sneumann/mzr

This is the git repository matching the Bioconductor package mzR: parser for netCDF, mzXML, mzData and mzML files (mass spectrometry data)

Continuous integration

The mzR project master branch is subjected to CI using travis:

The devel branch is tested on multiple architectures by the BioC build farm:

http://bioconductor.org/checkResults/devel/bioc-LATEST/mzR/

Installation

Installation on macOS

If you install from source, you first need to install the netCDF headers and libraries: brew install netcdf, and then instal mzR the BioC way via:

if (!requireNamespace("BiocManager", quietly=TRUE))
    install.packages("BiocManager")
BiocManager::install("mzR", suppressUpdates = TRUE)

Installation on Linux

We are not shipping the full set of boost headers due to size restrictions. This might cause compilation failure due to missing files. We have tested several OS and compiler build environments successfully, please report any compilation failures at https://github.com/sneumann/mzR/issues and we'll add the missing files.

mzR-2.9.1 with boost-1.59.0 has been tested on the following compilers:

On the BioC build farm (http://bioconductor.org/checkResults/devel/bioc-LATEST/mzR/)

• malbec2 (Ubuntu 16.04.1, gcc-5.4.0)
• tokay2 (Windows Server 2012 R2, MinGW-W64-4.9.3)
• Failling oaxaca (Apple clang 3.5svn / 600.0.57)

Also on:

• Debian stretch/sid (gcc-5.4.0)
• Ubuntu 16.04 (clang 3.8.0)
• Ubuntu 16.04 (gcc-5.4.0)
• Ubuntu 14.04 (gcc-4.8.2)
• Ubuntu 12.04 (gcc-4.6.3)

Contributions

Please read the contributions guide and code of conduct.

mzr's Issues

multiple definition of `strncasecmp' with the new toolschain

Hi, currently we have build issues on the windows machine of the build farm
for both http://bioconductor.org/checkResults/devel/bioc-LATEST/mzR/moscato2-buildsrc.html
and http://bioconductor.org/spb_reports/mzR_2.5.5.1_buildreport_20160404074007.html

Somehow, two the *.o from both *.c files (rnetCDF.c and R_init_mzR.o) include
the symbols from the stdlib, thus linking them results in multiple definition ofstrncasecmp'`.
I tried both the ULDAR and standard linker, both give the same issue. I failed to set up
a local working development on Windows, so I can't help much here.

Yours,
Steffen

netCDF backend should implement runInfo() and instrumentInfo()

We should implement something to at least return
some minimal information for:

> runInfo(ms)
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘runInfo’ for signature ‘"mzRnetCDF"’
> instrumentInfo(ms)
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘instrumentInfo’ for signature ‘"mzRnetCDF"’

Yours, Steffen

segfault in psms

The error initially happened with a bigger file (15 M) [1] in a more complex setup. The simplified example below systematically produces the segfault at the second call to psm. Below is a simple example with a small file (same as used in the openIDfile example). The number of iterations to get the error may vary.

> library("mzR")
Loading required package: Rcpp
> f <- system.file("mzid", "Tandem.mzid.gz", package="msdata")
> x <- openIDfile(f)
> tmp0 <- psms(x)
> tmp0 <- psms(x) ## crashes systematically with big file 
> tmp0 <- psms(x)
> tmp <- replicate(100, tmp0 <- psms(x))
> tmp <- replicate(100, tmp0 <- psms(x))
> tmp <- replicate(100, tmp0 <- psms(x))
 *** caught segfault ***
address 0x100000019, cause 'memory not mapped'

Traceback:
 1: .External(list(name = "CppMethod__invoke_notvoid", address = <pointer: 0x2139cf0>,     dll = list(name = "Rcpp", path = "/home/lg390/R/x86_64-unknown-linux-gnu-library/3.2/Rcpp/libs/Rcpp.so",         dynamicLookup = TRUE, handle = <pointer: 0x32cf740>,         info = <pointer: 0x7f62ef7a3920>), numParameters = -1L),     <pointer: 0x48e57a0>, <pointer: 0x48e5970>, .pointer)
 2: object@backend$getPsmInfo()
 3: psms(x)
 4: psms(x)
 5: FUN(c(0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L)[[64L]], ...)
 6: lapply(X = X, FUN = FUN, ...)
 7: sapply(integer(n), eval.parent(substitute(function(...) expr)),     simplify = simplify)
 8: replicate(100, tmp0 <- psms(x))

This is not an isolated case; I stumbled on this several times with different files. @thirdwing, could you have a look? Thanks.

[1] http://proteome.sysbiol.cam.ac.uk/lgatto/files/Adult_CD8Tcells_Gel_Elite_44_f01.mzid

Link warning outdated

Reported by Emma Schymanski:

Is the mzR warning message out of date?

Warning message:
In fun(libname, pkgname) :
  mzR has been built against a different Rcpp version (0.11.5)
than is installed on your system (0.11.6). This might lead to errors
when loading mzR. If you encounter such issues, please send a report,
including the output of sessionInfo() to the Bioc mailing list at 
http://www.bioconductor.org/help/mailing-list. For details see also
https://github.com/sneumann/mzR/wiki/mzR-Rcpp-compiler-linker-issue.

-> this points people to the mailing list, whereas now they should visit the support site?
https://support.bioconductor.org/

Proteowizard has a newer version of src/pwiz/data/common/cv.cpp that includes PeptideShaker

release mzR fails to install on debian with g++ 5.3.1-13

biocLite('mzR') fails on R-3.2.4 revised on Debian Stretch with g++ 5.3.1-13.

You can reproduce this with docker as follows:

docker run -ti --rm bioconductor/mzrprob bash

That will pull down the docker image and start a container and a bash shell inside it. You can then do:

R
biocLite('mzR')

When I do this, the end of my output looks like the following.
This is blocking the creation of Bioconductor's proteomics docker container.

Here are the last lines of the output:

./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<T>, boost::detail::thread_move_t<Args>...)
   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<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<class Function> 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<T>, boost::detail::thread_move_t<Args>...)
   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<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<class Function> 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 ‘/usr/local/lib/R/site-library/mzR’

File handles are not closed for backend pwiz

Apparently, the file handles are not closed for backend = "pwiz":

library(mzR)
library(msdata)
f <- msdata::proteomics(full.names = TRUE, pattern = "TMT_Erwinia")
for (i in 1:1000) {
    msd <- mzR::openMSfile(f, backend = "pwiz")
    mzR::close(msd)
}

Throws the error:

Error: failed opening file: Too many open files: unspecified iostream_category error

Re-instantiate ramp.R

During the migration to a current boost and pwiz code,
the ramp.R / rampR.cpp interface got dropped. Get the code back in,
modify rampR.cpp to compile with new boost.

Error in get(name, envir = asNamespace(pkg), inherits = FALSE) : 
  object 'rampIsFile' not found

Compilation of mzR fails

Hi can't figure out what's wrong. I

> biocLite("mzR")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.1 (BiocInstaller 1.18.3), R version
  3.2.0.
Installing package(s) ‘mzR’
trying URL 'http://bioconductor.org/packages/3.1/bioc/src/contrib/mzR_2.2.1.tar.gz'
Content type 'application/x-gzip' length 14657073 bytes (14.0 MB)
==================================================
downloaded 14.0 MB

* 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/data/common/MemoryIndex.o ./pwiz/data/common/CVTranslator.o ./pwiz/data/common/cv.o ./pwiz/data/common/ParamTypes.o ./pwiz/data/common/BinaryIndexStream.o ./pwiz/data/common/diff_std.o ./pwiz/data/common/Unimod.o ./pwiz/data/msdata/SpectrumList_MGF.o ./pwiz/data/msdata/DefaultReaderList.o ./pwiz/data/msdata/ChromatogramList_mzML.o ./pwiz/data/msdata/examples.o ./pwiz/data/msdata/Serializer_mzML.o ./pwiz/data/msdata/Serializer_MSn.o ./pwiz/data/msdata/Reader.o ./pwiz/data/msdata/Serializer_MGF.o ./pwiz/data/msdata/Serializer_mzXML.o ./pwiz/data/msdata/SpectrumList_mzML.o ./pwiz/data/msdata/SpectrumList_MSn.o ./pwiz/data/msdata/BinaryDataEncoder.o ./pwiz/data/msdata/Diff.o ./pwiz/data/msdata/MSData.o ./pwiz/data/msdata/References.o ./pwiz/data/msdata/SpectrumList_mzXML.o ./pwiz/data/msdata/IO.o ./pwiz/data/msdata/SpectrumList_BTDX.o ./pwiz/data/msdata/SpectrumInfo.o ./pwiz/data/msdata/RAMPAdapter.o ./pwiz/data/msdata/LegacyAdapter.o ./pwiz/data/msdata/SpectrumIterator.o ./pwiz/data/msdata/MSDataFile.o ./pwiz/data/msdata/MSNumpress.o ./pwiz/data/msdata/SpectrumListCache.o ./pwiz/data/msdata/Index_mzML.o ./pwiz/data/identdata/IdentDataFile.o ./pwiz/data/identdata/IdentData.o ./pwiz/data/identdata/DefaultReaderList.o ./pwiz/data/identdata/Reader.o ./pwiz/data/identdata/Serializer_protXML.o ./pwiz/data/identdata/Serializer_pepXML.o ./pwiz/data/identdata/Serializer_mzid.o ./pwiz/data/identdata/IO.o ./pwiz/data/identdata/Version.o ./pwiz/data/identdata/References.o ./pwiz/data/proteome/Modification.o ./pwiz/data/proteome/Digestion.o ./pwiz/data/proteome/Peptide.o ./pwiz/data/proteome/AminoAcid.o ./pwiz/utility/minimxml/XMLWriter.o ./pwiz/utility/minimxml/SAXParser.o ./pwiz/utility/chemistry/Chemistry.o ./pwiz/utility/chemistry/ChemistryData.o ./pwiz/utility/chemistry/MZTolerance.o ./pwiz/utility/misc/IntegerSet.o ./pwiz/utility/misc/Base64.o ./pwiz/utility/misc/IterationListener.o ./pwiz/utility/misc/MSIHandler.o ./pwiz/utility/misc/Filesystem.o ./pwiz/utility/misc/TabReader.o ./pwiz/utility/misc/random_access_compressed_ifstream.o ./pwiz/utility/misc/SHA1.o ./pwiz/utility/misc/SHA1Calculator.o ./pwiz/utility/misc/sha1calc.o ./random_access_gzFile.o rampR.o R_init_mzR.o
find . -name \*~ -exec rm {} \;   ## from cleanup
find . -name \*.o -exec rm {} \;  ## from cleanup
find . -name "#*#" -exec rm {} \; ## from cleanup
g++ -I/usr/include/R/ -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -D_FORTIFY_SOURCE=2 -I"/home/simion/R/x86_64-unknown-linux-gnu-library/3.2/Rcpp/include" -I"/home/simion/R/x86_64-unknown-linux-gnu-library/3.2/zlibbioc/include"   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4  -c cramp.cpp -o cramp.o
g++ -I/usr/include/R/ -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -D_FORTIFY_SOURCE=2 -I"/home/simion/R/x86_64-unknown-linux-gnu-library/3.2/Rcpp/include" -I"/home/simion/R/x86_64-unknown-linux-gnu-library/3.2/zlibbioc/include"   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4  -c ramp_base64.cpp -o ramp_base64.o
g++ -I/usr/include/R/ -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -D_FORTIFY_SOURCE=2 -I"/home/simion/R/x86_64-unknown-linux-gnu-library/3.2/Rcpp/include" -I"/home/simion/R/x86_64-unknown-linux-gnu-library/3.2/zlibbioc/include"   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4  -c ramp.cpp -o ramp.o
g++ -I/usr/include/R/ -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -D_FORTIFY_SOURCE=2 -I"/home/simion/R/x86_64-unknown-linux-gnu-library/3.2/Rcpp/include" -I"/home/simion/R/x86_64-unknown-linux-gnu-library/3.2/zlibbioc/include"   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4  -c RcppRamp.cpp -o RcppRamp.o
g++ -I/usr/include/R/ -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -D_FORTIFY_SOURCE=2 -I"/home/simion/R/x86_64-unknown-linux-gnu-library/3.2/Rcpp/include" -I"/home/simion/R/x86_64-unknown-linux-gnu-library/3.2/zlibbioc/include"   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4  -c RcppRampModule.cpp -o RcppRampModule.o
gcc -I/usr/include/R/ -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -D_FORTIFY_SOURCE=2 -I"/home/simion/R/x86_64-unknown-linux-gnu-library/3.2/Rcpp/include" -I"/home/simion/R/x86_64-unknown-linux-gnu-library/3.2/zlibbioc/include"   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4  -c rnetCDF.c -o rnetCDF.o
g++ -I/usr/include/R/ -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -D_FORTIFY_SOURCE=2 -I"/home/simion/R/x86_64-unknown-linux-gnu-library/3.2/Rcpp/include" -I"/home/simion/R/x86_64-unknown-linux-gnu-library/3.2/zlibbioc/include"   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4  -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/include/R/ -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -D_FORTIFY_SOURCE=2 -I"/home/simion/R/x86_64-unknown-linux-gnu-library/3.2/Rcpp/include" -I"/home/simion/R/x86_64-unknown-linux-gnu-library/3.2/zlibbioc/include"   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4  -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/include/R/ -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -D_FORTIFY_SOURCE=2 -I"/home/simion/R/x86_64-unknown-linux-gnu-library/3.2/Rcpp/include" -I"/home/simion/R/x86_64-unknown-linux-gnu-library/3.2/zlibbioc/include"   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4  -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/include/R/ -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -D_FORTIFY_SOURCE=2 -I"/home/simion/R/x86_64-unknown-linux-gnu-library/3.2/Rcpp/include" -I"/home/simion/R/x86_64-unknown-linux-gnu-library/3.2/zlibbioc/include"   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4  -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/include/R/ -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -D_FORTIFY_SOURCE=2 -I"/home/simion/R/x86_64-unknown-linux-gnu-library/3.2/Rcpp/include" -I"/home/simion/R/x86_64-unknown-linux-gnu-library/3.2/zlibbioc/include"   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4  -c boost/system/src/error_code.cpp -o boost/system/src/error_code.o
g++ -I/usr/include/R/ -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -D_FORTIFY_SOURCE=2 -I"/home/simion/R/x86_64-unknown-linux-gnu-library/3.2/Rcpp/include" -I"/home/simion/R/x86_64-unknown-linux-gnu-library/3.2/zlibbioc/include"   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4  -c boost/regex/src/posix_api.cpp -o boost/regex/src/posix_api.o
g++ -I/usr/include/R/ -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -D_FORTIFY_SOURCE=2 -I"/home/simion/R/x86_64-unknown-linux-gnu-library/3.2/Rcpp/include" -I"/home/simion/R/x86_64-unknown-linux-gnu-library/3.2/zlibbioc/include"   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4  -c boost/regex/src/fileiter.cpp -o boost/regex/src/fileiter.o
g++ -I/usr/include/R/ -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -D_FORTIFY_SOURCE=2 -I"/home/simion/R/x86_64-unknown-linux-gnu-library/3.2/Rcpp/include" -I"/home/simion/R/x86_64-unknown-linux-gnu-library/3.2/zlibbioc/include"   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4  -c boost/regex/src/regex_raw_buffer.cpp -o boost/regex/src/regex_raw_buffer.o
g++ -I/usr/include/R/ -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -D_FORTIFY_SOURCE=2 -I"/home/simion/R/x86_64-unknown-linux-gnu-library/3.2/Rcpp/include" -I"/home/simion/R/x86_64-unknown-linux-gnu-library/3.2/zlibbioc/include"   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4  -c boost/regex/src/cregex.cpp -o boost/regex/src/cregex.o
g++ -I/usr/include/R/ -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -D_FORTIFY_SOURCE=2 -I"/home/simion/R/x86_64-unknown-linux-gnu-library/3.2/Rcpp/include" -I"/home/simion/R/x86_64-unknown-linux-gnu-library/3.2/zlibbioc/include"   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4  -c boost/regex/src/regex_debug.cpp -o boost/regex/src/regex_debug.o
g++ -I/usr/include/R/ -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -D_FORTIFY_SOURCE=2 -I"/home/simion/R/x86_64-unknown-linux-gnu-library/3.2/Rcpp/include" -I"/home/simion/R/x86_64-unknown-linux-gnu-library/3.2/zlibbioc/include"   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4  -c boost/regex/src/instances.cpp -o boost/regex/src/instances.o
g++ -I/usr/include/R/ -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -D_FORTIFY_SOURCE=2 -I"/home/simion/R/x86_64-unknown-linux-gnu-library/3.2/Rcpp/include" -I"/home/simion/R/x86_64-unknown-linux-gnu-library/3.2/zlibbioc/include"   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4  -c boost/regex/src/icu.cpp -o boost/regex/src/icu.o
g++ -I/usr/include/R/ -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -D_FORTIFY_SOURCE=2 -I"/home/simion/R/x86_64-unknown-linux-gnu-library/3.2/Rcpp/include" -I"/home/simion/R/x86_64-unknown-linux-gnu-library/3.2/zlibbioc/include"   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4  -c boost/regex/src/usinstances.cpp -o boost/regex/src/usinstances.o
g++ -I/usr/include/R/ -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -D_FORTIFY_SOURCE=2 -I"/home/simion/R/x86_64-unknown-linux-gnu-library/3.2/Rcpp/include" -I"/home/simion/R/x86_64-unknown-linux-gnu-library/3.2/zlibbioc/include"   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4  -c boost/regex/src/regex.cpp -o boost/regex/src/regex.o
g++ -I/usr/include/R/ -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -D_FORTIFY_SOURCE=2 -I"/home/simion/R/x86_64-unknown-linux-gnu-library/3.2/Rcpp/include" -I"/home/simion/R/x86_64-unknown-linux-gnu-library/3.2/zlibbioc/include"   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4  -c boost/regex/src/wide_posix_api.cpp -o boost/regex/src/wide_posix_api.o
g++ -I/usr/include/R/ -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -D_FORTIFY_SOURCE=2 -I"/home/simion/R/x86_64-unknown-linux-gnu-library/3.2/Rcpp/include" -I"/home/simion/R/x86_64-unknown-linux-gnu-library/3.2/zlibbioc/include"   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4  -c boost/regex/src/regex_traits_defaults.cpp -o boost/regex/src/regex_traits_defaults.o
g++ -I/usr/include/R/ -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -D_FORTIFY_SOURCE=2 -I"/home/simion/R/x86_64-unknown-linux-gnu-library/3.2/Rcpp/include" -I"/home/simion/R/x86_64-unknown-linux-gnu-library/3.2/zlibbioc/include"   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4  -c boost/regex/src/winstances.cpp -o boost/regex/src/winstances.o
g++ -I/usr/include/R/ -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -D_FORTIFY_SOURCE=2 -I"/home/simion/R/x86_64-unknown-linux-gnu-library/3.2/Rcpp/include" -I"/home/simion/R/x86_64-unknown-linux-gnu-library/3.2/zlibbioc/include"   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4  -c boost/regex/src/wc_regex_traits.cpp -o boost/regex/src/wc_regex_traits.o
g++ -I/usr/include/R/ -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -D_FORTIFY_SOURCE=2 -I"/home/simion/R/x86_64-unknown-linux-gnu-library/3.2/Rcpp/include" -I"/home/simion/R/x86_64-unknown-linux-gnu-library/3.2/zlibbioc/include"   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4  -c boost/regex/src/c_regex_traits.cpp -o boost/regex/src/c_regex_traits.o
g++ -I/usr/include/R/ -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -D_FORTIFY_SOURCE=2 -I"/home/simion/R/x86_64-unknown-linux-gnu-library/3.2/Rcpp/include" -I"/home/simion/R/x86_64-unknown-linux-gnu-library/3.2/zlibbioc/include"   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4  -c boost/regex/src/cpp_regex_traits.cpp -o boost/regex/src/cpp_regex_traits.o
g++ -I/usr/include/R/ -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -D_FORTIFY_SOURCE=2 -I"/home/simion/R/x86_64-unknown-linux-gnu-library/3.2/Rcpp/include" -I"/home/simion/R/x86_64-unknown-linux-gnu-library/3.2/zlibbioc/include"   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4  -c boost/regex/src/static_mutex.cpp -o boost/regex/src/static_mutex.o
g++ -I/usr/include/R/ -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -D_FORTIFY_SOURCE=2 -I"/home/simion/R/x86_64-unknown-linux-gnu-library/3.2/Rcpp/include" -I"/home/simion/R/x86_64-unknown-linux-gnu-library/3.2/zlibbioc/include"   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4  -c boost/regex/src/w32_regex_traits.cpp -o boost/regex/src/w32_regex_traits.o
g++ -I/usr/include/R/ -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -D_FORTIFY_SOURCE=2 -I"/home/simion/R/x86_64-unknown-linux-gnu-library/3.2/Rcpp/include" -I"/home/simion/R/x86_64-unknown-linux-gnu-library/3.2/zlibbioc/include"   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4  -c boost/iostreams/src/zlib.cpp -o boost/iostreams/src/zlib.o
g++ -I/usr/include/R/ -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -D_FORTIFY_SOURCE=2 -I"/home/simion/R/x86_64-unknown-linux-gnu-library/3.2/Rcpp/include" -I"/home/simion/R/x86_64-unknown-linux-gnu-library/3.2/zlibbioc/include"   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4  -c boost/iostreams/src/file_descriptor.cpp -o boost/iostreams/src/file_descriptor.o
g++ -I/usr/include/R/ -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -D_FORTIFY_SOURCE=2 -I"/home/simion/R/x86_64-unknown-linux-gnu-library/3.2/Rcpp/include" -I"/home/simion/R/x86_64-unknown-linux-gnu-library/3.2/zlibbioc/include"   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4  -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/include/R/ -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -D_FORTIFY_SOURCE=2 -I"/home/simion/R/x86_64-unknown-linux-gnu-library/3.2/Rcpp/include" -I"/home/simion/R/x86_64-unknown-linux-gnu-library/3.2/zlibbioc/include"   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4  -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<typename... T>
                      ^
./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 <std::size_t...> 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<T>, boost::detail::thread_move_t<Args>...)
   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<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<class Function> 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<T>, boost::detail::thread_move_t<Args>...)
   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<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<class Function> 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/lib64/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’

mzR fails to install on debian with g++ (Ubuntu 5.3.1-14ubuntu2.1) 5.3.1

Installation of the mzR Package in R fails, because the mzr/src/Makevars script uses MAC specific parameter of the g++ compiler (-Wno-deprecated-register).

ERROR:
....
At global scope:
cc1plus: warning: unrecognized command line option ‘-Wno-deprecated-register’
....

A bugfix for me was the replacement of the -Wno-deprecated-register parameter with -Wno-deprecated (mzr/src/Makevars, line 105). This might occurs in some other error, but as a quick and dirty solution in works.

sessionInfo()

R version 3.3.1 (2016-06-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04 LTS

locale:
[1] LC_CTYPE=de_DE.UTF-8 LC_NUMERIC=C LC_TIME=de_DE.UTF-8 LC_COLLATE=de_DE.UTF-8
[5] LC_MONETARY=de_DE.UTF-8 LC_MESSAGES=de_DE.UTF-8 LC_PAPER=de_DE.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C

Error with openMSfile in RStudio

The following error occurs when trying to load files using RStudio. The same files work fine with the regular R gui:

> ms <- openMSfile('/Users/Thomas/Desktop/004-CM_005.mzML')
Error in rampModule$open(filename, declaredOnly = TRUE) : 
  [MSDataFile::readFile()] Unsupported file format.

The problem has been observed with a range of files and on a range of systems (both mac and win). The problem is not constant (sometimes a file works in RStudio), but has only been observed using RStudio.

close() missing for pwiz backend

> library(mzR)
Loading required package: Rcpp
> ms <- openMSfile("/vol/R/BioC/devel/msdata/inst/microtofq/MM8.mzML")
> close(ms)
Error in UseMethod("close") : 
  no applicable method for 'close' applied to an object of class "c('mzRpwiz', 'mzR', 'Versioned')"
> sessionInfo()
R version 3.1.1 (2014-07-10)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=de_DE.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=de_DE.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=de_DE.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] mzR_1.99.1  Rcpp_0.11.1

loaded via a namespace (and not attached):
[1] Biobase_2.22.0     BiocGenerics_0.8.0 codetools_0.2-9    parallel_3.1.1    

pwiz backend does not close file handles

I experienced problems processing a large dataset using MSnbase and was able to break that down to a problem most likely in the header call using the "pwiz" backend. A reproducible example and the error message are below. It might be related to the fact that for no dedicated close function seems to be present in the pwiz library.

library(MSnbase)
library(msdata)
fl <- proteomics(full.names = TRUE)[2]

for (i in 1:1000) {
    cat(i, "")
    ## readMSData2
    msd <- mzR::openMSfile(fl, backend = "pwiz")
    cat(" instrumentInfo ")
    inst <- instrumentInfo(msd)
    cat(" header ")
    head <- mzR::header(msd)
    gc()
    mzR::close(msd)
    rm(msd)
    cat(" spectra ")
    ## spectra
    msd <- mzR::openMSfile(fl, backend = "pwiz")
    sp <- mzR::peaks(msd)
    gc()
    mzR::close(msd)
    rm(msd)
    cat("OK\n")
}

The error:

## Error
243  instrumentInfo  header Error in object@backend$getAllScanHeaderInfo() :
  failed opening file: Too many open files: unspecified iostream_category error
>

There are no problems without the header call.

Support of ion mobility mzML

Hi,

currently mzR dies on ion mobility data with
Invalid cvParam accession "1002476"
where 1002476 is "ion mobility drift time"
http://www.ebi.ac.uk/ols/ontologies/ms/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FMS_1002476
using mzR_2.4.1
yours, Maria and Steffen

Please find an example data file https://www.dropbox.com/s/7m3hdw010twyun1/naringinMSlevel1.mzML?dl=0

Documenting system dependencies

Dan's advice

Hi Laurent,
If you list the system dependencies (and how to install them) in a top-level README file, the web site landing page will link to it.

I realize you have a SystemRequirements field (which also shows up on the landing page) but that is not always enough to tell people
how to install them. Also, are those requirements necessary on Mac and Windows, or only on Linux? In other words, are they compile-time or runtime dependencies? YOu could clarify in the README.

FYI
Dan

latest mzR from svn fails to build on mac

https://bioconductor.org/checkResults/devel/bioc-LATEST/mzR/morelia-install.html

raw data reading

Just curious, can mzR be extended to support the reading of vendor raw files?

Compilation fails on

mzR has been having compilation failures on moscato1
(the old Windows builder in Seattle) since the 2.7.4 update about
2 weeks ago:
https://bioconductor.org/checkResults/3.4/bioc-LATEST/mzR/moscato1-install.html

C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o mzR.dll tmp.def cramp.o ramp_base64.o ramp.o RcppRamp.o RcppRampModule.o rnetCDF.o RcppPwiz.o RcppPwizModule.o RcppIdent.o RcppIdentModule.o RcppExports.o R_init_mzR.o rampR.o -Wl,--dynamic-linker=/ld.exe -L./win//i386 -lws2_32 -lnetcdf -lpwiz -Lc:/local323/lib/i386 -Lc:/local323/lib -LD:/biocbld/BBS-3˜1.4-B/R/bin/i386 -lR
./win//i386/libpwiz.a(error_code.o):error_code.cpp:(.text+0x72): undefined reference to `__gxx_personality_sj0'
./win//i386/libpwiz.a(error_code.o):error_code.cpp:(.text+0x8b): undefined reference to `_Unwind_SjLj_Register'
./win//i386/libpwiz.a(error_code.o):error_code.cpp:(.text+0xdb): undefined reference to `_Unwind_SjLj_Unregister'
./win//i386/libpwiz.a(error_code.o):error_code.cpp:(.text+0x164): undefined reference to `_Unwind_SjLj_Resume'
./win//i386/libpwiz.a(error_code.o):error_code.cpp:(.text+0x1fb): undefined reference to `__gxx_personality_sj0'
./win//i386/libpwiz.a(error_code.o):error_code.cpp:(.text+0x20e): undefined reference to `_Unwind_SjLj_Register'
./win//i386/libpwiz.a(error_code.o):error_code.cpp:(.text+0x2a6): undefined reference to `_Unwind_SjLj_Unregister'
./win//i386/libpwiz.a(error_code.o):error_code.cpp:(.text+0x4d9): undefined reference to `_Unwind_SjLj_Resume'
...

These are undefined symbols because our Windows statically complied libpwiz.a
does not match the lib static-libgcc in the used toolchain on the BioC machines.
So 1) we need to recompile libpwiz.a using the correct (which ?!) toolchain.
In the long run, with the more powerful build machine tokay1 we could try "normal" compilation
on windows, just like we have on the other ARCH. This precompiling has always been a pain.
Happy to get rid of it :-) Yours, Steffen

Crashes reported on bioc-devel

From [Bioc-devel] msPurity build fail on Mac OS X (morelia), @mtmorgan offers the following patch.

Index: src/cramp.cpp
===================================================================
--- src/cramp.cpp   (revision 121179)
+++ src/cramp.cpp   (working copy)
@@ -95,7 +95,7 @@
          //      if (m_runInfo->m_data.scanCount < 0) { // undeclared 
scan count
          // this will provoke reading of index, which sets scan count
          rampScanInfo* tmp = getScanHeaderInfo ( 1 );
-        free(tmp);
+        delete(tmp);
          // }
          // END HENRY
      }

It's not clear to me yet if this is really the reason for the reported problem, so I haven't applied it yet. I will once we get to the bottom of the msPurity problem.

Add ionInjectionTime to header output

Hi,

Is it possible to add the functionality to extract the ionInjectionTime tag data from the header in converted Thermo files? It is stored in the scan header data along with the other details extracted with this function:

For example:

<scan num="9333"
msLevel="3"
scanEvent="0"
masterIndex="-1"
peaksCount="34"
ionInjectionTime="38.6763"
elapsedScanTime="0.13659"
polarity="+"

I can provide working files if necessary.

Thank you.
Chris

compiler/linker issue with Rcpp

Hi there,

I have been trying to re-install a package which has a lot of dependencies including "Rcpp" and "mzR". However, it seems that the current version of "mzR" (2.4.0) has compiler/linker issue with "Rcpp" (either version 0.12.2 or 0.12.3 which is most up-to-date). Below is the error messages along with session information when I load version 0.12.2 of "Rcpp". In my other slower machine, "mzR" (2.2.1) gets along with "Rcpp" (0.12.2) so I was wondering if there is anyway I can download the source file of version (2.2.1) of mzR for the purpose of urgency on my project.

library(mzR)
Error : .onLoad failed in loadNamespace() for 'mzR', details:
call: description[["RcppModules"]]
error: subscript out of bounds
In addition: Warning messages:
1: In fun(libname, pkgname) :
mzR has been built against a different Rcpp version (0.12.1)
than is installed on your system (0.12.2). This might lead to errors
when loading mzR. If you encounter such issues, please send a report,
including the output of sessionInfo() to the Bioc support forum at
https://support.bioconductor.org/. For details see also
https://github.com/sneumann/mzR/wiki/mzR-Rcpp-compiler-linker-issue.
2: In packageDescription(pkg, lib.loc = lib) : no package 'mzR' was found
Error: package or namespace load failed for ‘mzR’
sessionInfo()
R version 3.2.3 (2015-12-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] Rcpp_0.12.2

loaded via a namespace (and not attached):
[1] ProtGenerics_1.2.1 parallel_3.2.3 tools_3.2.3
[4] Biobase_2.30.0 BiocGenerics_0.16.1

Many thanks in advance,
Mike C.

Unify Makevars files

Hi, after #61 works on unixoid systems, we could re-unify
the Makevars and Makevars.win. The major differences are
in the definition of a few architecture-specific *.o files on Windows,
and a few platform specific compiler switches. Those could be handled
with a few Makefile if-statements. Yours, Steffen

mzR.so: undefined symbol: _intel_fast_memcpy

Dear all,
I am unable to install mzR package due to "undefined symbol: _intel_fast_memcpy" . I am including the whole error and my sessionInfo() below. I have followed all the discussion about the issues with mzR and tried to re-install mzR in different ways (e.g. indicating the mirror site, from source) but the problem persists. I will be grateful to get some guidance on how to solve this issue.
Best regards,
Lyamine

** R
** inst
** preparing package for lazy loading
Creating a generic function for 'close' from package 'base' in package 'mzR'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/san2/home/mqtlican/local/lib64/R/library/mzR/libs/mzR.so':
/san2/home/mqtlican/local/lib64/R/library/mzR/libs/mzR.so: undefined symbol: _intel_fast_memcpy
Error: loading failed
Execution halted

ERROR: loading failed

---

sessionInfo()
R version 3.2.1 (2015-06-18)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
[1] C

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] BiocInstaller_1.20.0

loaded via a namespace (and not attached):
[1] tools_3.2.1

extract the startTimeStamp from a run

Would be nice to add the possibility to extract also the startTimeStamp of a run from an mzML file (and report that e.g. also by the runInfo method).

warning: control may reach end of non-void function from clang++ in Serializer_pepXML.cpp

http://bioconductor.org/checkResults/devel/bioc-LATEST/mzR/morelia-checksrc.html

* checking whether package ‘mzR’ can be installed ... [362s/367s] WARNING
Found the following significant warnings:
  pwiz/data/identdata/Serializer_pepXML.cpp:1469:5: warning: control may reach end of non-void function [-Wreturn-type]
Found the following additional warnings:
  pwiz/data/identdata/Serializer_pepXML.cpp:1469:5: warning: control may reach end of non-void function [-Wreturn-type]
See ‘/Users/biocbuild/bbs-3.1-bioc/meat/mzR.Rcheck/00install.out’ for details.

Update pwiz

Recently, a bug had been fixed in pwiz that now allows to correctly refer to an MS3 precursor. This is an essential feature for downstream analyses, requiring an update to pwiz/mzR.

I am happy to do this when I am back from my travelling, by would appreciate any indication to any patches that need to be applied after checking out the latest pwiz. The process of updating pwiz should be well documented.

cc: @thirdwing @sneumann

warning: control may reach end of non-void function

Hi,
clang on macOS is complaining with a WARNING about

* checking whether package ‘mzR’ can be installed ... WARNING
Found the following significant warnings:
  pwiz/data/identdata/Serializer_pepXML.cpp:1545:5: warning: control may reach end of non-void function [-Wreturn-type]

in
https://github.com/sneumann/mzR/blob/master/src/pwiz/data/identdata/Serializer_pepXML.cpp#L1545

I guess the right return value at the end of the function should be return true

mzR cvParam accession error when reading PeptideShaker mzIdentML file

Hey,

I am trying to open a mzid file generated by peptideshaker but when using the openIDfile command, i get this error message :
Error: Invalid cvParam accession "1002458"

By opening my mzid file and searching that accession, I get one line match :
<cvParam cvRef="PSI-MS" accession="MS:1002458" name="PeptideShaker"/>

Is there any way to fix this issue ?

Best regards,
Vivian

note : by looking for the error on google, this code has been seen already when willing to use PeptideShaker mzIdentML file to OpenSWATH here

Crash with pwiz backend on Windows

mzR is crashing on windows when the pwiz back-end is used. The code works fine on other systems and using the Ramp back-end on Windows. The problem is that this does not happen on every system. The bug has been confirmed with other mzML files.

Reproduce the bug

library(AnnotationHub)
ah <- AnnotationHub()
rw <- ah[["AH49008"]] ## uses pwiz backend by default
head(peaks(rw, 1))

or, with a manual downlaod

url <- ""ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2012/03/PXD000001/TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01-20141210.mzML"
download.file(url, basename(url))
rw <- openMSfile(rw, backend = "pwiz")
head(peaks(rw, 1))

while the following works

url <- ""ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2012/03/PXD000001/TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01-20141210.mzML"
download.file(url, basename(url))
rw <- openMSfile(rw, backend = "Ramp")
head(peaks(rw, 1))

A detailed crash report provided by Dan Tenenbaum

So I debugged as follows:

x <- selectMethod("peaks", "mzRpwiz")
debug(x)
peaks(rw, 1)

Then I kept setting breakpoints deeper down till I got here (line 82 of mzR/R/methods-mzRpwiz.R):

return(object@backend$getPeakList(scans)$peaks)

Looking at the getPeakList function:

Browse[3]> object@backend$getPeakList
Class method definition for method getPeakList()
function (...)
{
    " Rcpp::List getPeakList(int)  \n   docstring : Performs a non-sequential parsing oper
ation on an indexed mzXML file to obtain the peak list for a numbered scan."
    .External(list(name = "CppMethod__invoke_notvoid", address = <pointer: 0x000000000a435
f70>,
        dll = list(name = "Rcpp", path = "E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/libs/x64/
Rcpp.dll",
            dynamicLookup = TRUE, handle = <pointer: 0x000000006abc0000>,
            info = <pointer: 0x000000006dfcbf20>), numParameters = -1L),
        <pointer: 0x000000000a43fa40>, <pointer: 0x0000000012338900>,
        .pointer, ...)
}
<environment: 0x000000001f42fb38>

When I then step into it, I get the crash. sessionInfo() (run right before the line that causes the crash) follows.

R Under development (unstable) (2015-12-14 r69775)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows Server 2008 R2 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
 [1] mzR_2.5.2                         Rcpp_0.12.2
 [3] ProteomicsAnnotationHubData_1.1.1 curl_0.9.4
 [5] AnnotationHubData_1.1.9           futile.logger_1.4.1
 [7] GenomicRanges_1.23.8              GenomeInfoDb_1.7.3
 [9] IRanges_2.5.18                    S4Vectors_0.9.15
[11] AnnotationHub_2.3.10              BiocGenerics_0.17.2
[13] BiocStyle_1.9.2

loaded via a namespace (and not attached):
 [1] Biobase_2.31.3               httr_1.0.0
 [3] vsn_3.39.1                   jsonlite_0.9.19
 [5] foreach_1.4.3                shiny_0.12.2
 [7] interactiveDisplayBase_1.9.0 affy_1.49.0
 [9] RBGL_1.47.0                  Rsamtools_1.23.1
[11] impute_1.45.0                RSQLite_1.0.0
[13] lattice_0.20-33              limma_3.27.7
[15] chron_2.3-47                 digest_0.6.8
[17] XVector_0.11.1               colorspace_1.2-6
[19] htmltools_0.3                httpuv_1.3.3
[21] preprocessCore_1.33.0        plyr_1.8.3
[23] OrganismDbi_1.13.2           GEOquery_2.37.0
[25] MALDIquant_1.14              XML_3.98-1.3
[27] biomaRt_2.27.2               rBiopaxParser_2.9.0
[29] zlibbioc_1.17.0              xtable_1.8-0
[31] scales_0.3.0                 affyio_1.41.0
[33] BiocParallel_1.5.12          ggplot2_2.0.0
[35] SummarizedExperiment_1.1.12  GenomicFeatures_1.23.15
[37] magrittr_1.5                 mime_0.4
[39] doParallel_1.0.10            graph_1.49.1
[41] BiocInstaller_1.21.2         tools_3.3.0
[43] data.table_1.9.6             stringr_1.0.0
[45] MSnbase_1.19.7               munsell_0.4.2
[47] AnnotationDbi_1.33.4         lambda.r_1.1.7
[49] Biostrings_2.39.6            pcaMethods_1.61.0
[51] mzID_1.9.0                   grid_3.3.0
[53] RCurl_1.95-4.7               iterators_1.0.8
[55] AnnotationForge_1.13.5       bitops_1.0-6
[57] gtable_0.1.2                 codetools_0.2-14
[59] DBI_0.3.1                    reshape2_1.4.1
[61] R6_2.1.1                     GenomicAlignments_1.7.8
[63] knitr_1.11                   rtracklayer_1.31.3
[65] ProtGenerics_1.3.3           futile.options_1.0.0
[67] stringi_1.0-1

In mzR

In openMSfile.Rd, we have.

 \dontrun{
    ## to use another backend
    mz <- openMSfile(file, backend = "pwiz")
    mz
  }

In mzR-class.Rd, we have

 library(msdata)
 filepath <- system.file("microtofq", package = "msdata")
 file <- list.files(filepath, pattern="MM14.mzML",
                     full.names=TRUE, recursive = TRUE)
 mzml <- openMSfile(file, backend = "pwiz")

which seems to work (albeit on a small test file).

What needs to be done

• Could @sneumann and @thirdwing have a go an see if they can reproduce. Note that I have an AWS that enables to reproduce the crash. Please email me if you wish to use it.
• Fix the bug.

Installing from source with the gcc 4.9.3 toolchain

Hi,

I am trying to set up an R installation built with the new toolchain based on gcc 4.9.3. See https://github.com/rwinlib/r-base#readme

My mzR installation fails. There is a seemingly endless stream of "undefined reference" message, but the one I see recurring is:

./win//x64/libpwiz.a(ChromatogramList_mzML.o):ChromatogramList_mzML.cpp:(.text+0x11b): undefined reference to `__gxx_personality_sj0'
./win//x64/libpwiz.a(ChromatogramList_mzML.o):ChromatogramList_mzML.cpp:(.text+0x167): undefined reference to `_Unwind_SjLj_Register'
./win//x64/libpwiz.a(ChromatogramList_mzML.o):ChromatogramList_mzML.cpp:(.text+0x1c8): undefined reference to `_Unwind_SjLj_Unregister'
./win//x64/libpwiz.a(ChromatogramList_mzML.o):ChromatogramList_mzML.cpp:(.text+0x302): undefined reference to `_Unwind_SjLj_Resume'

My Rcpp is built from source (like everything for the 4.9.3 build).

Is this a problem from my side or a possible issue with the new toolchain?

remove faahKO dependency

This dependency is only to check CDF import, but introduces a cyclic
dependency mzR -> faahKO -> xcms -> mzR which can cause trouble.
msdata >= 0.3.5 contains ko15.CDF, mzR 2.0.1 should fix this.

read data from file handles or connections

From what I can tell, mzR (and MSnBase, etc) all expect fully qualified file names.

It would be great to have methods that support connections from files, gzfiles, zip files, url's, etc.

Compilation on tokay1 / Windows

There is an installation issues on the upcoming build machines
at https://bioconductor.org/checkResults/3.4/RPCI/bioc-LATEST/ :

In file included from rnetCDF.c:2:0:
rnetCDF.h:1:20: fatal error: netcdf.h: No such file or directory
 #include <netcdf.h>
                    ^
compilation terminated.

=> This is missing one of the SystemRequirements: C++11, GNU make, NetCDF,
namely NetCDF.

Yours, Steffen

mzR timeouts on Windows

Recording a email exchange with @dtenenba re mzR, that often fails to install on windows within 40 minutes.

The suggestion by @thirdwing and @sneumann was to ship libpwiz.a for Windows in the package.

Has anyone time to tackle this at some point?

Add acquistionnum column to psms output

Hello,

as investigated in lgatto/msidmatching#2 (comment) the acquistionnum/scan number reported by mzR for mzML/mzXML files contains the same numbers as the spectrumID column in the psms output for mzIdentML files.

Would it be possible to add a acquisitionnum column to the psms output to allow easier matching of identification and quantitation data similar to this approach in mzID: https://github.com/thomasp85/mzID/pull/18/files? We use this column in MSnbase for the matching.

A possible solution (I am sure there is an Rcpp way as well):

## mzR/R/methods-mzRident.R
setMethod("psms",
signature=c("mzRident"),
function(object) { 
  psms <- object@backend$getPsmInfo()
  psms$acquisitionNum <- as.numeric(sub("^.*=([[:digit:]]+)$", "\\1", psms$spectrumID))
  return(psms)
})

Maybe it would be cleaner to look for these lines in the mzIdentML and parse them directly:

<cvParam accession="MS:1001115" cvRef="PSI-MS" value="9230" name="scan number(s)"/>

Best wishes,

Sebastian

Ionization polarity not right (source file from agilent)

Not sure if this belongs with XCMS or mzR but seems mzR doesn't get it right.

I have an mzML file (sample: https://drive.google.com/file/d/0BzbMKsT1SFGiUzVQNzhSM3VjRXc/view?usp=sharing) converted from agilents .d format with proteowizard.
I am trying to determine the ionisation polarity.

If I do:

mz <- openMSfile(file)
runInfo(mz)
header(mz)$polarity

I just get -1's. But this file is positive mode. XCMS reports unknown.

In the mzML file there is also a line for each spectrum that indicates as much:

<cvParam cvRef="MS" accession="MS:1000130" name="positive scan" value=""/>

pwiz version

Is the pwiz version recorded somewhere in the mzR package, possibly in ./srz/pwiz? I would suggest to make it somehow available to developers/users.

restore readout of polarity with old Ramp interface

As reported from Paul Benton:
"The latest mzR does not seem to be loading the polarity information with the loadRaw method."

Paul also provided a snippet which I modified into a unit test
mzR/inst/unitTests/runit.polarity.R-disabled

pwiz patches

We should be able to identify all patches to pwiz code applied within mzR so that anyone can re-apply them or, better, we can automate them, if possible. I have created the patch label for this. I suggest we use it to tag issues and/or relevant pull request and possibly refer to these in this issue.

Cc: @thirdwing @sneumann @jotsetung

convertion CSV to mzXML

Posting @sneumann's code, for reference.

  data <- data.matrix(read.csv( bzfile(ff), comment.char = "#", header=FALSE))

  X <- data[,-1]
  rownames(X) <- data[,1]

  ## subsampling for debugging
  # X <- X[seq(1,nrow(X),length.out=1000),]

  colnames(X) <- seq(from=wavelength[1], to=wavelength[2], length=ncol(X))

  ## Just for debugging:
  #  par( mar = par( "mar" ) + c( 2, 4, 0, 0 ) )
  #  image( X, xaxt= "n", yaxt= "n" )
  #  axis( 1, at=seq(0,1,length.out=8 ), labels= as.integer(rownames( X ))[seq(1,nrow(X),length.out=8 )], las= 1)
  #  axis( 2, at=seq(0,1,length.out=10 ), labels= as.integer(colnames( X ))[seq(1,ncol(X),length.out=10 )], las= 1 )


  xr <- new("xcmsRaw")

  xr@env$intensity <- as.vector(t(X))
  xr@env$mz <- rep(seq(from=wavelength[1], to=wavelength[2], length=ncol(X)),
                   times=nrow(X))

  xr@scantime <- as.integer(data[,1])
  xr@tic <- apply(X, 1, sum)
  xr@mzrange <- wavelength

  ## If downsampled, need to extract scantime from downsampled X
  # xr@scantime <- as.integer(rownames(X))

  xr@acquisitionNum <- seq(from=1, to=nrow(X))

  xr@scanindex <- as.integer(seq(from=0, to=length(X)-ncol(X), along.with=xr@acquisitionNum))

  ## Display works only for positive intensities
  # xr@env$intensity <- xr@env$intensity+abs(min(xr@env$intensity))
  # profStep(xr) <- 1
  # plotRaw(xr)

  write.cdf(xr, sub("csv.bz2", "cdf", ff))

Use spectra or scan instead of peaks

Once respective generics have been added to BiocGenerics, allow spectra() and/or scans() in addition (instead of) peaks(.).

error reading mzML files from Sciex triple tof 6600

When reading an mzML file from a sciex triple tof 6600 an error is produced :
Invalid cvParam accession "1002533"

This seems to be coming from the psi-ms.obo file which is in pwiz/common/psi-ms.obo . I've attempted to update the file directly and recompile mzR. This didn't seem to work and produced the same error.
I then tried the checkoutpwiz.sh and recompiled howver, mzR failed with multiple errors.

Checking the updated psi-ms.obo file the reference is as expected:
[Term]
id: MS:1002533
name: TripleTOF 6600
def: "SCIEX TripleTOF 6600, a quadrupole - quadrupole - time-of-flight mass spectrometer." [PSI:MS]
is_a: MS:1000121 ! SCIEX instrument model

Compile error assigning to 'const char *' from incompatible type 'char' on Mac

Hi,

This is easy to fix, and requires a fix in ramp.cpp

ramp.cpp:2261:40: error: assigning to 'const char *' from incompatible type 'char'
                        pEndAttrValue  = '\0';
                                       ^ ˜˜˜˜
ramp.cpp:2281:39: error: assigning to 'const char *' from incompatible type 'char'
                        pEndAttrValue = '\0';
                                      ^ ˜˜˜˜

Will do after passing build on windows.
Yours, Steffen

segfault when retrieving ´score()´

I get an segmentation fault when I'm trying to retrieve the score() from the folowing identifications with mzR. It works with all other files I tried. psms() works.

https://www.dropbox.com/s/lja86fwfa76okpb/d46e40d85d0cfff4___20080315_CPTAC6_22_6QC1.mzML.mgf.export.F113747.mzid?dl=0

sessionInfo()
R version 3.1.2 (2014-10-31)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
[1] MSnbase_1.14.1      BiocParallel_1.0.1  mzR_2.0.0          
[4] Rcpp_0.11.4         Biobase_2.26.0      BiocGenerics_0.12.1
[7] dplyr_0.4.1        

Greets

No close method for mzRident/mzRpwiz

@thirdwing I notices that there was no close for mzRident objects. Wouldn't it be safer to explicitly close such an instance? Is there a reason not to have one?

add protein length column to psms output

The mzIdentML format offers an attribute "length" (stores the number of bases of a protein, e.g. <DBSequence ... length="512">). It would be nice if psms could return this attribute as additional column.

This is needed for some label-free quantitation algorithms in MSnbase (see e.g. lgatto/MSnbase#48).

duplicated items in getAllScanHeaderInfo()

in the function getAllScanHeaderInfo(), there are several duplicated items like below:

  header.add("seqNum", seqNum);
  header.add("seqNum",                   seqNum);
  header.add("acquisitionNum",           acquisitionNum);
  header.add("msLevel",                  msLevel);
  header.add("polarity",               polarity);
  header.add("seqNum",                   seqNum);

Is there any special reason for this?

Rstudio package build and Rcpp::compileAttributes()

Hi,
I am bitten by http://lists.r-forge.r-project.org/pipermail/rcpp-devel/2013-February/005233.html
resulting in the following error when trying to build in Rstudio:

==> Rcpp::compileAttributes()
Error in eval(substitute(expr), envir, enclos) : 
  file already exists: 'D:/Dateien von Steffen/Desktop/R Packages/mzR-project/mzR/src/RcppExports.cpp'
Ruft auf: source ... withVisible -> eval -> eval -> <Anonymous> -> .Call
Execution stopped

The workaround suggested by JJ Allaire (http://lists.r-forge.r-project.org/pipermail/rcpp-devel/2013-February/005233.html) is:

- Use a custom SOURCES variable in Makevars to explicitly list the
source files to compile as part of the package
- Don't include RcppExports.cpp in that list
- Add another source file that in turn includes RcppExports.cpp but
wraps it in the required preprocessor directives.

Compiling without Rstudio simply on the command line works fine.
Yours, Steffen

mascot mzid file doesnt read

When I try to read this file ( https://www.dropbox.com/sh/nuwvqlc9bvg0ui0/AABG_3cED_Dm-o8tmjBp8RpWa?dl=0 ) I get this error:

> dat = openIDfile('./F004497.mzid')
Error: [References::resolve()] Failed to resolve reference.
  object type: N4pwiz9identdata7ContactE
  reference id: PERSON_DOC_OWNER
  referent list: 4


    ORG_MSL
    ORG_DOC_OWNER

The file could be read succesfully with mzID

sessioninfo

> sessionInfo()
R version 3.1.2 (2014-10-31)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
 [1] mzID_1.4.1          pracma_1.7.9        MSnbase_1.14.1     
 [4] BiocParallel_1.0.0  mzR_2.0.0           Rcpp_0.11.3        
 [7] Biobase_2.26.0      BiocGenerics_0.12.1 MSGFplus_1.1.3     
[10] dplyr_0.4.1        

mzR installation is failing on OS X

mzR fails to install on my machine (OS X Mavericks, R 3.1.0). I believe the requirements are all present and working, although I might be missing something that I don't know about. Here is a gist of the output from when I try to install.

From searching around it looks like you know about and are working on this problem, just wanted to let you know there was someone waiting on a fix (if there is a workaround for the time being I would be happy to use that).

If there is any additional config information that would help, let me know.