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CHECK report for flowWorkspace on tokay1

This page was generated on 2019-04-13 11:21:38 -0400 (Sat, 13 Apr 2019).

Package 554/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowWorkspace 3.30.2
Greg Finak ,Mike Jiang
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/flowWorkspace
Branch: RELEASE_3_8
Last Commit: eac7b2d
Last Changed Date: 2019-01-04 13:33:27 -0400 (Fri, 04 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: flowWorkspace
Version: 3.30.2
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flowWorkspace.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings flowWorkspace_3.30.2.tar.gz
StartedAt: 2019-04-13 02:20:03 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 02:24:16 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 253.9 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: flowWorkspace.Rcheck
Warnings: 2

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flowWorkspace.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings flowWorkspace_3.30.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/flowWorkspace.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-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 '3.30.2'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOgG1q4/R.INSTALL1bf4598c1d9c/flowWorkspace/man/estimateLogicle.GatingHierarchy.Rd:20: file link 'estimateLogicle' in package 'flowCore' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.8-bioc/meat/flowWorkspace.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
  installed size is 15.6Mb
  sub-directories of 1Mb or more:
    lib    7.2Mb
    libs   6.6Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
Versioned 'LinkingTo' values for
  'BH' 'RProtoBufLib' 'cytolib'
are only usable in R >= 3.0.2
* 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
Namespaces in Imports field not imported from:
  'RBGL' 'grDevices' 'graphics'
  All declared Imports should be used.
Unexported objects imported by ':::' calls:
  'flowCore:::.estimateLogicle' 'flowCore:::checkClass'
  'flowCore:::copyFlowSet' 'flowCore:::guid'
  'flowCore:::logicle_transform' 'flowCore:::updateTransformKeywords'
  '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:
  '.cpp_setIndices' '.getNodeInd'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
getGate,GatingSetList-character: warning in unlist(res, recur = FALSE):
  partial argument match of 'recur' to 'recursive'
.addGatingHierarchies: no visible global function definition for 'is'
.computeCV : <anonymous>: no visible binding for global variable
  'xml.count'
.computeCV : <anonymous>: no visible binding for global variable
  'openCyto.count'
.computeCV : <anonymous> : <anonymous>: no visible global function
  definition for 'IQR'
.computeCV : <anonymous> : <anonymous>: no visible global function
  definition for 'median'
.computeCV_gh : <anonymous>: no visible global function definition for
  'IQR'
.computeCV_gh : <anonymous>: no visible global function definition for
  'median'
.dropRedundantNodes : <anonymous>: no visible global function
  definition for 'is'
.getSingleCellExpression: no visible binding for global variable
  'parallel'
.graph_handler : asGraphNEL: no visible global function definition for
  'new'
.graph_handler : asGraphNEL: no visible global function definition for
  'validObject'
.load_gs: no visible global function definition for 'new'
.load_gs: no visible global function definition for '.hasSlot'
.load_gs: no visible global function definition for 'slot'
.load_gs: no visible global function definition for 'is'
.mergeGates : <anonymous>: no visible global function definition for
  'extends'
.parse.pData: no visible binding for global variable '.'
.plotGate: no visible global function definition for 'new'
.plotGate: no visible global function definition for 'as.formula'
.preplot: no visible global function definition for 'as'
.preprocessMap: no visible binding for global variable 'old'
.preprocessMap: no visible binding for global variable '.'
.preprocessor: no visible binding for global variable 'groupName'
GatingSetList: no visible global function definition for 'as'
GatingSetList: no visible global function definition for 'validObject'
booleanFilter: no visible global function definition for 'new'
booleanFilter: no visible global function definition for 'is'
char2booleanFilter: no visible global function definition for 'new'
dropRedundantNodes : <anonymous>: no visible global function definition
  for 'is'
flowWorkspace.par.init: no visible global function definition for
  'gray'
getMergedStats: no visible binding for global variable 'sampleName'
mkformula: no visible global function definition for 'as.formula'
pop.MFI: no visible binding for global variable 'desc'
save_gslist: no visible binding for global variable 'slot'
transformerList: no visible global function definition for 'is'
transformerList: no visible binding for global variable 'is'
GatingSet,GatingHierarchy-character: no visible global function
  definition for 'new'
GatingSet,character-character: no visible global function definition
  for 'new'
GatingSet,flowSet-ANY: no visible global function definition for 'new'
Rm,character-GatingSetList-character: no visible global function
  definition for 'selectMethod'
[,GatingSet-ANY: no visible global function definition for 'extends'
[,GatingSetList-ANY: no visible global function definition for
  'callNextMethod'
[,GatingSetList-ANY: no visible global function definition for 'as'
[[,GatingSet-character: no visible global function definition for 'new'
add,GatingHierarchy-logicalFilterResult: no visible global function
  definition for 'selectMethod'
add,GatingSet-filtersList: no visible global function definition for
  'selectMethod'
add,GatingSet-list: no visible global function definition for
  'selectMethod'
add,GatingSetList-filter: no visible global function definition for
  'selectMethod'
add,GatingSetList-filterList: no visible global function definition for
  'selectMethod'
add,GatingSetList-filters: no visible global function definition for
  'selectMethod'
add,GatingSetList-filtersList: no visible global function definition
  for 'selectMethod'
add,GatingSetList-list: no visible global function definition for
  'selectMethod'
getPopStats,GatingHierarchy: no visible binding for global variable
  'node'
keyword,GatingSetList-character: no visible global function definition
  for 'selectMethod'
keyword,GatingSetList-missing: no visible global function definition
  for 'selectMethod'
openWorkspace,character: no visible global function definition for
  'new'
pData<-,GatingSetList-data.frame: no visible global function definition
  for 'callNextMethod'
pData<-,GatingSetList-data.frame: no visible global function definition
  for 'as'
plotGate,GatingSetList-character: no visible global function definition
  for 'selectMethod'
rbind2,GatingSetList-missing: no visible global function definition for
  'new'
rbind2,GatingSetList-missing: no visible binding for global variable
  'slot'
recompute,GatingSetList: no visible global function definition for
  'selectMethod'
show,flowJoWorkspace: no visible global function definition for '.'
show,flowJoWorkspace: no visible binding for global variable
  'groupName'
transform,GatingSet: no visible global function definition for 'is'
transform,GatingSet : <anonymous>: no visible global function
  definition for 'is'
Undefined global functions or variables:
  . .hasSlot IQR as as.formula callNextMethod desc extends gray
  groupName is median new node old openCyto.count parallel sampleName
  selectMethod slot validObject xml.count
Consider adding
  importFrom("grDevices", "gray")
  importFrom("methods", ".hasSlot", "as", "callNextMethod", "extends",
             "is", "new", "selectMethod", "slot", "validObject")
  importFrom("stats", "IQR", "as.formula", "median")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 ... WARNING
Undocumented arguments in documentation object 'add,GatingSet,list-method'
  'cluster_method_name'

Undocumented arguments in documentation object 'plot_diff_tree'
  'path' '...'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in shell scripts ... 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 ... NOTE
GNU make is a SystemRequirements.
* 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 'C:/Users/biocbuild/bbs-3.8-bioc/R/library/flowWorkspace/libs/i386/flowWorkspace.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
  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 use Fortran I/O
nor system RNGs. 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 6 NOTEs
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/flowWorkspace.Rcheck/00check.log'
for details.

Installation output

flowWorkspace.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/flowWorkspace_3.30.2.tar.gz && rm -rf flowWorkspace.buildbin-libdir && mkdir flowWorkspace.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=flowWorkspace.buildbin-libdir flowWorkspace_3.30.2.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL flowWorkspace_3.30.2.zip && rm flowWorkspace_3.30.2.tar.gz flowWorkspace_3.30.2.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 2832k  100 2832k    0     0  41.0M      0 --:--:-- --:--:-- --:--:-- 43.2M

install for i386

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

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


** libs
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -IC:/libxml2//i386/include/libxml2 -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c R_API.cpp -o R_API.o
In file included from C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
                 from C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_API.cpp:9:
C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:103:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < x.size(); i++){
                     ^
C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:228:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < nEvents; i++)
                     ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -IC:/libxml2//i386/include/libxml2 -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c R_GatingHierarchy.cpp -o R_GatingHierarchy.o
In file included from C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
                 from C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from R_GatingHierarchy.cpp:17:
C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:103:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < x.size(); i++){
                     ^
C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:228:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < nEvents; i++)
                     ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -IC:/libxml2//i386/include/libxml2 -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c R_GatingSet.cpp -o R_GatingSet.o
In file included from ../inst/include/flowWorkspace/openWorkspace.hpp:12:0,
                 from R_GatingSet.cpp:10:
../inst/include/flowWorkspace/winFlowJoWorkspace.hpp:433:30: warning: "/*" within comment [-Wcomment]
     * "*[local-name()='edge']/*[local-name()='vertex']" is for ellipsoidGate
 ^
In file included from C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
                 from ../inst/include/flowWorkspace/wsNode.hpp:10,
                 from ../inst/include/flowWorkspace/workspace.hpp:14,
                 from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
                 from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
                 from R_GatingSet.cpp:10:
C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:103:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < x.size(); i++){
                     ^
C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:228:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < nEvents; i++)
                     ^
In file included from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11:0,
                 from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
                 from R_GatingSet.cpp:10:
../inst/include/flowWorkspace/workspace.hpp: In member function 'void workspace::toArray(std::string, std::vector<double>&, std::vector<double>&)':
../inst/include/flowWorkspace/workspace.hpp:108:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(unsigned i=0;i<nLen;i++)
                       ^
In file included from ../inst/include/flowWorkspace/openWorkspace.hpp:12:0,
                 from R_GatingSet.cpp:10:
../inst/include/flowWorkspace/winFlowJoWorkspace.hpp: In member function 'virtual trans_local xFlowJoWorkspace::getTransformation(wsRootNode, const compensation&, PARAM_VEC&, trans_global_vec*, biexpTrans*, linTrans*, bool)':
../inst/include/flowWorkspace/winFlowJoWorkspace.hpp:802:12: warning: unused variable 'minRange' [-Wunused-variable]
     double minRange=atof(transNode.getProperty("minRange").c_str());
            ^
In file included from C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15:0,
                 from C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/flowWorkspace/wsNode.hpp:10,
                 from ../inst/include/flowWorkspace/workspace.hpp:14,
                 from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
                 from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
                 from R_GatingSet.cpp:10:
C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp: In member function 'CurlyGuadGate* winFlowJoWorkspace::getGate(wsCurlyQuadGateNode&)':
C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:1314:94: warning: 'quad' may be used uninitialized in this function [-Wmaybe-uninitialized]
  CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),interpolated(false),quadrant(_quad){
                                                                                              ^
In file included from ../inst/include/flowWorkspace/openWorkspace.hpp:12:0,
                 from R_GatingSet.cpp:10:
../inst/include/flowWorkspace/winFlowJoWorkspace.hpp:410:10: note: 'quad' was declared here
     QUAD quad;
          ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -IC:/libxml2//i386/include/libxml2 -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
In file included from C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
                 from C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from ../inst/include/flowWorkspace.h:5,
                 from RcppExports.cpp:4:
C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:103:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < x.size(); i++){
                     ^
C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:228:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < nEvents; i++)
                     ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -IC:/libxml2//i386/include/libxml2 -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c getDescendants.cpp -o getDescendants.o
In file included from C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
                 from C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getDescendants.cpp:2:
C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:103:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < x.size(); i++){
                     ^
C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:228:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < nEvents; i++)
                     ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -IC:/libxml2//i386/include/libxml2 -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c getSingleCellExpression.cpp -o getSingleCellExpression.o
In file included from C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
                 from C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from getSingleCellExpression.cpp:2:
C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:103:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < x.size(); i++){
                     ^
C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:228:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < nEvents; i++)
                     ^
getSingleCellExpression.cpp: In function 'Rcpp::NumericMatrix getSingleCellExpressionByGate(Rcpp::XPtr<GatingSet>, std::string, Rcpp::List, Rcpp::NumericMatrix, Rcpp::CharacterVector, bool)':
getSingleCellExpression.cpp:73:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(unsigned j = 0; j < pops.size(); ++j){
                           ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -IC:/libxml2//i386/include/libxml2 -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c setCounts.cpp -o setCounts.o
In file included from C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
                 from C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from setCounts.cpp:2:
C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:103:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < x.size(); i++){
                     ^
C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:228:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < nEvents; i++)
                     ^
mkdir -p "C:/Users/biocbuild/bbs-3.8-bioc/meat/flowWorkspace.buildbin-libdir/flowWorkspace/lib/i386"
C:/Rtools/mingw_32/bin/ar rs "C:/Users/biocbuild/bbs-3.8-bioc/meat/flowWorkspace.buildbin-libdir/flowWorkspace/lib/i386/libflowWorkspace.a" R_API.o R_GatingHierarchy.o R_GatingSet.o RcppExports.o getDescendants.o getSingleCellExpression.o setCounts.o
C:\Rtools\mingw_32\bin\ar.exe: creating C:/Users/biocbuild/bbs-3.8-bioc/meat/flowWorkspace.buildbin-libdir/flowWorkspace/lib/i386/libflowWorkspace.a
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o flowWorkspace.dll tmp.def R_API.o R_GatingHierarchy.o R_GatingSet.o RcppExports.o getDescendants.o getSingleCellExpression.o setCounts.o C:/libxml2//i386/lib/libxml2.a C:/Users/biocbuild/bbs-3.8-bioc/R/library/RProtoBufLib/lib/i386/GatingSet.pb.o C:/Users/biocbuild/bbs-3.8-bioc/R/library/RProtoBufLib/lib/i386/libprotobuf.a -lws2_32 -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/flowWorkspace.buildbin-libdir/flowWorkspace/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'flowWorkspace'
    finding HTML links ... done
    GatingHierarchy-class                   html  
    GatingSet-class                         html  
    GatingSet-methods                       html  
    finding level-2 HTML links ... done

    GatingSetList-class                     html  
    add                                     html  
    asinh_Gml2                              html  
    asinhtGml2_trans                        html  
    booleanFilter-class                     html  
    checkRedundantNodes                     html  
    clone                                   html  
    compensate                              html  
    compute_timestep                        html  
    dropRedundantChannels                   html  
    dropRedundantNodes                      html  
    estimateLogicle.GatingHierarchy         html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOgG1q4/R.INSTALL1bf4598c1d9c/flowWorkspace/man/estimateLogicle.GatingHierarchy.Rd:20: file link 'estimateLogicle' in package 'flowCore' does not exist and so has been treated as a topic
    extract_cluster_pop_name_from_node      html  
    filterObject                            html  
    fix_channel_slash                       html  
    flowData                                html  
    flowJo.fasinh                           html  
    flowJo.flog                             html  
    flowJoTrans                             html  
    flowJoWorkspace-class                   html  
    flowJo_biexp_trans                      html  
    flowJo_fasinh_trans                     html  
    flowWorkspace-package                   html  
    flowWorkspace.par.get                   html  
    flowWorkspace.par.init                  html  
    flow_breaks                             html  
    flow_trans                              html  
    getCompensationMatrices                 html  
    getCompensationObj                      html  
    getData-methods                         html  
    getDescendants                          html  
    getFJWSubsetIndices                     html  
    getGate                                 html  
    getIndiceMat                            html  
    getIndices-GatingSet-name-method        html  
    getIndices                              html  
    getKeywords                             html  
    getMergedStats                          html  
    getNodes                                html  
    getParent                               html  
    getPopStats                             html  
    getSampleGroups                         html  
    getSamples                              html  
    getSingleCellExpression                 html  
    getStats                                html  
    getTransformations                      html  
    gh_check_cluster_node                   html  
    gh_get_cluster_labels                   html  
    groupByChannels                         html  
    groupByTree                             html  
    insertGate                              html  
    isNcdf                                  html  
    keyword                                 html  
    lapply-methods                          html  
    length                                  html  
    logicleGml2_trans                       html  
    logicle_trans                           html  
    loglevel                                html  
    logtGml2_trans                          html  
    markernames                             html  
    mkformula                               html  
    moveNode                                html  
    ncFlowSet-methods                       html  
    nodeflags                               html  
    openWorkspace                           html  
    pData-methods                           html  
    parseWorkspace                          html  
    plot-methods                            html  
    plotGate-methods                        html  
    plotPopCV                               html  
    plot_diff_tree                          html  
    prettyAxis                              html  
    recompute                               html  
    sampleNames                             html  
    save_gs                                 html  
    set.count.xml                           html  
    setGate                                 html  
    setNode-methods                         html  
    standardize-GatingSet                   html  
    stats.fun                               html  
    subset                                  html  
    transform                               html  
    transformerList                         html  
    updateChannels                          html  
    updateIndices-GatingHierarchy-character-logical-method
                                            html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

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

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


** libs
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -IC:/libxml2//x64/include/libxml2 -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c R_API.cpp -o R_API.o
In file included from C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
                 from C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_API.cpp:9:
C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:103:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < x.size(); i++){
                     ^
C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:228:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < nEvents; i++)
                     ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -IC:/libxml2//x64/include/libxml2 -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c R_GatingHierarchy.cpp -o R_GatingHierarchy.o
In file included from C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
                 from C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from R_GatingHierarchy.cpp:17:
C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:103:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < x.size(); i++){
                     ^
C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:228:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < nEvents; i++)
                     ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -IC:/libxml2//x64/include/libxml2 -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c R_GatingSet.cpp -o R_GatingSet.o
In file included from ../inst/include/flowWorkspace/openWorkspace.hpp:12:0,
                 from R_GatingSet.cpp:10:
../inst/include/flowWorkspace/winFlowJoWorkspace.hpp:433:30: warning: "/*" within comment [-Wcomment]
     * "*[local-name()='edge']/*[local-name()='vertex']" is for ellipsoidGate
 ^
In file included from C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
                 from ../inst/include/flowWorkspace/wsNode.hpp:10,
                 from ../inst/include/flowWorkspace/workspace.hpp:14,
                 from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
                 from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
                 from R_GatingSet.cpp:10:
C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:103:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < x.size(); i++){
                     ^
C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:228:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < nEvents; i++)
                     ^
In file included from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11:0,
                 from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
                 from R_GatingSet.cpp:10:
../inst/include/flowWorkspace/workspace.hpp: In member function 'void workspace::toArray(std::string, std::vector<double>&, std::vector<double>&)':
../inst/include/flowWorkspace/workspace.hpp:108:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(unsigned i=0;i<nLen;i++)
                       ^
In file included from ../inst/include/flowWorkspace/openWorkspace.hpp:12:0,
                 from R_GatingSet.cpp:10:
../inst/include/flowWorkspace/winFlowJoWorkspace.hpp: In member function 'virtual trans_local xFlowJoWorkspace::getTransformation(wsRootNode, const compensation&, PARAM_VEC&, trans_global_vec*, biexpTrans*, linTrans*, bool)':
../inst/include/flowWorkspace/winFlowJoWorkspace.hpp:802:12: warning: unused variable 'minRange' [-Wunused-variable]
     double minRange=atof(transNode.getProperty("minRange").c_str());
            ^
In file included from C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15:0,
                 from C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/flowWorkspace/wsNode.hpp:10,
                 from ../inst/include/flowWorkspace/workspace.hpp:14,
                 from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
                 from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
                 from R_GatingSet.cpp:10:
C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp: In member function 'CurlyGuadGate* winFlowJoWorkspace::getGate(wsCurlyQuadGateNode&)':
C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:1314:94: warning: 'quad' may be used uninitialized in this function [-Wmaybe-uninitialized]
  CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),interpolated(false),quadrant(_quad){
                                                                                              ^
In file included from ../inst/include/flowWorkspace/openWorkspace.hpp:12:0,
                 from R_GatingSet.cpp:10:
../inst/include/flowWorkspace/winFlowJoWorkspace.hpp:410:10: note: 'quad' was declared here
     QUAD quad;
          ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -IC:/libxml2//x64/include/libxml2 -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
In file included from C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
                 from C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from ../inst/include/flowWorkspace.h:5,
                 from RcppExports.cpp:4:
C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:103:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < x.size(); i++){
                     ^
C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:228:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < nEvents; i++)
                     ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -IC:/libxml2//x64/include/libxml2 -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c getDescendants.cpp -o getDescendants.o
In file included from C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
                 from C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getDescendants.cpp:2:
C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:103:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < x.size(); i++){
                     ^
C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:228:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < nEvents; i++)
                     ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -IC:/libxml2//x64/include/libxml2 -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c getSingleCellExpression.cpp -o getSingleCellExpression.o
In file included from C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
                 from C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from getSingleCellExpression.cpp:2:
C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:103:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < x.size(); i++){
                     ^
C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:228:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < nEvents; i++)
                     ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -IC:/libxml2//x64/include/libxml2 -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c setCounts.cpp -o setCounts.o
In file included from C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
                 from C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from setCounts.cpp:2:
C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:103:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < x.size(); i++){
                     ^
C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:228:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < nEvents; i++)
                     ^
mkdir -p "C:/Users/biocbuild/bbs-3.8-bioc/meat/flowWorkspace.buildbin-libdir/flowWorkspace/lib/x64"
C:/Rtools/mingw_64/bin/ar rs "C:/Users/biocbuild/bbs-3.8-bioc/meat/flowWorkspace.buildbin-libdir/flowWorkspace/lib/x64/libflowWorkspace.a" R_API.o R_GatingHierarchy.o R_GatingSet.o RcppExports.o getDescendants.o getSingleCellExpression.o setCounts.o
C:\Rtools\mingw_64\bin\ar.exe: creating C:/Users/biocbuild/bbs-3.8-bioc/meat/flowWorkspace.buildbin-libdir/flowWorkspace/lib/x64/libflowWorkspace.a
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o flowWorkspace.dll tmp.def R_API.o R_GatingHierarchy.o R_GatingSet.o RcppExports.o getDescendants.o getSingleCellExpression.o setCounts.o C:/libxml2//x64/lib/libxml2.a C:/Users/biocbuild/bbs-3.8-bioc/R/library/RProtoBufLib/lib/x64/GatingSet.pb.o C:/Users/biocbuild/bbs-3.8-bioc/R/library/RProtoBufLib/lib/x64/libprotobuf.a -lws2_32 -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/flowWorkspace.buildbin-libdir/flowWorkspace/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'flowWorkspace' as flowWorkspace_3.30.2.zip
* DONE (flowWorkspace)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'flowWorkspace' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

flowWorkspace.Rcheck/tests_i386/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(flowWorkspace)
Loading required package: flowCore
Loading required package: ncdfFlow
Loading required package: RcppArmadillo
Loading required package: BH
> 
> test_check("flowWorkspace")

Attaching package: 'dplyr'

The following objects are masked from 'package:data.table':

    between, first, last

The following object is masked from 'package:ncdfFlow':

    filter

The following object is masked from 'package:flowCore':

    filter

The following object is masked from 'package:testthat':

    matches

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:dplyr':

    combine, intersect, setdiff, union

The following object is masked from 'package:flowCore':

    normalize

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

mac version of flowJo workspace recognized.
== testthat results  ===========================================================
OK: 781 SKIPPED: 3 FAILED: 0
> 
> #devtools::test("˜/rglab/workspace/flowWorkspace")
> #devtools::check_man()
> #test_file("/home/wjiang2/rglab/workspace/flowWorkspace/tests/testthat/test-archive.R")
> #test_file("/home/wjiang2/rglab/workspace/flowWorkspace/tests/testthat/test-parseWorkspace.R")
> 
> #test_file("/home/wjiang2/rglab/workspace/flowWorkspace/tests/testthat/InternalTestSuite.R")
> 
> 
> proc.time()
   user  system elapsed 
  29.82    3.48   33.31

flowWorkspace.Rcheck/tests_x64/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(flowWorkspace)
Loading required package: flowCore
Loading required package: ncdfFlow
Loading required package: RcppArmadillo
Loading required package: BH
> 
> test_check("flowWorkspace")

Attaching package: 'dplyr'

The following objects are masked from 'package:data.table':

    between, first, last

The following object is masked from 'package:ncdfFlow':

    filter

The following object is masked from 'package:flowCore':

    filter

The following object is masked from 'package:testthat':

    matches

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:dplyr':

    combine, intersect, setdiff, union

The following object is masked from 'package:flowCore':

    normalize

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

mac version of flowJo workspace recognized.
== testthat results  ===========================================================
OK: 781 SKIPPED: 3 FAILED: 0
> 
> #devtools::test("˜/rglab/workspace/flowWorkspace")
> #devtools::check_man()
> #test_file("/home/wjiang2/rglab/workspace/flowWorkspace/tests/testthat/test-archive.R")
> #test_file("/home/wjiang2/rglab/workspace/flowWorkspace/tests/testthat/test-parseWorkspace.R")
> 
> #test_file("/home/wjiang2/rglab/workspace/flowWorkspace/tests/testthat/InternalTestSuite.R")
> 
> 
> proc.time()
   user  system elapsed 
  30.45    2.76   33.28

Example timings

flowWorkspace.Rcheck/examples_i386/flowWorkspace-Ex.timings

nameusersystemelapsed
GatingHierarchy-class2.010.142.16
GatingSet-class1.130.141.26
GatingSet-methods000
GatingSetList-class000
add000
asinh_Gml2000
asinhtGml2_trans000
booleanFilter-class0.010.000.01
checkRedundantNodes000
clone000
compensate000
dropRedundantChannels000
dropRedundantNodes000
estimateLogicle.GatingHierarchy000
extract_cluster_pop_name_from_node000
flowJo.fasinh000
flowJo.flog000
flowJoTrans000
flowJoWorkspace-class0.030.000.03
flowJo_biexp_trans0.880.020.89
flowJo_fasinh_trans000
flowWorkspace.par.get000
flow_breaks0.670.020.69
getCompensationMatrices000
getData-methods000
getDescendants0.010.000.01
getGate000
getIndices-GatingSet-name-method000
getIndices000
getKeywords0.160.010.46
getMergedStats000
getParent000
getPopStats000
getSampleGroups000
getSamples000
getSingleCellExpression000
getStats000
getTransformations000
groupByChannels000
groupByTree000
insertGate000
keyword000
logicleGml2_trans000
logicle_trans000
loglevel000
logtGml2_trans000
markernames000
mkformula000
moveNode0.060.000.06
openWorkspace000
parseWorkspace000
plot-methods000
plotGate-methods000
plotPopCV000
plot_diff_tree000
prettyAxis000
sampleNames000
save_gs000
set.count.xml000
setGate000
setNode-methods000
transform000
transformerList000
updateChannels000
updateIndices-GatingHierarchy-character-logical-method0.370.100.46

flowWorkspace.Rcheck/examples_x64/flowWorkspace-Ex.timings

nameusersystemelapsed
GatingHierarchy-class2.080.142.24
GatingSet-class1.310.141.46
GatingSet-methods000
GatingSetList-class000
add000
asinh_Gml2000
asinhtGml2_trans000
booleanFilter-class000
checkRedundantNodes000
clone000
compensate000
dropRedundantChannels000
dropRedundantNodes000
estimateLogicle.GatingHierarchy0.020.000.02
extract_cluster_pop_name_from_node000
flowJo.fasinh000
flowJo.flog000
flowJoTrans000
flowJoWorkspace-class0.020.020.03
flowJo_biexp_trans0.430.110.54
flowJo_fasinh_trans000
flowWorkspace.par.get000
flow_breaks0.490.040.54
getCompensationMatrices000
getData-methods000
getDescendants0.010.000.01
getGate000
getIndices-GatingSet-name-method000
getIndices000
getKeywords0.170.020.19
getMergedStats000
getParent000
getPopStats000
getSampleGroups000
getSamples000
getSingleCellExpression000
getStats000
getTransformations000
groupByChannels000
groupByTree000
insertGate000
keyword000
logicleGml2_trans000
logicle_trans000
loglevel000
logtGml2_trans000
markernames000
mkformula000
moveNode0.050.010.07
openWorkspace000
parseWorkspace000
plot-methods000
plotGate-methods000
plotPopCV000
plot_diff_tree000
prettyAxis000
sampleNames000
save_gs000
set.count.xml000
setGate000
setNode-methods000
transform000
transformerList0.010.000.01
updateChannels000
updateIndices-GatingHierarchy-character-logical-method0.520.160.67