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CHECK report for CytoML on tokay1

This page was generated on 2020-04-15 12:26:55 -0400 (Wed, 15 Apr 2020).

Package 401/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CytoML 1.12.1
Mike Jiang
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/CytoML
Branch: RELEASE_3_10
Last Commit: 2167017
Last Changed Date: 2020-03-26 14:39:11 -0400 (Thu, 26 Mar 2020)
malbec1 Linux (Ubuntu 18.04.4 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: CytoML
Version: 1.12.1
Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CytoML.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings CytoML_1.12.1.tar.gz
StartedAt: 2020-04-15 02:27:36 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 02:35:47 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 491.1 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: CytoML.Rcheck
Warnings: 2

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CytoML.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings CytoML_1.12.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/CytoML.Rcheck'
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CytoML/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CytoML' version '1.12.1'
* package encoding: UTF-8
* 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 'CytoML' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 13.8Mb
  sub-directories of 1Mb or more:
    extdata   4.8Mb
    lib       1.9Mb
    libs      5.8Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'methods'
A package should be listed in only one of these fields.
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:
  'RUnit' 'corpcor'
  All declared Imports should be used.
Unexported objects imported by ':::' calls:
  'flowWorkspace:::.addGatingHierarchies' 'lattice:::updateList'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.parse.pData: no visible binding for global variable '.'
DerivedParameterNode: no visible global function definition for
  'write.csv'
DerivedParametersNode: no visible global function definition for
  'gs_get_pop_paths'
addCustomInfo: no visible global function definition for
  'gh_get_transformations'
addGate: no visible binding for global variable 'id'
addGate: no visible binding for global variable 'gate_id'
addGate: no visible binding for global variable 'fcs'
addGate: no visible binding for global variable 'gate_def'
addGate: no visible binding for global variable 'name'
booleanNode: no visible global function definition for 'filter_to_list'
constructPopNode: no visible global function definition for
  'gh_pop_get_gate'
constructPopNode : <anonymous>: no visible global function definition
  for 'gh_pop_get_gate'
constructTree: no visible binding for global variable 'id'
constructTree: no visible binding for global variable 'name'
createTransformIdentifier: no visible global function definition for
  'slotNames'
cytobank_to_gatingset.cytobank_experiment: no visible binding for
  global variable 'desc'
diva_to_gatingset: no visible binding for global variable 'specimen'
diva_to_gatingset: no visible binding for global variable
  'sampleSelected'
export_comp_trans: no visible global function definition for
  'gh_get_compensations'
export_comp_trans: no visible global function definition for
  'gh_get_transformations'
export_gates_cytobank: no visible global function definition for
  'gs_get_pop_paths'
export_gates_cytobank: no visible global function definition for
  'gs_pop_get_gate'
extend.polygonGate: no visible binding for global variable '..dim'
extend.polygonGate : <anonymous>: no visible binding for global
  variable 'y'
extend.polygonGate : <anonymous>: no visible binding for global
  variable 'x'
extend.polygonGate: no visible binding for global variable 'id'
extend.polygonGate: no visible binding for global variable 'x'
extend.polygonGate: no visible binding for global variable 'y'
extend.polygonGate: no visible binding for global variable 'is.smaller'
flinTr: no visible global function definition for 'lintGml2'
flowjo_to_gatingset: no visible binding for global variable 'groupName'
fratioTr: no visible global function definition for 'ratiotGml2'
generate_trans: no visible global function definition for
  'flowjo_log_trans'
getSpilloverMat: no visible global function definition for
  'gh_get_compensations'
gs_compare_cytobank_counts: no visible binding for global variable
  'population'
gs_compare_cytobank_counts: no visible binding for global variable
  'parent'
gs_compare_cytobank_counts: no visible binding for global variable
  'count'
gs_compare_cytobank_counts: no visible binding for global variable
  'parent_count'
gs_compare_cytobank_counts: no visible global function definition for
  '.'
gs_compare_cytobank_counts: no visible binding for global variable
  'fcs_filename'
hyperlogTr: no visible global function definition for 'hyperlogtGml2'
open_cytobank_experiment: no visible global function definition for
  'unzip'
range.GatingHierarchy: no visible global function definition for
  'gh_get_transformations'
read.gatingML.cytobank: no visible binding for global variable 'id'
read.gatingML.cytobank: no visible binding for global variable
  'comp_ref'
sampleNode: no visible global function definition for 'gh_pop_get_gate'
sampleNode: no visible global function definition for
  'gh_get_transformations'
transDg1polynomial: no visible global function definition for
  'dg1polynomial'
transEH: no visible global function definition for 'EHtrans'
transExponential: no visible global function definition for
  'exponential'
transHyperLog: no visible global function definition for 'hyperlog'
transHyperbolicSin: no visible global function definition for 'sinht'
transInvSplitScale: no visible global function definition for
  'invsplitscale'
transInverseHyperbolicSin: no visible global function definition for
  'asinht'
transLogarithm: no visible global function definition for 'logarithm'
transQuadratic: no visible global function definition for 'quadratic'
transRatio: no visible global function definition for 'ratio'
transSplitScale: no visible global function definition for 'splitscale'
transSquareroot: no visible global function definition for 'squareroot'
transformationNode: no visible global function definition for
  'gh_get_transformations'
write.gatingML: no visible global function definition for 'sessionInfo'
identifyNode,http...www.isac.net.org.std.Gating.ML.v1.5.gating_DecisionTreeGate:
  no visible binding for global variable 'expressionFilter'
identifyNode,http...www.isac.net.org.std.Gating.ML.v1.5.gating_PolytopeGate:
  no visible global function definition for 'polytopeGate'
identifyNode,http...www.isac.net.org.std.Gating.ML.v2.0.transformations_spectrumMatrix:
  no visible global function definition for 'pseudoinverse'
show,flowjo_workspace: no visible global function definition for '.'
show,flowjo_workspace: no visible binding for global variable
  'groupName'
Undefined global functions or variables:
  . ..dim EHtrans asinht comp_ref count desc dg1polynomial exponential
  expressionFilter fcs fcs_filename filter_to_list flowjo_log_trans
  gate_def gate_id gh_get_compensations gh_get_transformations
  gh_pop_get_gate groupName gs_get_pop_paths gs_pop_get_gate hyperlog
  hyperlogtGml2 id invsplitscale is.smaller lintGml2 logarithm name
  parent parent_count polytopeGate population pseudoinverse quadratic
  ratio ratiotGml2 sampleSelected sessionInfo sinht slotNames specimen
  splitscale squareroot unzip write.csv x y
Consider adding
  importFrom("methods", "slotNames")
  importFrom("utils", "sessionInfo", "unzip", "write.csv")
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 ... WARNING
Undocumented code objects:
  'ce_get_cmpensations' 'ce_get_transformations' 'parseWorkspace'
Undocumented S4 methods:
  generic 'colnames' and siglist 'cytobank_experiment'
  generic 'markernames' and siglist 'cytobank_experiment'
  generic 'pData' and siglist 'cytobank_experiment'
  generic 'sampleNames' and siglist 'cytobank_experiment'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'diva_workspace-class'
  'name' 'subset' 'path' 'fast' 'worksheet' 'swap_cols' 'verbose'

Undocumented arguments in documentation object 'getSampleGroups'
  '...'

Undocumented arguments in documentation object 'parseWorkspace,flowjo_workspace-method'
  'name' 'subset' 'requiregates' 'sampNloc' 'additional.keys'
  'additional.sampleID' 'keywords' 'keywords.source' 'execute' 'path'
  'keyword.ignore.case'

Undocumented arguments in documentation object 'getSamples'
  '...'

Undocumented arguments in documentation object 'cytobankExperiment'
  '...'

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-3.10-bioc/R/library/CytoML/libs/i386/CytoML.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)
File 'C:/Users/biocbuild/bbs-3.10-bioc/R/library/CytoML/libs/x64/CytoML.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
Examples with CPU or elapsed time > 5s
                           user system elapsed
gs_compare_cytobank_counts  4.9    0.7    4.92
* 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-3.10-bioc/meat/CytoML.Rcheck/00check.log'
for details.

Installation output

CytoML.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/CytoML_1.12.1.tar.gz && rm -rf CytoML.buildbin-libdir && mkdir CytoML.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CytoML.buildbin-libdir CytoML_1.12.1.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL CytoML_1.12.1.zip && rm CytoML_1.12.1.tar.gz CytoML_1.12.1.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 6176k  100 6176k    0     0  24.8M      0 --:--:-- --:--:-- --:--:-- 25.2M

install for i386

* installing *source* package 'CytoML' ...
** using staged installation

   **********************************************
   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-3~1.10-/R/include" -DNDEBUG -DROUT -I../inst/include/ -IC:/libxml2//i386/include/libxml2 -DLIBXML_STATIC -DRCPP_PARALLEL_USE_TBB=1 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppParallel/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
In file included from ../inst/include/flowWorkspace/openWorkspace.hpp:12:0,
                 from ../inst/include/CytoML.h:5,
                 from RcppExports.cpp:4:
../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-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14:0,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from C:/Users/biocbuild/bbs-3.10-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 ../inst/include/CytoML.h:5,
                 from RcppExports.cpp:4:
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp: In member function 'virtual void logTrans::transforming(EVENT_DATA_TYPE*, int)':
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:697:20: warning: unused variable 'thisMin' [-Wunused-variable]
    EVENT_DATA_TYPE thisMin=0;//input.min();
                    ^
In file included from C:/Users/biocbuild/bbs-3.10-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 ../inst/include/CytoML.h:5,
                 from RcppExports.cpp:4:
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.10-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-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.10-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 ../inst/include/CytoML.h:5,
                 from RcppExports.cpp:4:
../inst/include/flowWorkspace/workspace.hpp: In member function 'void workspace::toArray(std::string, std::vector<double>&, std::vector<double>&)':
../inst/include/flowWorkspace/workspace.hpp:107:23: 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 ../inst/include/CytoML.h:5,
                 from RcppExports.cpp:4:
../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:808:12: warning: unused variable 'minRange' [-Wunused-variable]
     double minRange=atof(transNode.getProperty("minRange").c_str());
            ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -DROUT -I../inst/include/ -IC:/libxml2//i386/include/libxml2 -DLIBXML_STATIC -DRCPP_PARALLEL_USE_TBB=1 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppParallel/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c parseFlowJoWorkspace.cpp -o parseFlowJoWorkspace.o
In file included from ../inst/include/flowWorkspace/openWorkspace.hpp:12:0,
                 from parseFlowJoWorkspace.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-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14:0,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from C:/Users/biocbuild/bbs-3.10-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 parseFlowJoWorkspace.cpp:10:
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp: In member function 'virtual void logTrans::transforming(EVENT_DATA_TYPE*, int)':
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:697:20: warning: unused variable 'thisMin' [-Wunused-variable]
    EVENT_DATA_TYPE thisMin=0;//input.min();
                    ^
In file included from C:/Users/biocbuild/bbs-3.10-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 parseFlowJoWorkspace.cpp:10:
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.10-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-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.10-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 parseFlowJoWorkspace.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:107:23: 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 parseFlowJoWorkspace.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:808:12: warning: unused variable 'minRange' [-Wunused-variable]
     double minRange=atof(transNode.getProperty("minRange").c_str());
            ^
In file included from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15:0,
                 from C:/Users/biocbuild/bbs-3.10-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 parseFlowJoWorkspace.cpp:10:
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp: In member function 'CurlyGuadGate* winFlowJoWorkspace::getGate(wsCurlyQuadGateNode&)':
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:1270:94: 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 parseFlowJoWorkspace.cpp:10:
../inst/include/flowWorkspace/winFlowJoWorkspace.hpp:410:10: note: 'quad' was declared here
     QUAD quad;
          ^
mkdir -p "C:/Users/biocbuild/bbs-3.10-bioc/meat/CytoML.buildbin-libdir/00LOCK-CytoML/00new/CytoML/lib/i386"
C:/Rtools/mingw_32/bin/ar rs "C:/Users/biocbuild/bbs-3.10-bioc/meat/CytoML.buildbin-libdir/00LOCK-CytoML/00new/CytoML/lib/i386/libflowWorkspace.a" RcppExports.o parseFlowJoWorkspace.o
C:\Rtools\mingw_32\bin\ar.exe: creating C:/Users/biocbuild/bbs-3.10-bioc/meat/CytoML.buildbin-libdir/00LOCK-CytoML/00new/CytoML/lib/i386/libflowWorkspace.a
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o CytoML.dll tmp.def RcppExports.o parseFlowJoWorkspace.o C:/libxml2//i386/lib/libxml2.a C:/Users/biocbuild/bbs-3.10-bioc/R/library/RProtoBufLib/lib/i386/GatingSet.pb.o C:/Users/biocbuild/bbs-3.10-bioc/R/library/RProtoBufLib/lib/i386/libprotobuf.a -LC:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppParallel/lib/i386 -ltbb -ltbbmalloc -lws2_32 -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/CytoML.buildbin-libdir/00LOCK-CytoML/00new/CytoML/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for 'gating' from package 'openCyto' in package 'CytoML'
** help
*** installing help indices
  converting help for package 'CytoML'
    finding HTML links ... done
    CytoML.par.get                          html  
    CytoML.par.init                         html  
    GatingSet-methods                       html  
    finding level-2 HTML links ... done

    addCustomInfo                           html  
    compensate-GatingSet-graphGML-method    html  
    constructTree                           html  
    cytobank_to_gatingset                   html  
    diva_workspace-class                    html  
    extend                                  html  
    fj_ws_get_keywords                      html  
    fj_ws_get_sample_groups                 html  
    flowjo_to_gatingset                     html  
    flowjo_workspace-class                  html  
    gating-methods                          html  
    gatingset_to_cytobank                   html  
    gatingset_to_flowjo                     html  
    getChildren-graphGML-character-method   html  
    getCompensationMatrices.graphGML        html  
    getFJWSubsetIndices                     html  
    getGate-graphGML-character-method       html  
    getNodes-graphGML-method                html  
    getParent-graphGML-character-method     html  
    getSamples                              html  
    getTransformations.graphGML             html  
    graphGML-class                          html  
    gs_compare_cytobank_counts              html  
    matchPath                               html  
    open_cytobank_experiment                html  
    open_diva_xml                           html  
    open_flowjo_xml                         html  
    parse.gateInfo                          html  
    plot-graphGML-missing-method            html  
    range.GatingHierarchy                   html  
    read.gatingML.cytobank                  html  
    show-graphGML-method                    html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'CytoML' ...

   **********************************************
   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-3~1.10-/R/include" -DNDEBUG -DROUT -I../inst/include/ -IC:/libxml2//x64/include/libxml2 -DLIBXML_STATIC -DRCPP_PARALLEL_USE_TBB=1 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppParallel/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
In file included from ../inst/include/flowWorkspace/openWorkspace.hpp:12:0,
                 from ../inst/include/CytoML.h:5,
                 from RcppExports.cpp:4:
../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-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14:0,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from C:/Users/biocbuild/bbs-3.10-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 ../inst/include/CytoML.h:5,
                 from RcppExports.cpp:4:
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp: In member function 'virtual void logTrans::transforming(EVENT_DATA_TYPE*, int)':
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:697:20: warning: unused variable 'thisMin' [-Wunused-variable]
    EVENT_DATA_TYPE thisMin=0;//input.min();
                    ^
In file included from C:/Users/biocbuild/bbs-3.10-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 ../inst/include/CytoML.h:5,
                 from RcppExports.cpp:4:
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.10-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-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.10-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 ../inst/include/CytoML.h:5,
                 from RcppExports.cpp:4:
../inst/include/flowWorkspace/workspace.hpp: In member function 'void workspace::toArray(std::string, std::vector<double>&, std::vector<double>&)':
../inst/include/flowWorkspace/workspace.hpp:107:23: 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 ../inst/include/CytoML.h:5,
                 from RcppExports.cpp:4:
../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:808:12: warning: unused variable 'minRange' [-Wunused-variable]
     double minRange=atof(transNode.getProperty("minRange").c_str());
            ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -DROUT -I../inst/include/ -IC:/libxml2//x64/include/libxml2 -DLIBXML_STATIC -DRCPP_PARALLEL_USE_TBB=1 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppParallel/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c parseFlowJoWorkspace.cpp -o parseFlowJoWorkspace.o
In file included from ../inst/include/flowWorkspace/openWorkspace.hpp:12:0,
                 from parseFlowJoWorkspace.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-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14:0,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from C:/Users/biocbuild/bbs-3.10-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 parseFlowJoWorkspace.cpp:10:
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp: In member function 'virtual void logTrans::transforming(EVENT_DATA_TYPE*, int)':
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:697:20: warning: unused variable 'thisMin' [-Wunused-variable]
    EVENT_DATA_TYPE thisMin=0;//input.min();
                    ^
In file included from C:/Users/biocbuild/bbs-3.10-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 parseFlowJoWorkspace.cpp:10:
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.10-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-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.10-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 parseFlowJoWorkspace.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:107:23: 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 parseFlowJoWorkspace.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:808:12: warning: unused variable 'minRange' [-Wunused-variable]
     double minRange=atof(transNode.getProperty("minRange").c_str());
            ^
In file included from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15:0,
                 from C:/Users/biocbuild/bbs-3.10-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 parseFlowJoWorkspace.cpp:10:
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp: In member function 'CurlyGuadGate* winFlowJoWorkspace::getGate(wsCurlyQuadGateNode&)':
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:1270:94: 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 parseFlowJoWorkspace.cpp:10:
../inst/include/flowWorkspace/winFlowJoWorkspace.hpp:410:10: note: 'quad' was declared here
     QUAD quad;
          ^
mkdir -p "C:/Users/biocbuild/bbs-3.10-bioc/meat/CytoML.buildbin-libdir/CytoML/lib/x64"
C:/Rtools/mingw_64/bin/ar rs "C:/Users/biocbuild/bbs-3.10-bioc/meat/CytoML.buildbin-libdir/CytoML/lib/x64/libflowWorkspace.a" RcppExports.o parseFlowJoWorkspace.o
C:\Rtools\mingw_64\bin\ar.exe: creating C:/Users/biocbuild/bbs-3.10-bioc/meat/CytoML.buildbin-libdir/CytoML/lib/x64/libflowWorkspace.a
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o CytoML.dll tmp.def RcppExports.o parseFlowJoWorkspace.o C:/libxml2//x64/lib/libxml2.a C:/Users/biocbuild/bbs-3.10-bioc/R/library/RProtoBufLib/lib/x64/GatingSet.pb.o C:/Users/biocbuild/bbs-3.10-bioc/R/library/RProtoBufLib/lib/x64/libprotobuf.a -LC:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppParallel/lib/x64 -ltbb -ltbbmalloc -lws2_32 -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/CytoML.buildbin-libdir/CytoML/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CytoML' as CytoML_1.12.1.zip
* DONE (CytoML)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'CytoML' successfully unpacked and MD5 sums checked

Tests output

CytoML.Rcheck/tests_i386/testthat.Rout


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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(CytoML)
> 
> 
> test_check("CytoML")
Loading required package: ggplot2
Loading required package: flowCore
Loading required package: ncdfFlow
Loading required package: RcppArmadillo
Loading required package: BH
windows version of flowJo workspace recognized.
version X
windows version of flowJo workspace recognized.
version X
windows version of flowJo workspace recognized.
version X
windows version of flowJo workspace recognized.
version X
windows version of flowJo workspace recognized.
version X
Failed to use spillover/spectrum matrix Spill_defaultCompensation for compensated parameter FSC-A. It seems that the matrix was not properly defined in the Gating-ML file.

Failed to use spillover/spectrum matrix Spill_defaultCompensation for compensated parameter FSC-H. It seems that the matrix was not properly defined in the Gating-ML file.

Failed to use spillover/spectrum matrix Spill_defaultCompensation for compensated parameter FSC-A. It seems that the matrix was not properly defined in the Gating-ML file.

Failed to use spillover/spectrum matrix Spill_defaultCompensation for compensated parameter SSC-A. It seems that the matrix was not properly defined in the Gating-ML file.

Failed to use spillover/spectrum matrix Spill_defaultCompensation for compensated parameter FSC-A. It seems that the matrix was not properly defined in the Gating-ML file.

mac version of flowJo workspace recognized.
== testthat results  ===========================================================
[ OK: 97 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 0 ]
> 
> #devtools::test()
> 
> # test_file("~/rglab/workspace/CytoML/tests/testthat/flowjo2gs_internalTestSuite.R")
> # test_file("~/rglab/workspace/CytoML/tests/testthat/Cytobank2GatingSet-InternalTestSuite.R")
> # test_file("~/rglab/workspace/CytoML/tests/testthat/GatingSet2flowJo-InternalTestSuite.R")
> # test_file("~/rglab/workspace/CytoML/tests/testthat/diva2gs-InternalTestSuite.R")
> # test_file("~/rglab/workspace/CytoML/tests/testthat/test-cytobank.R")
> # test_file("~/rglab/workspace/CytoML/tests/testthat/test-diva2gs.R")
> # test_file("~/rglab/workspace/CytoML/tests/testthat/test-extend.R")
> # test_file("~/rglab/workspace/CytoML/tests/testthat/test-GatingSet2flowJo.R")
> # test_file("~/rglab/workspace/CytoML/tests/testthat/test-flowjo2gs.R")
> 
> proc.time()
   user  system elapsed 
 111.07   12.67  118.93

CytoML.Rcheck/tests_x64/testthat.Rout


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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(CytoML)
> 
> 
> test_check("CytoML")
Loading required package: ggplot2
Loading required package: flowCore
Loading required package: ncdfFlow
Loading required package: RcppArmadillo
Loading required package: BH
windows version of flowJo workspace recognized.
version X
windows version of flowJo workspace recognized.
version X
windows version of flowJo workspace recognized.
version X
windows version of flowJo workspace recognized.
version X
windows version of flowJo workspace recognized.
version X
Failed to use spillover/spectrum matrix Spill_defaultCompensation for compensated parameter FSC-A. It seems that the matrix was not properly defined in the Gating-ML file.

Failed to use spillover/spectrum matrix Spill_defaultCompensation for compensated parameter FSC-H. It seems that the matrix was not properly defined in the Gating-ML file.

Failed to use spillover/spectrum matrix Spill_defaultCompensation for compensated parameter FSC-A. It seems that the matrix was not properly defined in the Gating-ML file.

Failed to use spillover/spectrum matrix Spill_defaultCompensation for compensated parameter SSC-A. It seems that the matrix was not properly defined in the Gating-ML file.

Failed to use spillover/spectrum matrix Spill_defaultCompensation for compensated parameter FSC-A. It seems that the matrix was not properly defined in the Gating-ML file.

mac version of flowJo workspace recognized.
== testthat results  ===========================================================
[ OK: 97 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 0 ]
> 
> #devtools::test()
> 
> # test_file("~/rglab/workspace/CytoML/tests/testthat/flowjo2gs_internalTestSuite.R")
> # test_file("~/rglab/workspace/CytoML/tests/testthat/Cytobank2GatingSet-InternalTestSuite.R")
> # test_file("~/rglab/workspace/CytoML/tests/testthat/GatingSet2flowJo-InternalTestSuite.R")
> # test_file("~/rglab/workspace/CytoML/tests/testthat/diva2gs-InternalTestSuite.R")
> # test_file("~/rglab/workspace/CytoML/tests/testthat/test-cytobank.R")
> # test_file("~/rglab/workspace/CytoML/tests/testthat/test-diva2gs.R")
> # test_file("~/rglab/workspace/CytoML/tests/testthat/test-extend.R")
> # test_file("~/rglab/workspace/CytoML/tests/testthat/test-GatingSet2flowJo.R")
> # test_file("~/rglab/workspace/CytoML/tests/testthat/test-flowjo2gs.R")
> 
> proc.time()
   user  system elapsed 
 131.50   11.54  134.73

Example timings

CytoML.Rcheck/examples_i386/CytoML-Ex.timings

nameusersystemelapsed
CytoML.par.get000
cytobank_to_gatingset0.010.000.01
extend0.130.030.13
fj_ws_get_keywords0.220.081.01
fj_ws_get_sample_groups000
flowjo_to_gatingset000
flowjo_workspace-class0.110.110.30
gatingset_to_cytobank1.110.171.28
gatingset_to_flowjo1.220.061.56
getChildren-graphGML-character-method000
getNodes-graphGML-method000
getSamples000
gs_compare_cytobank_counts3.730.784.25
open_diva_xml000
open_flowjo_xml000
plot-graphGML-missing-method000
range.GatingHierarchy000
read.gatingML.cytobank000

CytoML.Rcheck/examples_x64/CytoML-Ex.timings

nameusersystemelapsed
CytoML.par.get000
cytobank_to_gatingset000
extend0.230.050.20
fj_ws_get_keywords0.190.040.24
fj_ws_get_sample_groups000
flowjo_to_gatingset000
flowjo_workspace-class0.140.110.25
gatingset_to_cytobank1.980.052.04
gatingset_to_flowjo1.880.031.91
getChildren-graphGML-character-method000
getNodes-graphGML-method000
getSamples000
gs_compare_cytobank_counts4.900.704.92
open_diva_xml000
open_flowjo_xml000
plot-graphGML-missing-method000
range.GatingHierarchy000
read.gatingML.cytobank000