Package: CytoML

Version: 1.12.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CytoML.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CytoML_1.12.1.tar.gz

StartedAt: 2020-04-15 01:36:17 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 01:41:30 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 313.1 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: CytoML.Rcheck

Warnings: 2

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CytoML.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CytoML_1.12.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/CytoML.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘CytoML’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 15.7Mb
  sub-directories of 1Mb or more:
    extdata   4.8Mb
    lib       7.5Mb
    libs      2.2Mb
* 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
* 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 ... NOTE
Package has both ‘src/Makevars.in’ and ‘src/Makevars’.
Installation with --no-configure' is unlikely to work.  If you intended
‘src/Makevars’ to be used on Windows, rename it to ‘src/Makevars.win’
otherwise remove it.  If ‘configure’ created ‘src/Makevars’, you need a
‘cleanup’ script.
* checking for 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 is not available
File ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/CytoML/libs/CytoML.so’:
  Found ‘__ZNSt3__14coutE’, possibly from ‘std::cout’ (C++)
  Found ‘___assert_rtn’, possibly from ‘assert’ (C)
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘_printf’, possibly from ‘printf’ (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 ... OK
Examples with CPU or elapsed time > 5s
                             user system elapsed
gs_compare_cytobank_counts 14.247  9.874    5.82
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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, 7 NOTEs
See
  ‘/Users/biocbuild/bbs-3.10-bioc/meat/CytoML.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL CytoML
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘CytoML’ ...
** using staged installation
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether clang++ -std=gnu++11 accepts -g... yes
checking for gcc... clang
checking whether we are using the GNU C compiler... yes
checking whether clang accepts -g... yes
checking for clang option to accept ISO C89... none needed
configure: setting xml2 flags...
configure: No directory was specified for --with-xml2. Trying to find xml2 using other methods.
checking for xml2-config... /usr/bin/xml2-config
configure: Using the following compilation and linking flags
configure:    PKG_CPPFLAGS=-I/usr/include/libxml2 -ftemplate-depth=900
configure:    PKG_LIBS=-lxml2 -lz -lpthread -licucore -lm
configure: creating ./config.status
config.status: creating src/Makevars
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include/ -I/usr/include/libxml2 -ftemplate-depth=900 -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RProtoBufLib/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppParallel/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:4:
In file included from ./../inst/include/CytoML.h:5:
In file included from ../inst/include/flowWorkspace/openWorkspace.hpp:11:
In file included from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10:
In file included from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11:
In file included from ../inst/include/flowWorkspace/workspace.hpp:14:
In file included from ../inst/include/flowWorkspace/wsNode.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/nodeProperties.hpp:11:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/POPINDICES.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/gate.hpp:14:
/Library/Frameworks/R.framework/Versions/3.6/Resources/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 RcppExports.cpp:4:
In file included from ./../inst/include/CytoML.h:5:
In file included from ../inst/include/flowWorkspace/openWorkspace.hpp:12:
../inst/include/flowWorkspace/winFlowJoWorkspace.hpp:433:30: warning: '/*' within block comment [-Wcomment]
           * "*[local-name()='edge']/*[local-name()='vertex']" is for ellipsoidGate
                                    ^
../inst/include/flowWorkspace/winFlowJoWorkspace.hpp:417:13: warning: variable 'quad' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
                else if(quadPattern == "--")
                        ^~~~~~~~~~~~~~~~~~~
../inst/include/flowWorkspace/winFlowJoWorkspace.hpp:425:45: note: uninitialized use occurs here
                CurlyGuadGate * g=new CurlyGuadGate(pp, quad);
                                                        ^~~~
../inst/include/flowWorkspace/winFlowJoWorkspace.hpp:417:10: note: remove the 'if' if its condition is always true
                else if(quadPattern == "--")
                     ^~~~~~~~~~~~~~~~~~~~~~~
../inst/include/flowWorkspace/winFlowJoWorkspace.hpp:410:5: note: variable 'quad' is declared here
                QUAD quad;
                ^
../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 RcppExports.cpp:4:
In file included from ./../inst/include/CytoML.h:5:
In file included from ../inst/include/flowWorkspace/openWorkspace.hpp:11:
In file included from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10:
In file included from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11:
In file included from ../inst/include/flowWorkspace/workspace.hpp:10:
In file included from /usr/local/clang7/include/c++/v1/vector:270:
In file included from /usr/local/clang7/include/c++/v1/__bit_reference:15:
In file included from /usr/local/clang7/include/c++/v1/algorithm:644:
/usr/local/clang7/include/c++/v1/memory:1866:58: warning: destructor called on non-final 'trans_global' that has virtual functions but non-virtual destructor [-Wdelete-non-virtual-dtor]
    _LIBCPP_INLINE_VISIBILITY void destroy(pointer __p) {__p->~_Tp();}
                                                         ^
/usr/local/clang7/include/c++/v1/memory:1728:18: note: in instantiation of member function 'std::__1::allocator<trans_global>::destroy' requested here
            {__a.destroy(__p);}
                 ^
/usr/local/clang7/include/c++/v1/memory:1596:14: note: in instantiation of function template specialization 'std::__1::allocator_traits<std::__1::allocator<trans_global> >::__destroy<trans_global>' requested here
            {__destroy(__has_destroy<allocator_type, _Tp*>(), __a, __p);}
             ^
/usr/local/clang7/include/c++/v1/vector:421:25: note: in instantiation of function template specialization 'std::__1::allocator_traits<std::__1::allocator<trans_global> >::destroy<trans_global>' requested here
        __alloc_traits::destroy(__alloc(), _VSTD::__to_raw_pointer(--__soon_to_be_end));
                        ^
/usr/local/clang7/include/c++/v1/vector:364:29: note: in instantiation of member function 'std::__1::__vector_base<trans_global, std::__1::allocator<trans_global> >::__destruct_at_end' requested here
    void clear() _NOEXCEPT {__destruct_at_end(__begin_);}
                            ^
/usr/local/clang7/include/c++/v1/vector:458:9: note: in instantiation of member function 'std::__1::__vector_base<trans_global, std::__1::allocator<trans_global> >::clear' requested here
        clear();
        ^
/usr/local/clang7/include/c++/v1/iterator:1427:74: note: in instantiation of member function 'std::__1::__vector_base<trans_global, std::__1::allocator<trans_global> >::~__vector_base' requested here
    template <class _Tp, class _Alloc> friend class _LIBCPP_TEMPLATE_VIS vector;
                                                                         ^
/usr/local/clang7/include/c++/v1/memory:1866:64: note: qualify call to silence this warning
    _LIBCPP_INLINE_VISIBILITY void destroy(pointer __p) {__p->~_Tp();}
                                                               ^
5 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include/ -I/usr/include/libxml2 -ftemplate-depth=900 -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RProtoBufLib/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppParallel/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c parseFlowJoWorkspace.cpp -o parseFlowJoWorkspace.o
In file included from parseFlowJoWorkspace.cpp:10:
In file included from ../inst/include/flowWorkspace/openWorkspace.hpp:11:
In file included from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10:
In file included from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11:
In file included from ../inst/include/flowWorkspace/workspace.hpp:14:
In file included from ../inst/include/flowWorkspace/wsNode.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/nodeProperties.hpp:11:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/POPINDICES.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/gate.hpp:14:
/Library/Frameworks/R.framework/Versions/3.6/Resources/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 parseFlowJoWorkspace.cpp:10:
In file included from ../inst/include/flowWorkspace/openWorkspace.hpp:12:
../inst/include/flowWorkspace/winFlowJoWorkspace.hpp:433:30: warning: '/*' within block comment [-Wcomment]
           * "*[local-name()='edge']/*[local-name()='vertex']" is for ellipsoidGate
                                    ^
../inst/include/flowWorkspace/winFlowJoWorkspace.hpp:417:13: warning: variable 'quad' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
                else if(quadPattern == "--")
                        ^~~~~~~~~~~~~~~~~~~
../inst/include/flowWorkspace/winFlowJoWorkspace.hpp:425:45: note: uninitialized use occurs here
                CurlyGuadGate * g=new CurlyGuadGate(pp, quad);
                                                        ^~~~
../inst/include/flowWorkspace/winFlowJoWorkspace.hpp:417:10: note: remove the 'if' if its condition is always true
                else if(quadPattern == "--")
                     ^~~~~~~~~~~~~~~~~~~~~~~
../inst/include/flowWorkspace/winFlowJoWorkspace.hpp:410:5: note: variable 'quad' is declared here
                QUAD quad;
                ^
../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 parseFlowJoWorkspace.cpp:10:
In file included from ../inst/include/flowWorkspace/openWorkspace.hpp:11:
In file included from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10:
In file included from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11:
In file included from ../inst/include/flowWorkspace/workspace.hpp:10:
In file included from /usr/local/clang7/include/c++/v1/vector:270:
In file included from /usr/local/clang7/include/c++/v1/__bit_reference:15:
In file included from /usr/local/clang7/include/c++/v1/algorithm:644:
/usr/local/clang7/include/c++/v1/memory:1866:58: warning: destructor called on non-final 'trans_global' that has virtual functions but non-virtual destructor [-Wdelete-non-virtual-dtor]
    _LIBCPP_INLINE_VISIBILITY void destroy(pointer __p) {__p->~_Tp();}
                                                         ^
/usr/local/clang7/include/c++/v1/memory:1728:18: note: in instantiation of member function 'std::__1::allocator<trans_global>::destroy' requested here
            {__a.destroy(__p);}
                 ^
/usr/local/clang7/include/c++/v1/memory:1596:14: note: in instantiation of function template specialization 'std::__1::allocator_traits<std::__1::allocator<trans_global> >::__destroy<trans_global>' requested here
            {__destroy(__has_destroy<allocator_type, _Tp*>(), __a, __p);}
             ^
/usr/local/clang7/include/c++/v1/vector:421:25: note: in instantiation of function template specialization 'std::__1::allocator_traits<std::__1::allocator<trans_global> >::destroy<trans_global>' requested here
        __alloc_traits::destroy(__alloc(), _VSTD::__to_raw_pointer(--__soon_to_be_end));
                        ^
/usr/local/clang7/include/c++/v1/vector:364:29: note: in instantiation of member function 'std::__1::__vector_base<trans_global, std::__1::allocator<trans_global> >::__destruct_at_end' requested here
    void clear() _NOEXCEPT {__destruct_at_end(__begin_);}
                            ^
/usr/local/clang7/include/c++/v1/vector:458:9: note: in instantiation of member function 'std::__1::__vector_base<trans_global, std::__1::allocator<trans_global> >::clear' requested here
        clear();
        ^
/usr/local/clang7/include/c++/v1/iterator:1427:74: note: in instantiation of member function 'std::__1::__vector_base<trans_global, std::__1::allocator<trans_global> >::~__vector_base' requested here
    template <class _Tp, class _Alloc> friend class _LIBCPP_TEMPLATE_VIS vector;
                                                                         ^
/usr/local/clang7/include/c++/v1/memory:1866:64: note: qualify call to silence this warning
    _LIBCPP_INLINE_VISIBILITY void destroy(pointer __p) {__p->~_Tp();}
                                                               ^
5 warnings generated.
mkdir -p "/Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-CytoML/00new/CytoML/lib"
ar rs "/Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-CytoML/00new/CytoML/lib/libflowWorkspace.a" RcppExports.o parseFlowJoWorkspace.o
ar: creating archive /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-CytoML/00new/CytoML/lib/libflowWorkspace.a
clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o CytoML.so RcppExports.o parseFlowJoWorkspace.o /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RProtoBufLib/lib/GatingSet.pb.o /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RProtoBufLib/lib/libprotobuf.a -lxml2 -lz -lpthread -licucore -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
if [ `uname -s` = 'Darwin' ]; then install_name_tool -change /usr/local/clang4/lib/libc++.1.dylib /usr/lib/libc++.1.dylib CytoML.so; fi
installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-CytoML/00new/CytoML/libs
** 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
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (CytoML)

R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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 
257.407 144.754 142.060 

name	user	system	elapsed
CytoML.par.get	0.001	0.001	0.001
cytobank_to_gatingset	0	0	0
extend	0.554	0.729	0.210
fj_ws_get_keywords	0.624	0.785	0.558
fj_ws_get_sample_groups	0.001	0.000	0.000
flowjo_to_gatingset	0.000	0.000	0.001
flowjo_workspace-class	1.075	0.296	0.547
gatingset_to_cytobank	2.110	0.501	2.045
gatingset_to_flowjo	1.786	0.098	1.900
getChildren-graphGML-character-method	0	0	0
getNodes-graphGML-method	0	0	0
getSamples	0	0	0
gs_compare_cytobank_counts	14.247	9.874	5.820
open_diva_xml	0.001	0.001	0.001
open_flowjo_xml	0.001	0.001	0.000
plot-graphGML-missing-method	0.001	0.000	0.001
range.GatingHierarchy	0.001	0.000	0.000
read.gatingML.cytobank	0.001	0.000	0.000