This page was generated on 2020-04-15 12:19:53 -0400 (Wed, 15 Apr 2020).
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### Running command:
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### C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flowWorkspace.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings flowWorkspace_3.34.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/flowWorkspace.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 '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 whether package 'flowWorkspace' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpCqwvNP/R.INSTALL1d3c4fffcdf/flowWorkspace/man/flowjo_biexp_trans.Rd:13: file link 'flowJoTrans' in package 'flowWorkspace' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.10-bioc/meat/flowWorkspace.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
installed size is 13.2Mb
sub-directories of 1Mb or more:
lib 7.3Mb
libs 4.4Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
Versioned 'LinkingTo' values for
'BH' 'RProtoBufLib' 'cytolib'
are only usable in R >= 3.0.2
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
'RBGL' 'grDevices' 'graphics' '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 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/flowWorkspace/libs/i386/flowWorkspace.dll':
Found '_exit', possibly from '_exit' (C)
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.10-bioc/R/library/flowWorkspace/libs/x64/flowWorkspace.dll':
Found '_exit', possibly from '_exit' (C)
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
Running 'testthat.R'
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 4 WARNINGs, 6 NOTEs
See
'C:/Users/biocbuild/bbs-3.10-bioc/meat/flowWorkspace.Rcheck/00check.log'
for details.
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/flowWorkspace_3.34.1.tar.gz && rm -rf flowWorkspace.buildbin-libdir && mkdir flowWorkspace.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=flowWorkspace.buildbin-libdir flowWorkspace_3.34.1.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL flowWorkspace_3.34.1.zip && rm flowWorkspace_3.34.1.tar.gz flowWorkspace_3.34.1.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
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100 2642k 100 2642k 0 0 28.0M 0 --:--:-- --:--:-- --:--:-- 29.3M
install for i386
* installing *source* package 'flowWorkspace' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -DROUT -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 R_API.cpp -o R_API.o
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 C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
from R_API.cpp:9:
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 C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
from R_API.cpp:9:
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++)
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -DROUT -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 R_GatingHierarchy.cpp -o R_GatingHierarchy.o
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 C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
from R_GatingHierarchy.cpp:17:
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 C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
from R_GatingHierarchy.cpp:17:
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++)
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -DROUT -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 R_GatingSet.cpp -o R_GatingSet.o
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 C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
from R_GatingSet.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 C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
from R_GatingSet.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++)
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -DROUT -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 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 C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
from ../inst/include/flowWorkspace.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 C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
from ../inst/include/flowWorkspace.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++)
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -DROUT -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 getDescendants.cpp -o getDescendants.o
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 C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
from getDescendants.cpp:1:
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 C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
from getDescendants.cpp:1:
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++)
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -DROUT -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 getPopStats.cpp -o getPopStats.o
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 C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
from getPopStats.cpp:1:
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 C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
from getPopStats.cpp:1:
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++)
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -DROUT -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 getSingleCellExpression.cpp -o getSingleCellExpression.o
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 C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
from getSingleCellExpression.cpp:1:
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 C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
from getSingleCellExpression.cpp:1:
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++)
^
getSingleCellExpression.cpp: In function 'Rcpp::NumericMatrix getSingleCellExpressionByGate(Rcpp::XPtr<GatingSet>, std::string, Rcpp::List, Rcpp::NumericMatrix, Rcpp::CharacterVector, bool)':
getSingleCellExpression.cpp:73:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(unsigned j = 0; j < pops.size(); ++j){
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -DROUT -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 setCounts.cpp -o setCounts.o
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 C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
from setCounts.cpp:1:
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 C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
from setCounts.cpp:1:
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++)
^
mkdir -p "C:/Users/biocbuild/bbs-3.10-bioc/meat/flowWorkspace.buildbin-libdir/00LOCK-flowWorkspace/00new/flowWorkspace/lib/i386"
C:/Rtools/mingw_32/bin/ar rs "C:/Users/biocbuild/bbs-3.10-bioc/meat/flowWorkspace.buildbin-libdir/00LOCK-flowWorkspace/00new/flowWorkspace/lib/i386/libflowWorkspace.a" R_API.o R_GatingHierarchy.o R_GatingSet.o RcppExports.o getDescendants.o getPopStats.o getSingleCellExpression.o setCounts.o
C:\Rtools\mingw_32\bin\ar.exe: creating C:/Users/biocbuild/bbs-3.10-bioc/meat/flowWorkspace.buildbin-libdir/00LOCK-flowWorkspace/00new/flowWorkspace/lib/i386/libflowWorkspace.a
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o flowWorkspace.dll tmp.def R_API.o R_GatingHierarchy.o R_GatingSet.o RcppExports.o getDescendants.o getPopStats.o getSingleCellExpression.o setCounts.o 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/flowWorkspace.buildbin-libdir/00LOCK-flowWorkspace/00new/flowWorkspace/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'flowWorkspace'
finding HTML links ... done
GatingHierarchy-class html
GatingSet-class html
GatingSet-methods html
GatingSetList-class html
asinh_Gml2 html
asinhtGml2_trans html
booleanFilter-class html
finding level-2 HTML links ... done
compensate html
compute_timestep html
estimateLogicle.GatingHierarchy html
extract_cluster_pop_name_from_node html
filterObject html
fix_channel_slash html
flowJo_flog html
flowWorkspace-deprecated html
flowWorkspace-package html
flowWorkspace.par.get html
flowWorkspace.par.init html
flow_breaks html
flow_trans html
flowjo_biexp html
flowjo_biexp_trans html
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpCqwvNP/R.INSTALL1d3c4fffcdf/flowWorkspace/man/flowjo_biexp_trans.Rd:13: file link 'flowJoTrans' in package 'flowWorkspace' does not exist and so has been treated as a topic
flowjo_fasinh html
flowjo_fasinh_trans html
gh_apply_to_new_fcs html
gh_copy_gate html
gh_get_cluster_labels html
gh_get_compensations html
gh_get_transformations html
gh_pop_compare_stats html
gh_pop_get_cluster_name html
gh_pop_get_descendants html
gh_pop_get_full_path html
gh_pop_get_gate html
gh_pop_get_indices html
gh_pop_get_indices_mat html
gh_pop_get_proportion html
gh_pop_move html
gh_pop_set_indices html
gh_pop_set_xml_count html
gs_check_redundant_nodes html
gs_clone html
gs_cyto_data html
gs_get_compensation_internal html
gs_get_leaf_nodes html
gs_get_pop_paths html
gs_get_singlecell_expression html
gs_is_h5 html
gs_plot_diff_tree html
gs_plot_pop_count_cv html
gs_pop_add html
gs_pop_get_children html
gs_pop_get_count_fast html
gs_pop_get_data html
gs_pop_get_stats html
gs_pop_set_gate html
gs_pop_set_name html
gs_pop_set_visibility html
gs_remove_redundant_channels html
gs_remove_redundant_nodes html
gs_split_by_channels html
gs_split_by_tree html
gs_update_channels html
gslist_to_gs html
keyword html
lapply-methods html
length html
logicleGml2_trans html
logicle_trans html
loglevel html
logtGml2_trans html
markernames html
mkformula html
ncFlowSet-methods html
nodeflags html
openWorkspace html
pData-methods html
plot-methods html
plotGate-methods html
pop_add html
prettyAxis html
recompute html
rotate_gate html
sampleNames html
save_gs html
scale_gate html
shift_gate html
standardize-GatingSet html
stats.fun html
subset html
swap_data_cols html
transform html
transform_gate html
transformerList 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 'flowWorkspace' ...
** libs
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -DROUT -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 R_API.cpp -o R_API.o
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 C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
from R_API.cpp:9:
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 C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
from R_API.cpp:9:
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++)
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -DROUT -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 R_GatingHierarchy.cpp -o R_GatingHierarchy.o
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 C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
from R_GatingHierarchy.cpp:17:
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 C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
from R_GatingHierarchy.cpp:17:
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++)
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -DROUT -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 R_GatingSet.cpp -o R_GatingSet.o
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 C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
from R_GatingSet.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 C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
from R_GatingSet.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++)
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -DROUT -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 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 C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
from ../inst/include/flowWorkspace.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 C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
from ../inst/include/flowWorkspace.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++)
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -DROUT -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 getDescendants.cpp -o getDescendants.o
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 C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
from getDescendants.cpp:1:
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 C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
from getDescendants.cpp:1:
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++)
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -DROUT -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 getPopStats.cpp -o getPopStats.o
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 C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
from getPopStats.cpp:1:
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 C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
from getPopStats.cpp:1:
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++)
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -DROUT -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 getSingleCellExpression.cpp -o getSingleCellExpression.o
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 C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
from getSingleCellExpression.cpp:1:
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 C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
from getSingleCellExpression.cpp:1:
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++)
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -DROUT -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 setCounts.cpp -o setCounts.o
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 C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
from setCounts.cpp:1:
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 C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
from setCounts.cpp:1:
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++)
^
mkdir -p "C:/Users/biocbuild/bbs-3.10-bioc/meat/flowWorkspace.buildbin-libdir/flowWorkspace/lib/x64"
C:/Rtools/mingw_64/bin/ar rs "C:/Users/biocbuild/bbs-3.10-bioc/meat/flowWorkspace.buildbin-libdir/flowWorkspace/lib/x64/libflowWorkspace.a" R_API.o R_GatingHierarchy.o R_GatingSet.o RcppExports.o getDescendants.o getPopStats.o getSingleCellExpression.o setCounts.o
C:\Rtools\mingw_64\bin\ar.exe: creating C:/Users/biocbuild/bbs-3.10-bioc/meat/flowWorkspace.buildbin-libdir/flowWorkspace/lib/x64/libflowWorkspace.a
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o flowWorkspace.dll tmp.def R_API.o R_GatingHierarchy.o R_GatingSet.o RcppExports.o getDescendants.o getPopStats.o getSingleCellExpression.o setCounts.o 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/flowWorkspace.buildbin-libdir/flowWorkspace/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'flowWorkspace' as flowWorkspace_3.34.1.zip
* DONE (flowWorkspace)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'flowWorkspace' successfully unpacked and MD5 sums checked
flowWorkspace.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(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
29.73 3.95 34.70
|
flowWorkspace.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(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
31.93 3.73 35.71
|