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BioC 2.13: CHECK report for rTANDEM on zin1

This page was generated on 2014-04-05 09:48:32 -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: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings rTANDEM_1.2.1.tar.gz
StartedAt: 2014-04-05 03:46:20 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 03:48:54 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 153.6 seconds
RetCode: 0
Status:  OK 
CheckDir: rTANDEM.Rcheck
Warnings: 0

Command output

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/rTANDEM.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘rTANDEM’ can be installed ... [121s/125s] OK
* checking installed package size ... NOTE
  installed size is 13.3Mb
  sub-directories of 1Mb or more:
    extdata   2.9Mb
    libs     10.1Mb
* 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
* 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
File ‘/home/biocbuild/bbs-2.13-bioc/meat/rTANDEM.Rcheck/rTANDEM/libs/rTANDEM.so’:
  Found non-API call to R: ‘R_CStackLimit’

Compiled code should not call non-API entry points in R.

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 ... [3s/3s] 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
  ‘/home/biocbuild/bbs-2.13-bioc/meat/rTANDEM.Rcheck/00check.log’
for details.

rTANDEM.Rcheck/00install.out:

* installing *source* package ‘rTANDEM’ ...
** libs
g++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c base64.cpp -o base64.o
g++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c dataLoader.cpp -o dataLoader.o
g++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -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++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c masscalc.cpp -o masscalc.o
g++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c mbiomlreport.cpp -o mbiomlreport.o
g++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -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++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c mplugin.cpp -o mplugin.o
g++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -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++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -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++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -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++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -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++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -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++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -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++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c msequencecollection.cpp -o msequencecollection.o
g++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c msequenceserver.cpp -o msequenceserver.o
g++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c msequtilities.cpp -o msequtilities.o
g++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -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++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -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++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -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++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -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++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -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++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -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++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -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++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -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++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -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++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -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++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -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++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -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++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -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++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c stdafx.cpp -o stdafx.o
g++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -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++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -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++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -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++ -shared -L/usr/local/lib -o rTANDEM.so 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 -lpthread -lexpat -L/home/biocbuild/bbs-2.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.13-bioc/meat/rTANDEM.Rcheck/rTANDEM/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (rTANDEM)

rTANDEM.Rcheck/rTANDEM-Ex.timings:

nameusersystemelapsed
accessor0.6840.0080.694
conversion0.0600.0000.059
rTANDEM-package0.4880.0000.488
rTResult-class0.0040.0000.004
tandem0.4560.0240.484