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BioC 3.2: CHECK report for mzR on moscato1

This page was generated on 2016-04-23 10:18:02 -0700 (Sat, 23 Apr 2016).

Package 693/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mzR 2.4.1
Bernd Fischer , Steffen Neumann , Laurent Gatto , Qiang Kou
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/mzR
Last Changed Rev: 114283 / Revision: 116712
Last Changed Date: 2016-03-05 22:50:11 -0800 (Sat, 05 Mar 2016)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  TIMEOUT  OK [ OK ] OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: mzR
Version: 2.4.1
Command: rm -rf mzR.buildbin-libdir mzR.Rcheck && mkdir mzR.buildbin-libdir mzR.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=mzR.buildbin-libdir mzR_2.4.1.tar.gz >mzR.Rcheck\00install.out 2>&1 && cp mzR.Rcheck\00install.out mzR-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=mzR.buildbin-libdir --install="check:mzR-install.out" --force-multiarch --no-vignettes --timings mzR_2.4.1.tar.gz
StartedAt: 2016-04-23 05:14:23 -0700 (Sat, 23 Apr 2016)
EndedAt: 2016-04-23 05:34:14 -0700 (Sat, 23 Apr 2016)
EllapsedTime: 1190.9 seconds
RetCode: 0
Status:  OK  
CheckDir: mzR.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf mzR.buildbin-libdir mzR.Rcheck && mkdir mzR.buildbin-libdir mzR.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=mzR.buildbin-libdir mzR_2.4.1.tar.gz >mzR.Rcheck\00install.out 2>&1 && cp mzR.Rcheck\00install.out mzR-install.out  && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=mzR.buildbin-libdir --install="check:mzR-install.out" --force-multiarch --no-vignettes --timings mzR_2.4.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/mzR.Rcheck'
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'mzR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'mzR' version '2.4.1'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'mzR' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 12.4Mb
  sub-directories of 1Mb or more:
    libs  11.9Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'D:/biocbld/bbs-3.2-bioc/meat/mzR.buildbin-libdir/mzR/libs/i386/mzR.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'D:/biocbld/bbs-3.2-bioc/meat/mzR.buildbin-libdir/mzR/libs/x64/mzR.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
The detected symbols are linked into the code but might come from
libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [15s] OK
Examples with CPU or elapsed time > 5s
         user system elapsed
metadata  1.3   0.05   11.17
** running examples for arch 'x64' ... [5s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R' [17s]
 [17s] OK
** running tests for arch 'x64' ...
  Running 'runTests.R' [7s]
 [8s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  'D:/biocbld/bbs-3.2-bioc/meat/mzR.Rcheck/00check.log'
for details.

mzR.Rcheck/00install.out:


install for i386

* 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 R_init_mzR.o rampR.o
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB  -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE     -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"d:/RCompile/r-compiling/local/local323/include" -c cramp.cpp -o cramp.o
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB  -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE     -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"d:/RCompile/r-compiling/local/local323/include" -c ramp_base64.cpp -o ramp_base64.o
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB  -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE     -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"d:/RCompile/r-compiling/local/local323/include" -c ramp.cpp -o ramp.o
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB  -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE     -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"d:/RCompile/r-compiling/local/local323/include" -c RcppRamp.cpp -o RcppRamp.o
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB  -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE     -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"d:/RCompile/r-compiling/local/local323/include" -c RcppRampModule.cpp -o RcppRampModule.o
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB  -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE     -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"d:/RCompile/r-compiling/local/local323/include"  -D_LARGEFILE_SOURCE -I./win//i386 -D_MSC_VER  -fgnu89-inline   -O3 -Wall  -std=gnu99 -mtune=core2 -c rnetCDF.c -o rnetCDF.o
cc1.exe: warning: command line option '-fpermissive' is valid for C++/ObjC++ but not for C [enabled by default]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB  -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE     -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"d:/RCompile/r-compiling/local/local323/include" -c RcppPwiz.cpp -o RcppPwiz.o
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB  -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE     -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"d:/RCompile/r-compiling/local/local323/include" -c RcppPwizModule.cpp -o RcppPwizModule.o
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB  -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE     -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"d:/RCompile/r-compiling/local/local323/include" -c RcppIdent.cpp -o RcppIdent.o
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB  -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE     -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"d:/RCompile/r-compiling/local/local323/include" -c RcppIdentModule.cpp -o RcppIdentModule.o
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB  -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE     -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"d:/RCompile/r-compiling/local/local323/include"  -D_LARGEFILE_SOURCE -I./win//i386 -D_MSC_VER  -fgnu89-inline   -O3 -Wall  -std=gnu99 -mtune=core2 -c R_init_mzR.c -o R_init_mzR.o
cc1.exe: warning: command line option '-fpermissive' is valid for C++/ObjC++ but not for C [enabled by default]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB  -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE     -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"d:/RCompile/r-compiling/local/local323/include" -c rampR.cpp -o rampR.o
g++ -m32 -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 R_init_mzR.o rampR.o -L./win//i386 -lws2_32 -lnetcdf -lpwiz -Ld:/RCompile/r-compiling/local/local323/lib/i386 -Ld:/RCompile/r-compiling/local/local323/lib -LD:/biocbld/BBS-3˜1.2-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-3.2-bioc/meat/mzR.buildbin-libdir/mzR/libs/i386
** 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

install for x64

* 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 R_init_mzR.o rampR.o
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB  -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE     -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"d:/RCompile/r-compiling/local/local323/include" -c cramp.cpp -o cramp.o
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB  -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE     -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"d:/RCompile/r-compiling/local/local323/include" -c ramp_base64.cpp -o ramp_base64.o
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB  -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE     -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"d:/RCompile/r-compiling/local/local323/include" -c ramp.cpp -o ramp.o
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB  -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE     -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"d:/RCompile/r-compiling/local/local323/include" -c RcppRamp.cpp -o RcppRamp.o
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB  -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE     -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"d:/RCompile/r-compiling/local/local323/include" -c RcppRampModule.cpp -o RcppRampModule.o
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB  -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE     -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"d:/RCompile/r-compiling/local/local323/include"  -D_LARGEFILE_SOURCE -I./win//x64 -D_MSC_VER  -fgnu89-inline   -O2 -Wall  -std=gnu99 -mtune=core2 -c rnetCDF.c -o rnetCDF.o
cc1.exe: warning: command line option '-fpermissive' is valid for C++/ObjC++ but not for C [enabled by default]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB  -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE     -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"d:/RCompile/r-compiling/local/local323/include" -c RcppPwiz.cpp -o RcppPwiz.o
In file included from D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include/RcppCommon.h:179:0,
                 from D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppPwiz.h:4,
                 from RcppPwiz.cpp:1:
D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include/Rcpp/internal/wrap.h: In function 'SEXPREC* Rcpp::internal::wrap_dispatch_unknown_iterable(const T&, Rcpp::traits::false_type) [with T = long long unsigned int, SEXP = SEXPREC*, Rcpp::traits::false_type = Rcpp::traits::integral_constant<bool, false>]':
D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include/Rcpp/internal/wrap.h:732:98:   instantiated from 'SEXPREC* Rcpp::internal::wrap_dispatch_unknown(const T&, Rcpp::traits::false_type) [with T = long long unsigned int, SEXP = SEXPREC*, Rcpp::traits::false_type = Rcpp::traits::integral_constant<bool, false>]'
D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include/Rcpp/internal/wrap.h:770:96:   instantiated from 'SEXPREC* Rcpp::internal::wrap_dispatch_eigen(const T&, Rcpp::traits::false_type) [with T = long long unsigned int, SEXP = SEXPREC*, Rcpp::traits::false_type = Rcpp::traits::integral_constant<bool, false>]'
D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include/Rcpp/internal/wrap.h:787:80:   instantiated from 'SEXPREC* Rcpp::internal::wrap_dispatch_unknown_importable(const T&, Rcpp::traits::false_type) [with T = long long unsigned int, SEXP = SEXPREC*, Rcpp::traits::false_type = Rcpp::traits::integral_constant<bool, false>]'
D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include/Rcpp/internal/wrap.h:807:99:   instantiated from 'SEXPREC* Rcpp::internal::wrap_dispatch(const T&, Rcpp::traits::wrap_type_unknown_tag) [with T = long long unsigned int, SEXP = SEXPREC*]'
D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include/Rcpp/internal/wrap_end.h:30:110:   instantiated from 'SEXPREC* Rcpp::wrap(const T&) [with T = long long unsigned int, SEXP = SEXPREC*]'
D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include/Rcpp/vector/converter.h:80:31:   instantiated from 'static SEXPREC* Rcpp::internal::generic_element_converter<RTYPE>::get(const T&) [with T = long long unsigned int, int RTYPE = 19, SEXP = SEXPREC*]'
D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include/Rcpp/vector/Vector.h:506:9:   instantiated from 'static void Rcpp::Vector<RTYPE, StoragePolicy>::replace_element__dispatch__isArgument(Rcpp::traits::false_type, Rcpp::Vector<RTYPE, StoragePolicy>::iterator, SEXP, R_xlen_t, const U&) [with U = Rcpp::traits::named_object<long long unsigned int>, int RTYPE = 19, StoragePolicy = Rcpp::PreserveStorage, Rcpp::traits::false_type = Rcpp::traits::integral_constant<bool, false>, Rcpp::Vector<RTYPE, StoragePolicy>::iterator = Rcpp::internal::Proxy_Iterator<Rcpp::internal::generic_proxy<19> >, SEXP = SEXPREC*, R_xlen_t = long long int]'
D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include/Rcpp/vector/Vector.h:499:9:   instantiated from 'static void Rcpp::Vector<RTYPE, StoragePolicy>::replace_element__dispatch(Rcpp::traits::true_type, Rcpp::Vector<RTYPE, StoragePolicy>::iterator, SEXP, R_xlen_t, const U&) [with U = Rcpp::traits::named_object<long long unsigned int>, int RTYPE = 19, StoragePolicy = Rcpp::PreserveStorage, Rcpp::traits::true_type = Rcpp::traits::integral_constant<bool, true>, Rcpp::Vector<RTYPE, StoragePolicy>::iterator = Rcpp::internal::Proxy_Iterator<Rcpp::internal::generic_proxy<19> >, SEXP = SEXPREC*, R_xlen_t = long long int]'
D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include/Rcpp/vector/Vector.h:488:9:   instantiated from 'static void Rcpp::Vector<RTYPE, StoragePolicy>::replace_element(Rcpp::Vector<RTYPE, StoragePolicy>::iterator, SEXP, R_xlen_t, const U&) [with U = Rcpp::traits::named_object<long long unsigned int>, int RTYPE = 19, StoragePolicy = Rcpp::PreserveStorage, Rcpp::Vector<RTYPE, StoragePolicy>::iterator = Rcpp::internal::Proxy_Iterator<Rcpp::internal::generic_proxy<19> >, SEXP = SEXPREC*, R_xlen_t = long long int]'
D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include/Rcpp/generated/Vector__create.h:138:2:   instantiated from 'static Rcpp::Vector<RTYPE, StoragePolicy> Rcpp::Vector<RTYPE, StoragePolicy>::create__dispatch(Rcpp::traits::true_type, const T1&, const T2&) [with T1 = Rcpp::traits::named_object<long long unsigned int>, T2 = Rcpp::traits::named_object<Rcpp::Matrix<14> >, int RTYPE = 19, StoragePolicy = Rcpp::PreserveStorage, Rcpp::Vector<RTYPE, StoragePolicy> = Rcpp::Vector<19>, Rcpp::traits::true_type = Rcpp::traits::integral_constant<bool, true>]'
D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include/Rcpp/generated/Vector__create.h:112:21:   instantiated from 'static Rcpp::Vector<RTYPE, StoragePolicy> Rcpp::Vector<RTYPE, StoragePolicy>::create(const T1&, const T2&) [with T1 = Rcpp::traits::named_object<long long unsigned int>, T2 = Rcpp::traits::named_object<Rcpp::Matrix<14> >, int RTYPE = 19, StoragePolicy = Rcpp::PreserveStorage, Rcpp::Vector<RTYPE, StoragePolicy> = Rcpp::Vector<19>]'
RcppPwiz.cpp:351:16:   instantiated from here
D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include/Rcpp/internal/wrap.h:525:11: warning: invalid conversion from 'long long unsigned int' to 'SEXP' [-fpermissive]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB  -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE     -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"d:/RCompile/r-compiling/local/local323/include" -c RcppPwizModule.cpp -o RcppPwizModule.o
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB  -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE     -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"d:/RCompile/r-compiling/local/local323/include" -c RcppIdent.cpp -o RcppIdent.o
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB  -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE     -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"d:/RCompile/r-compiling/local/local323/include" -c RcppIdentModule.cpp -o RcppIdentModule.o
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB  -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE     -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"d:/RCompile/r-compiling/local/local323/include"  -D_LARGEFILE_SOURCE -I./win//x64 -D_MSC_VER  -fgnu89-inline   -O2 -Wall  -std=gnu99 -mtune=core2 -c R_init_mzR.c -o R_init_mzR.o
cc1.exe: warning: command line option '-fpermissive' is valid for C++/ObjC++ but not for C [enabled by default]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB  -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE     -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -I"d:/RCompile/r-compiling/local/local323/include" -c rampR.cpp -o rampR.o
g++ -m64 -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 R_init_mzR.o rampR.o -L./win//x64 -lws2_32 -lnetcdf -lpwiz -Ld:/RCompile/r-compiling/local/local323/lib/x64 -Ld:/RCompile/r-compiling/local/local323/lib -LD:/biocbld/BBS-3˜1.2-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-3.2-bioc/meat/mzR.buildbin-libdir/mzR/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'mzR' as mzR_2.4.1.zip
* DONE (mzR)

mzR.Rcheck/examples_i386/mzR-Ex.timings:

nameusersystemelapsed
metadata 1.30 0.0511.17
mzR-class0.150.020.17
openMSfile1.030.041.30
peaks0.130.000.12

mzR.Rcheck/examples_x64/mzR-Ex.timings:

nameusersystemelapsed
metadata0.810.032.21
mzR-class0.100.020.11
openMSfile0.610.030.64
peaks0.110.010.12