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BioC 3.0: CHECK report for flowWorkspace on moscato1

This page was generated on 2015-04-10 09:47:07 -0700 (Fri, 10 Apr 2015).

Package 324/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowWorkspace 3.12.06
Greg Finak ,Mike Jiang
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/flowWorkspace
Last Changed Rev: 100927 / Revision: 102249
Last Changed Date: 2015-03-20 10:30:59 -0700 (Fri, 20 Mar 2015)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  WARNINGS 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK [ WARNINGS ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  WARNINGS  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  WARNINGS  OK 

Summary

Package: flowWorkspace
Version: 3.12.06
Command: rm -rf flowWorkspace.buildbin-libdir flowWorkspace.Rcheck && mkdir flowWorkspace.buildbin-libdir flowWorkspace.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=flowWorkspace.buildbin-libdir flowWorkspace_3.12.06.tar.gz >flowWorkspace.Rcheck\00install.out 2>&1 && cp flowWorkspace.Rcheck\00install.out flowWorkspace-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=flowWorkspace.buildbin-libdir --install="check:flowWorkspace-install.out" --force-multiarch --no-vignettes --timings flowWorkspace_3.12.06.tar.gz
StartedAt: 2015-04-10 01:11:32 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 01:32:55 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 1283.0 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: flowWorkspace.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf flowWorkspace.buildbin-libdir flowWorkspace.Rcheck && mkdir flowWorkspace.buildbin-libdir flowWorkspace.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=flowWorkspace.buildbin-libdir flowWorkspace_3.12.06.tar.gz >flowWorkspace.Rcheck\00install.out 2>&1 && cp flowWorkspace.Rcheck\00install.out flowWorkspace-install.out  && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=flowWorkspace.buildbin-libdir --install="check:flowWorkspace-install.out" --force-multiarch --no-vignettes --timings flowWorkspace_3.12.06.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/flowWorkspace.Rcheck'
* using R version 3.1.3 (2015-03-09)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'flowWorkspace/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'flowWorkspace' version '3.12.06'
* 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 'flowWorkspace' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 14.3Mb
  sub-directories of 1Mb or more:
    libs   10.1Mb
    tests   2.8Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'graph' 'Biobase' 'gridExtra'
A package should be listed in only one of these fields.
* 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
'library' or 'require' call to 'RSVGTipsDevice' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespaces in Imports field not imported from:
  'Cairo' 'IDPmisc' 'RBGL' 'graphics'
  All declared Imports should be used.
Unexported objects imported by ':::' calls:
  'Rgraphviz:::getRenderPar' 'flowCore:::checkClass'
  'flowCore:::copyFlowSet' 'flowCore:::guid' 'graph:::.makeEdgeKeys'
  'lattice:::updateList' 'ncdfFlow:::.isValidSamples'
  'stats:::.splinefun'
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  '.addTrans' '.load_gs' '.uuid_gen' 'isNegated'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.addGatingHierarchies: no visible global function definition for
  'read.ncdfFlowSet'
.addGatingHierarchies : <anonymous>: no visible global function
  definition for 'flowFrame'
.addGatingHierarchies: no visible global function definition for
  'flowSet'
.computeCV : <anonymous>: no visible binding for global variable
  'flowJo.count'
.computeCV : <anonymous>: no visible binding for global variable
  'flowCore.count'
.getTransformations : <anonymous> : f: no visible binding for global
  variable 'max_val'
.getTransformations : <anonymous> : f: no visible binding for global
  variable 'decade'
.getTransformations : <anonymous> : f: no visible binding for global
  variable 'min_val'
.plotGate: no visible global function definition for 'sampleNames<-'
.plotGate : <anonymous>: no visible global function definition for
  'sampleNames<-'
.renderNodes.svgAnno: no visible global function definition for 'nodes'
GatingSetList: no visible global function definition for 'ncdfFlowList'
getData,GatingSetList-ANY: no visible global function definition for
  'ncdfFlowList'
pData<-,GatingSet-data.frame: no visible global function definition for
  'varMetadata'
pData<-,GatingSet-data.frame: no visible global function definition for
  'phenoData'
pData<-,GatingSet-data.frame: no visible global function definition for
  'varMetadata<-'
pData<-,GatingSet-data.frame: no visible global function definition for
  'phenoData<-'
rbind2,GatingSetList-missing: no visible global function definition for
  'ncdfFlowList'
sampleNames<-,GatingSet-ANY: no visible global function definition for
  'sampleNames<-'
* 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 ... WARNING
Found the following file(s) containing GNU extensions:
  src/Makevars.in
Portable Makefiles do not use GNU extensions such as +=, :=, $(shell),
$(wildcard), ifeq ... endif. See section 'Writing portable packages' in
the 'Writing R Extensions' manual.
* 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-3.0-bioc/meat/flowWorkspace.buildbin-libdir/flowWorkspace/libs/i386/flowWorkspace.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'puts', possibly from 'printf' (C), 'puts' (C)
File 'D:/biocbld/bbs-3.0-bioc/meat/flowWorkspace.buildbin-libdir/flowWorkspace/libs/x64/flowWorkspace.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'puts', possibly from 'printf' (C), 'puts' (C)

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' ... [21s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
GatingHierarchy-class 5.00   0.11    7.69
GatingSet-class       4.08   0.10    6.25
** running examples for arch 'x64' ... [16s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
GatingHierarchy-class 5.59   0.16    5.74
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'run-all.R' [308s]
 [309s] OK
** running tests for arch 'x64' ...
  Running 'run-all.R' [195s]
 [195s] 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

WARNING: There was 1 warning.
NOTE: There were 5 notes.
See
  'D:/biocbld/bbs-3.0-bioc/meat/flowWorkspace.Rcheck/00check.log'
for details.

flowWorkspace.Rcheck/00install.out:


install for i386

* installing *source* package 'flowWorkspace' ...

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
g++ -m32 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -DROUT -Wno-deprecated -Ic:/libxml2//i386/include/libxml2  -Ic:/boost//i386/include -DLIBXML_STATIC   -I"D:/biocbld/bbs-3.0-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c GatingHierarchy.cpp -o GatingHierarchy.o
g++ -m32 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -DROUT -Wno-deprecated -Ic:/libxml2//i386/include/libxml2  -Ic:/boost//i386/include -DLIBXML_STATIC   -I"D:/biocbld/bbs-3.0-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c GatingSet.cpp -o GatingSet.o
g++ -m32 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -DROUT -Wno-deprecated -Ic:/libxml2//i386/include/libxml2  -Ic:/boost//i386/include -DLIBXML_STATIC   -I"D:/biocbld/bbs-3.0-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c POPINDICES.cpp -o POPINDICES.o
g++ -m32 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -DROUT -Wno-deprecated -Ic:/libxml2//i386/include/libxml2  -Ic:/boost//i386/include -DLIBXML_STATIC   -I"D:/biocbld/bbs-3.0-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c R_API.cpp -o R_API.o
g++ -m32 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -DROUT -Wno-deprecated -Ic:/libxml2//i386/include/libxml2  -Ic:/boost//i386/include -DLIBXML_STATIC   -I"D:/biocbld/bbs-3.0-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c R_GatingHierarchy.cpp -o R_GatingHierarchy.o
g++ -m32 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -DROUT -Wno-deprecated -Ic:/libxml2//i386/include/libxml2  -Ic:/boost//i386/include -DLIBXML_STATIC   -I"D:/biocbld/bbs-3.0-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c R_GatingSet.cpp -o R_GatingSet.o
g++ -m32 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -DROUT -Wno-deprecated -Ic:/libxml2//i386/include/libxml2  -Ic:/boost//i386/include -DLIBXML_STATIC   -I"D:/biocbld/bbs-3.0-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
g++ -m32 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -DROUT -Wno-deprecated -Ic:/libxml2//i386/include/libxml2  -Ic:/boost//i386/include -DLIBXML_STATIC   -I"D:/biocbld/bbs-3.0-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c calibrationTable.cpp -o calibrationTable.o
g++ -m32 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -DROUT -Wno-deprecated -Ic:/libxml2//i386/include/libxml2  -Ic:/boost//i386/include -DLIBXML_STATIC   -I"D:/biocbld/bbs-3.0-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c flowData.cpp -o flowData.o
g++ -m32 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -DROUT -Wno-deprecated -Ic:/libxml2//i386/include/libxml2  -Ic:/boost//i386/include -DLIBXML_STATIC   -I"D:/biocbld/bbs-3.0-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c flowJoWorkspace.cpp -o flowJoWorkspace.o
g++ -m32 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -DROUT -Wno-deprecated -Ic:/libxml2//i386/include/libxml2  -Ic:/boost//i386/include -DLIBXML_STATIC   -I"D:/biocbld/bbs-3.0-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c gate.cpp -o gate.o
g++ -m32 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -DROUT -Wno-deprecated -Ic:/libxml2//i386/include/libxml2  -Ic:/boost//i386/include -DLIBXML_STATIC   -I"D:/biocbld/bbs-3.0-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c global.cpp -o global.o
g++ -m32 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -DROUT -Wno-deprecated -Ic:/libxml2//i386/include/libxml2  -Ic:/boost//i386/include -DLIBXML_STATIC   -I"D:/biocbld/bbs-3.0-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c macFlowJoWorkspace.cpp -o macFlowJoWorkspace.o
g++ -m32 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -DROUT -Wno-deprecated -Ic:/libxml2//i386/include/libxml2  -Ic:/boost//i386/include -DLIBXML_STATIC   -I"D:/biocbld/bbs-3.0-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c nodeProperties.cpp -o nodeProperties.o
g++ -m32 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -DROUT -Wno-deprecated -Ic:/libxml2//i386/include/libxml2  -Ic:/boost//i386/include -DLIBXML_STATIC   -I"D:/biocbld/bbs-3.0-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c spline.cpp -o spline.o
g++ -m32 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -DROUT -Wno-deprecated -Ic:/libxml2//i386/include/libxml2  -Ic:/boost//i386/include -DLIBXML_STATIC   -I"D:/biocbld/bbs-3.0-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c transformation.cpp -o transformation.o
g++ -m32 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -DROUT -Wno-deprecated -Ic:/libxml2//i386/include/libxml2  -Ic:/boost//i386/include -DLIBXML_STATIC   -I"D:/biocbld/bbs-3.0-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c winFlowJoWorkspace.cpp -o winFlowJoWorkspace.o
winFlowJoWorkspace.cpp:488:27: warning: "/*" within comment [-Wcomment]
g++ -m32 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -DROUT -Wno-deprecated -Ic:/libxml2//i386/include/libxml2  -Ic:/boost//i386/include -DLIBXML_STATIC   -I"D:/biocbld/bbs-3.0-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c workspace.cpp -o workspace.o
g++ -m32 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -DROUT -Wno-deprecated -Ic:/libxml2//i386/include/libxml2  -Ic:/boost//i386/include -DLIBXML_STATIC   -I"D:/biocbld/bbs-3.0-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c wsNode.cpp -o wsNode.o
g++ -m32 -shared -s -static-libgcc -o flowWorkspace.dll tmp.def GatingHierarchy.o GatingSet.o POPINDICES.o R_API.o R_GatingHierarchy.o R_GatingSet.o RcppExports.o calibrationTable.o flowData.o flowJoWorkspace.o gate.o global.o macFlowJoWorkspace.o nodeProperties.o spline.o transformation.o winFlowJoWorkspace.o workspace.o wsNode.o -L/usr/lib/x86_64-linux-gnu -Lc:/libxml2//i386/lib c:/libxml2//i386/lib/libxml2.a c:/boost//i386/lib/libboost_serialization-mgw46-mt-1_52.a c:/boost//i386/lib/libboost_regex-mgw46-mt-1_52.a -lws2_32 -Ld:/RCompile/CRANpkg/extralibs64/local/lib/i386 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LD:/biocbld/BBS-3˜1.0-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-3.0-bioc/meat/flowWorkspace.buildbin-libdir/flowWorkspace/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 'flowWorkspace' ...

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
g++ -m64 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -DROUT -Wno-deprecated -Ic:/libxml2//x64/include/libxml2  -Ic:/boost//x64/include -DLIBXML_STATIC   -I"D:/biocbld/bbs-3.0-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c GatingHierarchy.cpp -o GatingHierarchy.o
g++ -m64 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -DROUT -Wno-deprecated -Ic:/libxml2//x64/include/libxml2  -Ic:/boost//x64/include -DLIBXML_STATIC   -I"D:/biocbld/bbs-3.0-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c GatingSet.cpp -o GatingSet.o
g++ -m64 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -DROUT -Wno-deprecated -Ic:/libxml2//x64/include/libxml2  -Ic:/boost//x64/include -DLIBXML_STATIC   -I"D:/biocbld/bbs-3.0-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c POPINDICES.cpp -o POPINDICES.o
g++ -m64 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -DROUT -Wno-deprecated -Ic:/libxml2//x64/include/libxml2  -Ic:/boost//x64/include -DLIBXML_STATIC   -I"D:/biocbld/bbs-3.0-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c R_API.cpp -o R_API.o
g++ -m64 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -DROUT -Wno-deprecated -Ic:/libxml2//x64/include/libxml2  -Ic:/boost//x64/include -DLIBXML_STATIC   -I"D:/biocbld/bbs-3.0-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c R_GatingHierarchy.cpp -o R_GatingHierarchy.o
g++ -m64 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -DROUT -Wno-deprecated -Ic:/libxml2//x64/include/libxml2  -Ic:/boost//x64/include -DLIBXML_STATIC   -I"D:/biocbld/bbs-3.0-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c R_GatingSet.cpp -o R_GatingSet.o
g++ -m64 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -DROUT -Wno-deprecated -Ic:/libxml2//x64/include/libxml2  -Ic:/boost//x64/include -DLIBXML_STATIC   -I"D:/biocbld/bbs-3.0-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
g++ -m64 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -DROUT -Wno-deprecated -Ic:/libxml2//x64/include/libxml2  -Ic:/boost//x64/include -DLIBXML_STATIC   -I"D:/biocbld/bbs-3.0-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c calibrationTable.cpp -o calibrationTable.o
g++ -m64 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -DROUT -Wno-deprecated -Ic:/libxml2//x64/include/libxml2  -Ic:/boost//x64/include -DLIBXML_STATIC   -I"D:/biocbld/bbs-3.0-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c flowData.cpp -o flowData.o
g++ -m64 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -DROUT -Wno-deprecated -Ic:/libxml2//x64/include/libxml2  -Ic:/boost//x64/include -DLIBXML_STATIC   -I"D:/biocbld/bbs-3.0-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c flowJoWorkspace.cpp -o flowJoWorkspace.o
g++ -m64 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -DROUT -Wno-deprecated -Ic:/libxml2//x64/include/libxml2  -Ic:/boost//x64/include -DLIBXML_STATIC   -I"D:/biocbld/bbs-3.0-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c gate.cpp -o gate.o
g++ -m64 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -DROUT -Wno-deprecated -Ic:/libxml2//x64/include/libxml2  -Ic:/boost//x64/include -DLIBXML_STATIC   -I"D:/biocbld/bbs-3.0-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c global.cpp -o global.o
g++ -m64 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -DROUT -Wno-deprecated -Ic:/libxml2//x64/include/libxml2  -Ic:/boost//x64/include -DLIBXML_STATIC   -I"D:/biocbld/bbs-3.0-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c macFlowJoWorkspace.cpp -o macFlowJoWorkspace.o
g++ -m64 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -DROUT -Wno-deprecated -Ic:/libxml2//x64/include/libxml2  -Ic:/boost//x64/include -DLIBXML_STATIC   -I"D:/biocbld/bbs-3.0-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c nodeProperties.cpp -o nodeProperties.o
g++ -m64 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -DROUT -Wno-deprecated -Ic:/libxml2//x64/include/libxml2  -Ic:/boost//x64/include -DLIBXML_STATIC   -I"D:/biocbld/bbs-3.0-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c spline.cpp -o spline.o
g++ -m64 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -DROUT -Wno-deprecated -Ic:/libxml2//x64/include/libxml2  -Ic:/boost//x64/include -DLIBXML_STATIC   -I"D:/biocbld/bbs-3.0-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c transformation.cpp -o transformation.o
g++ -m64 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -DROUT -Wno-deprecated -Ic:/libxml2//x64/include/libxml2  -Ic:/boost//x64/include -DLIBXML_STATIC   -I"D:/biocbld/bbs-3.0-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c winFlowJoWorkspace.cpp -o winFlowJoWorkspace.o
winFlowJoWorkspace.cpp:488:27: warning: "/*" within comment [-Wcomment]
g++ -m64 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -DROUT -Wno-deprecated -Ic:/libxml2//x64/include/libxml2  -Ic:/boost//x64/include -DLIBXML_STATIC   -I"D:/biocbld/bbs-3.0-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c workspace.cpp -o workspace.o
g++ -m64 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -DROUT -Wno-deprecated -Ic:/libxml2//x64/include/libxml2  -Ic:/boost//x64/include -DLIBXML_STATIC   -I"D:/biocbld/bbs-3.0-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c wsNode.cpp -o wsNode.o
g++ -m64 -shared -s -static-libgcc -o flowWorkspace.dll tmp.def GatingHierarchy.o GatingSet.o POPINDICES.o R_API.o R_GatingHierarchy.o R_GatingSet.o RcppExports.o calibrationTable.o flowData.o flowJoWorkspace.o gate.o global.o macFlowJoWorkspace.o nodeProperties.o spline.o transformation.o winFlowJoWorkspace.o workspace.o wsNode.o -L/usr/lib/x86_64-linux-gnu -Lc:/libxml2//x64/lib c:/libxml2//x64/lib/libxml2.a c:/boost//x64/lib/libboost_serialization-mgw46-mt-1_52.a c:/boost//x64/lib/libboost_regex-mgw46-mt-1_52.a -lws2_32 -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LD:/biocbld/BBS-3˜1.0-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-3.0-bioc/meat/flowWorkspace.buildbin-libdir/flowWorkspace/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'flowWorkspace' as flowWorkspace_3.12.06.zip
* DONE (flowWorkspace)

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

nameusersystemelapsed
GatingHierarchy-class5.000.117.69
GatingSet-class4.080.106.25
GatingSet-methods000
GatingSetList-class000
add0.020.000.02
clone000
flowJoWorkspace-class0.080.010.09
flowWorkspace.par.get000
getCompensationMatrices000
getData-methods000
getGate000
getIndices-GatingSet-name-method000
getIndices000
getKeywords0.420.021.68
getNodes000
getParent000
getPopStats000
getSample000
getSampleGroups000
getSamples000
getSingleCellExpression000
getTransformations000
insertGate000
keyword000
loglevel000
mkformula000
openWorkspace000
parseWorkspace000
plot-methods000
plotGate-methods000
plotPopCV000
prettyAxis000
sampleNames000
save_gs000
setGate000
setNode-methods000
transform000

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

nameusersystemelapsed
GatingHierarchy-class5.590.165.74
GatingSet-class3.850.214.29
GatingSet-methods000
GatingSetList-class000
add0.020.000.02
clone000
flowJoWorkspace-class0.060.000.06
flowWorkspace.par.get000
getCompensationMatrices000
getData-methods000
getGate000
getIndices-GatingSet-name-method000
getIndices000
getKeywords0.220.070.28
getNodes000
getParent000
getPopStats000
getSample000
getSampleGroups000
getSamples000
getSingleCellExpression000
getTransformations000
insertGate000
keyword000
loglevel000
mkformula000
openWorkspace000
parseWorkspace000
plot-methods0.020.000.02
plotGate-methods000
plotPopCV000
prettyAxis000
sampleNames000
save_gs000
setGate000
setNode-methods000
transform0.010.000.01