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BioC 3.3: INSTALL report for mzR on moscato2

This page was generated on 2016-10-13 12:50:07 -0700 (Thu, 13 Oct 2016).

Package 767/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mzR 2.6.3
Bernd Fischer , Steffen Neumann , Laurent Gatto , Qiang Kou
Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/mzR
Last Changed Rev: 119743 / Revision: 122332
Last Changed Date: 2016-07-29 13:21:03 -0700 (Fri, 29 Jul 2016)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 [ OK ] TIMEOUT  skipped  skipped 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: mzR
Version: 2.6.3
Command: rm -rf mzR.buildbin-libdir && mkdir mzR.buildbin-libdir && C:\cygwin\bin\curl.exe -O http://zin2/BBS/3.3/bioc/src/contrib/mzR_2.6.3.tar.gz && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --library=mzR.buildbin-libdir --merge-multiarch mzR_2.6.3.tar.gz && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL mzR_2.6.3.zip && rm mzR_2.6.3.tar.gz mzR_2.6.3.zip
StartedAt: 2016-10-12 18:48:09 -0700 (Wed, 12 Oct 2016)
EndedAt: 2016-10-12 19:26:23 -0700 (Wed, 12 Oct 2016)
EllapsedTime: 2294.1 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   rm -rf mzR.buildbin-libdir && mkdir mzR.buildbin-libdir  && C:\cygwin\bin\curl.exe -O http://zin2/BBS/3.3/bioc/src/contrib/mzR_2.6.3.tar.gz && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --library=mzR.buildbin-libdir --merge-multiarch mzR_2.6.3.tar.gz && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL mzR_2.6.3.zip  && rm mzR_2.6.3.tar.gz mzR_2.6.3.zip
###
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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
C:/Rtools/mingw_32/bin/g++  -std=c++0x -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB  -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/local323/include" -c cramp.cpp -o cramp.o
C:/Rtools/mingw_32/bin/g++  -std=c++0x -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB  -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/local323/include" -c ramp_base64.cpp -o ramp_base64.o
C:/Rtools/mingw_32/bin/g++  -std=c++0x -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB  -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/local323/include" -c ramp.cpp -o ramp.o
C:/Rtools/mingw_32/bin/g++  -std=c++0x -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB  -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/local323/include" -c RcppRamp.cpp -o RcppRamp.o
C:/Rtools/mingw_32/bin/g++  -std=c++0x -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB  -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/local323/include" -c RcppRampModule.cpp -o RcppRampModule.o
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB  -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/local323/include"  -D_LARGEFILE_SOURCE -I./win//i386 -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
C:/Rtools/mingw_32/bin/g++  -std=c++0x -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB  -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/local323/include" -c RcppPwiz.cpp -o RcppPwiz.o
C:/Rtools/mingw_32/bin/g++  -std=c++0x -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB  -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/local323/include" -c RcppPwizModule.cpp -o RcppPwizModule.o
C:/Rtools/mingw_32/bin/g++  -std=c++0x -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB  -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/local323/include" -c RcppIdent.cpp -o RcppIdent.o
C:/Rtools/mingw_32/bin/g++  -std=c++0x -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB  -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/local323/include" -c RcppIdentModule.cpp -o RcppIdentModule.o
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB  -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/local323/include"  -D_LARGEFILE_SOURCE -I./win//i386 -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
C:/Rtools/mingw_32/bin/g++  -std=c++0x -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB  -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/local323/include" -c rampR.cpp -o rampR.o
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 R_init_mzR.o rampR.o -Wl,--dynamic-linker=c:/uldar/ld.exe -L./win//i386 -lws2_32 -lnetcdf -lpwiz -Lc:/local323/lib/i386 -Lc:/local323/lib -LE:/biocbld/BBS-3˜1.3-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-3.3-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
C:/Rtools/mingw_64/bin/g++  -std=c++0x -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB  -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/local323/include" -c cramp.cpp -o cramp.o
C:/Rtools/mingw_64/bin/g++  -std=c++0x -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB  -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/local323/include" -c ramp_base64.cpp -o ramp_base64.o
C:/Rtools/mingw_64/bin/g++  -std=c++0x -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB  -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/local323/include" -c ramp.cpp -o ramp.o
C:/Rtools/mingw_64/bin/g++  -std=c++0x -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB  -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/local323/include" -c RcppRamp.cpp -o RcppRamp.o
C:/Rtools/mingw_64/bin/g++  -std=c++0x -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB  -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/local323/include" -c RcppRampModule.cpp -o RcppRampModule.o
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB  -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/local323/include"  -D_LARGEFILE_SOURCE -I./win//x64 -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
C:/Rtools/mingw_64/bin/g++  -std=c++0x -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB  -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/local323/include" -c RcppPwiz.cpp -o RcppPwiz.o
C:/Rtools/mingw_64/bin/g++  -std=c++0x -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB  -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/local323/include" -c RcppPwizModule.cpp -o RcppPwizModule.o
C:/Rtools/mingw_64/bin/g++  -std=c++0x -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB  -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/local323/include" -c RcppIdent.cpp -o RcppIdent.o
C:/Rtools/mingw_64/bin/g++  -std=c++0x -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB  -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/local323/include" -c RcppIdentModule.cpp -o RcppIdentModule.o
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB  -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/local323/include"  -D_LARGEFILE_SOURCE -I./win//x64 -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
C:/Rtools/mingw_64/bin/g++  -std=c++0x -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB  -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/local323/include" -c rampR.cpp -o rampR.o
C:/Rtools/mingw_64/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 R_init_mzR.o rampR.o -Wl,--dynamic-linker=c:/uldar/ld.exe -L./win//x64 -lws2_32 -lnetcdf -lpwiz -Lc:/local323/lib/x64 -Lc:/local323/lib -LE:/biocbld/BBS-3˜1.3-B/R/bin/x64 -lR
installing to E:/biocbld/bbs-3.3-bioc/meat/mzR.buildbin-libdir/mzR/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'mzR' as mzR_2.6.3.zip
* DONE (mzR)
* installing to library 'E:/biocbld/bbs-3.3-bioc/R/library'
package 'mzR' successfully unpacked and MD5 sums checked