CHECK report for flowWorkspace on merida1
This page was generated on 2020-04-15 12:36:58 -0400 (Wed, 15 Apr 2020).
flowWorkspace 3.34.1
Greg Finak ,Mike Jiang
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/flowWorkspace |
| Branch: RELEASE_3_10 |
| Last Commit: a7fb3ad |
| Last Changed Date: 2020-01-02 14:38:02 -0400 (Thu, 02 Jan 2020) |
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | WARNINGS | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK | |
Summary
Command output
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###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:flowWorkspace.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings flowWorkspace_3.34.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/flowWorkspace.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 ‘flowWorkspace/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowWorkspace’ version ‘3.34.1’
* 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 ‘flowWorkspace’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 31.6Mb
sub-directories of 1Mb or more:
lib 28.0Mb
libs 2.7Mb
* 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
* 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’ ‘utils’
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.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.addGatingHierarchies: no visible global function definition for ‘is’
.addGatingHierarchies : <anonymous>: no visible global function
definition for ‘fj_ws_get_keywords’
.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’
.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’
.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 ‘.’
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’
flowWorkspace.par.init: no visible global function definition for
‘gray’
gh_apply_to_new_fcs: no visible global function definition for ‘new’
gh_pop_compare_stats: no visible binding for global variable ‘node’
gh_pop_get_count: no visible binding for global variable ‘count’
gh_pop_get_proportion: no visible binding for global variable ‘percent’
gh_pop_get_stats_tfilter: no visible global function definition for
‘is’
gs_get_singlecell_expression: no visible global function definition for
‘is’
gs_get_singlecell_expression: no visible binding for global variable
‘parallel’
gs_pop_add: no visible global function definition for ‘is’
gs_pop_get_count_fast: no visible global function definition for ‘is’
gs_pop_get_count_with_meta: no visible binding for global variable
‘sampleName’
gs_pop_set_gate: no visible global function definition for ‘is’
gs_remove_redundant_nodes : <anonymous>: no visible global function
definition for ‘is’
gslist_to_gs: no visible global function definition for ‘new’
gslist_to_gs: no visible binding for global variable ‘slot’
mkformula: no visible global function definition for ‘as.formula’
parse_transformer: no visible global function definition for ‘is’
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,flowSet-ANY: no visible global function definition for ‘new’
[,GatingSet-ANY: no visible global function definition for ‘new’
[,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 ‘as’
flowData,GatingSet: no visible binding for global variable ‘obj’
gs_cyto_data,GatingSet: no visible global function definition for ‘is’
keyword,GatingSetList-character: no visible global function definition
for ‘selectMethod’
keyword,GatingSetList-missing: no visible global function definition
for ‘selectMethod’
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’
recompute,GatingSetList: no visible global function definition for
‘selectMethod’
setNode,GatingSet-character-ANY: no visible global function definition
for ‘is’
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 count desc extends
fj_ws_get_keywords gray is median new node obj old openCyto.count
parallel percent 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 ... WARNING
Undocumented code objects:
‘getChildren’ ‘getData’ ‘getGate’ ‘getNodes’ ‘getParent’
‘getPopStats’ ‘gh_pop_get_stats_tfilter’ ‘gs_cyto_data<-’
‘gs_pop_get_stats_tfilter’
Undocumented S4 methods:
generic 'flowData<-' and siglist 'GatingSet'
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 ... WARNING
S4 class codoc mismatches from documentation object 'GatingSet-class':
Slots for class 'GatingSet'
Code: FCSPath axis compensation data flag guid name pointer
transformation
Docs: FCSPath axis compensation data flag guid pointer transformation
* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'GatingSet-class'
‘value’
Undocumented arguments in documentation object 'GatingSet,flowSet,ANY-method'
‘x’
Undocumented arguments in documentation object 'flowjo_log_trans'
‘n’ ‘equal.space’ ‘max_val’ ‘min_val’
Documented arguments not in \usage in documentation object 'GatingSet,GatingHierarchy,character-method':
‘swap_cols’
Undocumented arguments in documentation object 'flowData'
‘...’
Duplicated \argument entries in documentation object 'getPopStats,GatingSet-method':
‘x’ ‘...’
Documented arguments not in \usage in documentation object 'isGated':
‘...’
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 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 is not available
File ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/flowWorkspace/libs/flowWorkspace.so’:
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
* 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: 3 WARNINGs, 6 NOTEs
See
‘/Users/biocbuild/bbs-3.10-bioc/meat/flowWorkspace.Rcheck/00check.log’
for details.
Installation output
flowWorkspace.Rcheck/00install.out
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###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL flowWorkspace
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘flowWorkspace’ ...
** using staged installation
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -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 R_API.cpp -o R_API.o
In file included from R_API.cpp:9:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/GatingSet.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/GatingHierarchy.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/populationTree.hpp:11:
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 R_API.cpp:9:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/GatingSet.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/GatingHierarchy.hpp:10:
In file included from /usr/local/clang7/include/c++/v1/iostream:38:
In file included from /usr/local/clang7/include/c++/v1/ios:216:
In file included from /usr/local/clang7/include/c++/v1/__locale:15:
In file included from /usr/local/clang7/include/c++/v1/string:500:
In file included from /usr/local/clang7/include/c++/v1/string_view:176:
In file included from /usr/local/clang7/include/c++/v1/__string:56:
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();}
^
2 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -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 R_GatingHierarchy.cpp -o R_GatingHierarchy.o
In file included from R_GatingHierarchy.cpp:17:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/GatingHierarchy.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/populationTree.hpp:11:
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 R_GatingHierarchy.cpp:17:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/GatingHierarchy.hpp:10:
In file included from /usr/local/clang7/include/c++/v1/iostream:38:
In file included from /usr/local/clang7/include/c++/v1/ios:216:
In file included from /usr/local/clang7/include/c++/v1/__locale:15:
In file included from /usr/local/clang7/include/c++/v1/string:500:
In file included from /usr/local/clang7/include/c++/v1/string_view:176:
In file included from /usr/local/clang7/include/c++/v1/__string:56:
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();}
^
2 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -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 R_GatingSet.cpp -o R_GatingSet.o
In file included from R_GatingSet.cpp:10:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/GatingSet.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/GatingHierarchy.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/populationTree.hpp:11:
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 R_GatingSet.cpp:10:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/GatingSet.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/GatingHierarchy.hpp:10:
In file included from /usr/local/clang7/include/c++/v1/iostream:38:
In file included from /usr/local/clang7/include/c++/v1/ios:216:
In file included from /usr/local/clang7/include/c++/v1/__locale:15:
In file included from /usr/local/clang7/include/c++/v1/string:500:
In file included from /usr/local/clang7/include/c++/v1/string_view:176:
In file included from /usr/local/clang7/include/c++/v1/__string:56:
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();}
^
2 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -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/flowWorkspace.h:5:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/GatingSet.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/GatingHierarchy.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/populationTree.hpp:11:
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/flowWorkspace.h:5:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/GatingSet.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/GatingHierarchy.hpp:10:
In file included from /usr/local/clang7/include/c++/v1/iostream:38:
In file included from /usr/local/clang7/include/c++/v1/ios:216:
In file included from /usr/local/clang7/include/c++/v1/__locale:15:
In file included from /usr/local/clang7/include/c++/v1/string:500:
In file included from /usr/local/clang7/include/c++/v1/string_view:176:
In file included from /usr/local/clang7/include/c++/v1/__string:56:
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();}
^
2 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -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 getDescendants.cpp -o getDescendants.o
In file included from getDescendants.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/GatingSet.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/GatingHierarchy.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/populationTree.hpp:11:
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 getDescendants.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/GatingSet.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/GatingHierarchy.hpp:10:
In file included from /usr/local/clang7/include/c++/v1/iostream:38:
In file included from /usr/local/clang7/include/c++/v1/ios:216:
In file included from /usr/local/clang7/include/c++/v1/__locale:15:
In file included from /usr/local/clang7/include/c++/v1/string:500:
In file included from /usr/local/clang7/include/c++/v1/string_view:176:
In file included from /usr/local/clang7/include/c++/v1/__string:56:
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();}
^
2 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -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 getPopStats.cpp -o getPopStats.o
In file included from getPopStats.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/GatingSet.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/GatingHierarchy.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/populationTree.hpp:11:
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 getPopStats.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/GatingSet.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/GatingHierarchy.hpp:10:
In file included from /usr/local/clang7/include/c++/v1/iostream:38:
In file included from /usr/local/clang7/include/c++/v1/ios:216:
In file included from /usr/local/clang7/include/c++/v1/__locale:15:
In file included from /usr/local/clang7/include/c++/v1/string:500:
In file included from /usr/local/clang7/include/c++/v1/string_view:176:
In file included from /usr/local/clang7/include/c++/v1/__string:56:
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();}
^
2 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -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 getSingleCellExpression.cpp -o getSingleCellExpression.o
In file included from getSingleCellExpression.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/GatingHierarchy.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/populationTree.hpp:11:
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 getSingleCellExpression.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/GatingHierarchy.hpp:10:
In file included from /usr/local/clang7/include/c++/v1/iostream:38:
In file included from /usr/local/clang7/include/c++/v1/ios:216:
In file included from /usr/local/clang7/include/c++/v1/__locale:15:
In file included from /usr/local/clang7/include/c++/v1/string:500:
In file included from /usr/local/clang7/include/c++/v1/string_view:176:
In file included from /usr/local/clang7/include/c++/v1/__string:56:
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();}
^
2 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -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 setCounts.cpp -o setCounts.o
In file included from setCounts.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/GatingSet.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/GatingHierarchy.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/populationTree.hpp:11:
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 setCounts.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/GatingSet.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/GatingHierarchy.hpp:10:
In file included from /usr/local/clang7/include/c++/v1/iostream:38:
In file included from /usr/local/clang7/include/c++/v1/ios:216:
In file included from /usr/local/clang7/include/c++/v1/__locale:15:
In file included from /usr/local/clang7/include/c++/v1/string:500:
In file included from /usr/local/clang7/include/c++/v1/string_view:176:
In file included from /usr/local/clang7/include/c++/v1/__string:56:
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();}
^
2 warnings generated.
mkdir -p "/Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-flowWorkspace/00new/flowWorkspace/lib"
ar rs "/Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-flowWorkspace/00new/flowWorkspace/lib/libflowWorkspace.a" R_API.o R_GatingHierarchy.o R_GatingSet.o RcppExports.o getDescendants.o getPopStats.o getSingleCellExpression.o setCounts.o
ar: creating archive /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-flowWorkspace/00new/flowWorkspace/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 flowWorkspace.so R_API.o R_GatingHierarchy.o R_GatingSet.o RcppExports.o getDescendants.o getPopStats.o getSingleCellExpression.o setCounts.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 -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 flowWorkspace.so; fi
installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-flowWorkspace/00new/flowWorkspace/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** 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 (flowWorkspace)
Tests output
flowWorkspace.Rcheck/tests/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-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(flowWorkspace)
> library(flowCore)
> library(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, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, 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")'.
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 903 | SKIPPED: 3 | WARNINGS: 40 | 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/GatingHierarchy-testSuite.R")
> # test_file("/home/wjiang2/rglab/workspace/flowWorkspace/tests/testthat/GatingSet-testSuite.R")
>
> proc.time()
user system elapsed
49.824 20.082 44.699
Example timings
flowWorkspace.Rcheck/flowWorkspace-Ex.timings