecomment-299412692, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AbFYtyCoVBMuOrVFYh9L9hdZMbj7xDz8ks5r2uEegaJpZM4NQ5l4.

[sneumann]

Cool, thanks for letting me know. Yours, Steffen