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BioC 2.13: CHECK report for rTANDEM on moscato1

This page was generated on 2014-04-05 09:51:09 -0700 (Sat, 05 Apr 2014).

Package 630/750HostnameOS / ArchBUILDCHECKBUILD BIN
rTANDEM 1.2.1
Frederic Fournier
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/rTANDEM
Last Changed Rev: 86057 / Revision: 88450
Last Changed Date: 2014-02-04 10:03:14 -0800 (Tue, 04 Feb 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK [ OK ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: rTANDEM
Version: 1.2.1
Command: rm -rf rTANDEM.buildbin-libdir && mkdir rTANDEM.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=rTANDEM.buildbin-libdir rTANDEM_1.2.1.tar.gz >rTANDEM-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=rTANDEM.buildbin-libdir --install="check:rTANDEM-install.out" --force-multiarch --no-vignettes --timings rTANDEM_1.2.1.tar.gz && mv rTANDEM.buildbin-libdir/* rTANDEM.Rcheck/ && rmdir rTANDEM.buildbin-libdir
StartedAt: 2014-04-05 06:32:47 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 06:38:22 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 335.8 seconds
RetCode: 0
Status:  OK  
CheckDir: rTANDEM.Rcheck
Warnings: 0

Command output

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/rTANDEM.Rcheck'
* using R version 3.0.3 (2014-03-06)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'rTANDEM/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'rTANDEM' version '1.2.1'
* 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 'rTANDEM' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.7Mb
  sub-directories of 1Mb or more:
    extdata   2.9Mb
    libs      2.5Mb
* 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 ... NOTE
Namespace in Imports field not imported from: 'methods'
  All declared Imports should be used.
Packages in Depends field not imported from:
  'Rcpp' 'XML' 'data.table'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* 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 ... NOTE
Package has both 'src/Makevars.in' and 'src/Makevars'.
Installation with --no-configure' is unlikely to work.  If you intended
'src/Makevars' to be used on Windows, rename it to 'src/Makevars.win'
otherwise remove it.  If 'configure' created 'src/Makevars', you need a
'cleanup' script.
* 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-2.13-bioc/meat/rTANDEM.buildbin-libdir/rTANDEM/libs/i386/rTANDEM.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'D:/biocbld/bbs-2.13-bioc/meat/rTANDEM.buildbin-libdir/rTANDEM/libs/x64/rTANDEM.dll':
  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.  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 for old-style vignette sources ... NOTE
Vignette sources only in 'inst/doc':
  'rTANDEM.Rnw'
A 'vignettes' directory will be required as from R 3.1.0
* checking examples ...
** running examples for arch 'i386' ... [4s] OK
** running examples for arch 'x64' ... [6s] 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

NOTE: There were 5 notes.
See
  'D:/biocbld/bbs-2.13-bioc/meat/rTANDEM.Rcheck/00check.log'
for details.

rTANDEM.Rcheck/00install.out:


install for i386

* installing *source* package 'rTANDEM' ...
** libs
g++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c base64.cpp -o base64.o
g++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c dataLoader.cpp -o dataLoader.o
g++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c loadmspectrum.cpp -o loadmspectrum.o
In file included from mspectrum.h:142:0,
                 from loadmspectrum.cpp:142:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
g++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c masscalc.cpp -o masscalc.o
g++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c mbiomlreport.cpp -o mbiomlreport.o
g++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c mpam.cpp -o mpam.o
In file included from mspectrum.h:142:0,
                 from mspectrumcondition.h:153,
                 from mprocess.h:143,
                 from mpam.cpp:137:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
g++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c mplugin.cpp -o mplugin.o
g++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c mpmods.cpp -o mpmods.o
In file included from mspectrum.h:142:0,
                 from mspectrumcondition.h:153,
                 from mprocess.h:143,
                 from mpmods.cpp:137:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
g++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c mprocess.cpp -o mprocess.o
In file included from mspectrum.h:142:0,
                 from mprocess.cpp:157:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
mprocess.cpp: In member function 'virtual bool mprocess::create_score(const msequence&, size_t, size_t, long int, bool)':
mprocess.cpp:440:7: warning: unused variable 'bC' [-Wunused-variable]
mprocess.cpp: In member function 'bool mprocess::report_valid(double)':
mprocess.cpp:2472:9: warning: unused variable 'c' [-Wunused-variable]
mprocess.cpp:2476:9: warning: unused variable 'tLast' [-Wunused-variable]
mprocess.cpp: In member function 'bool mprocess::score_single(const msequence&)':
mprocess.cpp:3390:64: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
mprocess.cpp: In member function 'bool mprocess::initialize_crc()':
mprocess.cpp:4843:14: warning: unused variable 'crc' [-Wunused-variable]
g++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c mrefine.cpp -o mrefine.o
In file included from mspectrum.h:142:0,
                 from mrefine.cpp:137:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
mrefine.cpp: In member function 'virtual bool mrefine::refine()':
mrefine.cpp:250:9: warning: unused variable 'a' [-Wunused-variable]
mrefine.cpp:251:9: warning: unused variable 'tActiveNow' [-Wunused-variable]
g++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c mreport.cpp -o mreport.o
In file included from mspectrum.h:142:0,
                 from saxhandler.h:137,
                 from saxsaphandler.h:140,
                 from mreport.cpp:143:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
mreport.cpp: In member function 'bool mreport::masses(msequtilities&)':
mreport.cpp:655:78: warning: array subscript has type 'char' [-Wchar-subscripts]
mreport.cpp:646:9: warning: unused variable 'a' [-Wunused-variable]
g++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c mscore.cpp -o mscore.o
In file included from mspectrum.h:142:0,
                 from mscore.cpp:153:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
g++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c mscore_tandem.cpp -o mscore_tandem.o
In file included from mspectrum.h:142:0,
                 from mscore_tandem.cpp:135:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
mscore_tandem.cpp: In member function 'bool mscore_tandem::blur(std::vector<mi>&)':
mscore_tandem.cpp:288:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
mscore_tandem.cpp: In member function 'virtual double mscore_tandem::dot(long unsigned int*)':
mscore_tandem.cpp:358:8: warning: unused variable 'fValue0' [-Wunused-variable]
mscore_tandem.cpp:362:9: warning: unused variable 'b' [-Wunused-variable]
mscore_tandem.cpp: In member function 'virtual float mscore_tandem::ion_check(long unsigned int, size_t)':
mscore_tandem.cpp:581:16: warning: unused variable 'a' [-Wunused-variable]
mscore_tandem.cpp:582:16: warning: unused variable 'lCount' [-Wunused-variable]
mscore_tandem.cpp:583:7: warning: unused variable 'lType' [-Wunused-variable]
mscore_tandem.cpp:584:9: warning: unused variable 'b' [-Wunused-variable]
g++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c msequencecollection.cpp -o msequencecollection.o
g++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c msequenceserver.cpp -o msequenceserver.o
g++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c msequtilities.cpp -o msequtilities.o
g++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c mspectrumcondition.cpp -o mspectrumcondition.o
In file included from mspectrum.h:142:0,
                 from mspectrumcondition.cpp:154:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
g++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c mtermmods.cpp -o mtermmods.o
In file included from mspectrum.h:142:0,
                 from mspectrumcondition.h:153,
                 from mprocess.h:143,
                 from mtermmods.cpp:137:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
g++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c mxxcleavage.cpp -o mxxcleavage.o
In file included from mspectrum.h:142:0,
                 from mspectrumcondition.h:153,
                 from mprocess.h:143,
                 from mxxcleavage.cpp:137:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
g++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c saxbiomlhandler.cpp -o saxbiomlhandler.o
In file included from mspectrum.h:142:0,
                 from saxhandler.h:137,
                 from saxbiomlhandler.h:140,
                 from saxbiomlhandler.cpp:140:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
g++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c saxgamlhandler.cpp -o saxgamlhandler.o
In file included from mspectrum.h:142:0,
                 from saxhandler.h:137,
                 from saxgamlhandler.h:140,
                 from saxgamlhandler.cpp:139:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
g++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c saxhandler.cpp -o saxhandler.o
In file included from mspectrum.h:142:0,
                 from saxhandler.h:137,
                 from saxhandler.cpp:132:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
g++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c saxmodhandler.cpp -o saxmodhandler.o
In file included from mspectrum.h:142:0,
                 from saxhandler.h:137,
                 from saxmodhandler.h:140,
                 from saxmodhandler.cpp:140:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
g++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c saxmzdatahandler.cpp -o saxmzdatahandler.o
In file included from mspectrum.h:142:0,
                 from saxhandler.h:137,
                 from saxmzdatahandler.h:4,
                 from saxmzdatahandler.cpp:28:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
g++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c saxmzmlhandler.cpp -o saxmzmlhandler.o
In file included from mspectrum.h:142:0,
                 from saxhandler.h:137,
                 from saxmzmlhandler.h:4,
                 from saxmzmlhandler.cpp:33:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
g++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c saxmzxmlhandler.cpp -o saxmzxmlhandler.o
In file included from mspectrum.h:142:0,
                 from saxhandler.h:137,
                 from saxmzxmlhandler.h:4,
                 from saxmzxmlhandler.cpp:20:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
g++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c saxsaphandler.cpp -o saxsaphandler.o
In file included from mspectrum.h:142:0,
                 from saxhandler.h:137,
                 from saxsaphandler.h:140,
                 from saxsaphandler.cpp:140:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
g++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c saxtandeminputhandler.cpp -o saxtandeminputhandler.o
In file included from mspectrum.h:142:0,
                 from saxhandler.h:137,
                 from saxtandeminputhandler.h:140,
                 from saxtandeminputhandler.cpp:139:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
g++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c saxtaxhandler.cpp -o saxtaxhandler.o
In file included from mspectrum.h:142:0,
                 from saxhandler.h:137,
                 from saxtaxhandler.h:140,
                 from saxtaxhandler.cpp:139:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
g++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c stdafx.cpp -o stdafx.o
g++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c tandem.cpp -o tandem.o
In file included from mspectrum.h:142:0,
                 from tandem.h:15,
                 from tandem.cpp:143:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
tandem.cpp: In function 'SEXPREC* tandem(SEXP, SEXP, SEXP, SEXP, SEXP)':
tandem.cpp:277:12: warning: unused variable 'tCount' [-Wunused-variable]
g++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c xmlparameter.cpp -o xmlparameter.o
In file included from mspectrum.h:142:0,
                 from saxhandler.h:137,
                 from saxtandeminputhandler.h:140,
                 from xmlparameter.cpp:144:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
g++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c xmltaxonomy.cpp -o xmltaxonomy.o
In file included from mspectrum.h:142:0,
                 from saxhandler.h:137,
                 from saxtaxhandler.h:140,
                 from xmltaxonomy.cpp:160:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
g++ -m32 -shared -s -static-libgcc -o rTANDEM.dll tmp.def base64.o dataLoader.o loadmspectrum.o masscalc.o mbiomlreport.o mpam.o mplugin.o mpmods.o mprocess.o mrefine.o mreport.o mscore.o mscore_tandem.o msequencecollection.o msequenceserver.o msequtilities.o mspectrumcondition.o mtermmods.o mxxcleavage.o saxbiomlhandler.o saxgamlhandler.o saxhandler.o saxmodhandler.o saxmzdatahandler.o saxmzmlhandler.o saxmzxmlhandler.o saxsaphandler.o saxtandeminputhandler.o saxtaxhandler.o stdafx.o tandem.o xmlparameter.o xmltaxonomy.o -L -L -LC:/test_libexpata/i386/lib -shared -lexpat -lpthread -Ld:/RCompile/CRANpkg/extralibs64/local/lib/i386 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LD:/biocbld/BBS-2˜1.13-/R/bin/i386 -lR
c:/rtools31/gcc-4.6.3/bin/../lib/gcc/i686-w64-mingw32/4.6.3/../../../../i686-w64-mingw32/bin/ld.exe: skipping incompatible C:/test_libexpata/i386/lib/libexpat.a when searching for -lexpat
installing to D:/biocbld/bbs-2.13-bioc/meat/rTANDEM.buildbin-libdir/rTANDEM/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'rTANDEM' ...
** libs
g++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c base64.cpp -o base64.o
g++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c dataLoader.cpp -o dataLoader.o
g++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c loadmspectrum.cpp -o loadmspectrum.o
In file included from mspectrum.h:142:0,
                 from loadmspectrum.cpp:142:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
g++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c masscalc.cpp -o masscalc.o
g++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c mbiomlreport.cpp -o mbiomlreport.o
g++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c mpam.cpp -o mpam.o
In file included from mspectrum.h:142:0,
                 from mspectrumcondition.h:153,
                 from mprocess.h:143,
                 from mpam.cpp:137:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
g++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c mplugin.cpp -o mplugin.o
g++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c mpmods.cpp -o mpmods.o
In file included from mspectrum.h:142:0,
                 from mspectrumcondition.h:153,
                 from mprocess.h:143,
                 from mpmods.cpp:137:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
g++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c mprocess.cpp -o mprocess.o
In file included from mspectrum.h:142:0,
                 from mprocess.cpp:157:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
mprocess.cpp: In member function 'virtual bool mprocess::create_score(const msequence&, size_t, size_t, long int, bool)':
mprocess.cpp:440:7: warning: unused variable 'bC' [-Wunused-variable]
mprocess.cpp: In member function 'bool mprocess::report_valid(double)':
mprocess.cpp:2472:9: warning: unused variable 'c' [-Wunused-variable]
mprocess.cpp:2476:9: warning: unused variable 'tLast' [-Wunused-variable]
mprocess.cpp: In member function 'bool mprocess::score_single(const msequence&)':
mprocess.cpp:3390:64: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
mprocess.cpp: In member function 'bool mprocess::initialize_crc()':
mprocess.cpp:4843:14: warning: unused variable 'crc' [-Wunused-variable]
g++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c mrefine.cpp -o mrefine.o
In file included from mspectrum.h:142:0,
                 from mrefine.cpp:137:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
mrefine.cpp: In member function 'virtual bool mrefine::refine()':
mrefine.cpp:250:9: warning: unused variable 'a' [-Wunused-variable]
mrefine.cpp:251:9: warning: unused variable 'tActiveNow' [-Wunused-variable]
g++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c mreport.cpp -o mreport.o
In file included from mspectrum.h:142:0,
                 from saxhandler.h:137,
                 from saxsaphandler.h:140,
                 from mreport.cpp:143:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
mreport.cpp: In member function 'bool mreport::masses(msequtilities&)':
mreport.cpp:655:78: warning: array subscript has type 'char' [-Wchar-subscripts]
mreport.cpp:646:9: warning: unused variable 'a' [-Wunused-variable]
g++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c mscore.cpp -o mscore.o
In file included from mspectrum.h:142:0,
                 from mscore.cpp:153:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
g++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c mscore_tandem.cpp -o mscore_tandem.o
In file included from mspectrum.h:142:0,
                 from mscore_tandem.cpp:135:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
mscore_tandem.cpp: In member function 'bool mscore_tandem::blur(std::vector<mi>&)':
mscore_tandem.cpp:288:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
mscore_tandem.cpp: In member function 'virtual double mscore_tandem::dot(long unsigned int*)':
mscore_tandem.cpp:358:8: warning: unused variable 'fValue0' [-Wunused-variable]
mscore_tandem.cpp:362:9: warning: unused variable 'b' [-Wunused-variable]
mscore_tandem.cpp: In member function 'virtual float mscore_tandem::ion_check(long unsigned int, size_t)':
mscore_tandem.cpp:581:16: warning: unused variable 'a' [-Wunused-variable]
mscore_tandem.cpp:582:16: warning: unused variable 'lCount' [-Wunused-variable]
mscore_tandem.cpp:583:7: warning: unused variable 'lType' [-Wunused-variable]
mscore_tandem.cpp:584:9: warning: unused variable 'b' [-Wunused-variable]
g++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c msequencecollection.cpp -o msequencecollection.o
g++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c msequenceserver.cpp -o msequenceserver.o
g++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c msequtilities.cpp -o msequtilities.o
g++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c mspectrumcondition.cpp -o mspectrumcondition.o
In file included from mspectrum.h:142:0,
                 from mspectrumcondition.cpp:154:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
g++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c mtermmods.cpp -o mtermmods.o
In file included from mspectrum.h:142:0,
                 from mspectrumcondition.h:153,
                 from mprocess.h:143,
                 from mtermmods.cpp:137:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
g++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c mxxcleavage.cpp -o mxxcleavage.o
In file included from mspectrum.h:142:0,
                 from mspectrumcondition.h:153,
                 from mprocess.h:143,
                 from mxxcleavage.cpp:137:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
g++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c saxbiomlhandler.cpp -o saxbiomlhandler.o
In file included from mspectrum.h:142:0,
                 from saxhandler.h:137,
                 from saxbiomlhandler.h:140,
                 from saxbiomlhandler.cpp:140:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
g++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c saxgamlhandler.cpp -o saxgamlhandler.o
In file included from mspectrum.h:142:0,
                 from saxhandler.h:137,
                 from saxgamlhandler.h:140,
                 from saxgamlhandler.cpp:139:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
g++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c saxhandler.cpp -o saxhandler.o
In file included from mspectrum.h:142:0,
                 from saxhandler.h:137,
                 from saxhandler.cpp:132:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
g++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c saxmodhandler.cpp -o saxmodhandler.o
In file included from mspectrum.h:142:0,
                 from saxhandler.h:137,
                 from saxmodhandler.h:140,
                 from saxmodhandler.cpp:140:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
g++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c saxmzdatahandler.cpp -o saxmzdatahandler.o
In file included from mspectrum.h:142:0,
                 from saxhandler.h:137,
                 from saxmzdatahandler.h:4,
                 from saxmzdatahandler.cpp:28:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
g++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c saxmzmlhandler.cpp -o saxmzmlhandler.o
In file included from mspectrum.h:142:0,
                 from saxhandler.h:137,
                 from saxmzmlhandler.h:4,
                 from saxmzmlhandler.cpp:33:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
g++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c saxmzxmlhandler.cpp -o saxmzxmlhandler.o
In file included from mspectrum.h:142:0,
                 from saxhandler.h:137,
                 from saxmzxmlhandler.h:4,
                 from saxmzxmlhandler.cpp:20:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
g++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c saxsaphandler.cpp -o saxsaphandler.o
In file included from mspectrum.h:142:0,
                 from saxhandler.h:137,
                 from saxsaphandler.h:140,
                 from saxsaphandler.cpp:140:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
g++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c saxtandeminputhandler.cpp -o saxtandeminputhandler.o
In file included from mspectrum.h:142:0,
                 from saxhandler.h:137,
                 from saxtandeminputhandler.h:140,
                 from saxtandeminputhandler.cpp:139:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
g++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c saxtaxhandler.cpp -o saxtaxhandler.o
In file included from mspectrum.h:142:0,
                 from saxhandler.h:137,
                 from saxtaxhandler.h:140,
                 from saxtaxhandler.cpp:139:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
g++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c stdafx.cpp -o stdafx.o
g++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c tandem.cpp -o tandem.o
In file included from mspectrum.h:142:0,
                 from tandem.h:15,
                 from tandem.cpp:143:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
tandem.cpp: In function 'SEXPREC* tandem(SEXP, SEXP, SEXP, SEXP, SEXP)':
tandem.cpp:277:12: warning: unused variable 'tCount' [-Wunused-variable]
g++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c xmlparameter.cpp -o xmlparameter.o
In file included from mspectrum.h:142:0,
                 from saxhandler.h:137,
                 from saxtandeminputhandler.h:140,
                 from xmlparameter.cpp:144:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
g++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c xmltaxonomy.cpp -o xmltaxonomy.o
In file included from mspectrum.h:142:0,
                 from saxhandler.h:137,
                 from saxtaxhandler.h:140,
                 from xmltaxonomy.cpp:160:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
g++ -m64 -shared -s -static-libgcc -o rTANDEM.dll tmp.def base64.o dataLoader.o loadmspectrum.o masscalc.o mbiomlreport.o mpam.o mplugin.o mpmods.o mprocess.o mrefine.o mreport.o mscore.o mscore_tandem.o msequencecollection.o msequenceserver.o msequtilities.o mspectrumcondition.o mtermmods.o mxxcleavage.o saxbiomlhandler.o saxgamlhandler.o saxhandler.o saxmodhandler.o saxmzdatahandler.o saxmzmlhandler.o saxmzxmlhandler.o saxsaphandler.o saxtandeminputhandler.o saxtaxhandler.o stdafx.o tandem.o xmlparameter.o xmltaxonomy.o -L -L -LC:/test_libexpata/x64/lib -shared -lexpat -lpthread -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LD:/biocbld/BBS-2˜1.13-/R/bin/x64 -lR
installing to D:/biocbld/bbs-2.13-bioc/meat/rTANDEM.buildbin-libdir/rTANDEM/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'rTANDEM' as rTANDEM_1.2.1.zip
* DONE (rTANDEM)

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

nameusersystemelapsed
accessor0.850.040.92
conversion000
rTANDEM-package0.670.000.70
rTResult-class000
tandem0.930.020.95

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

nameusersystemelapsed
accessor1.440.001.70
conversion0.000.010.02
rTANDEM-package0.810.020.82
rTResult-class0.020.000.02
tandem0.960.031.09