flowWorkspace 3.28.2
Greg Finak ,Mike Jiang
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/flowWorkspace |
| Branch: RELEASE_3_7 |
| Last Commit: bd5ee4c |
| Last Changed Date: 2018-09-12 18:32:05 -0400 (Wed, 12 Sep 2018) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | |
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
##############################################################################
##############################################################################
###
### Running command:
###
### C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flowWorkspace.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings flowWorkspace_3.28.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/flowWorkspace.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* 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 '3.28.2'
* 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-3.7-bioc/tmpdir/RtmpeKdHJV/R.INSTALLf101cdf7f8a/flowWorkspace/man/estimateLogicle.GatingHierarchy.Rd:20: file link 'estimateLogicle' in package 'flowCore' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.7-bioc/meat/flowWorkspace.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
installed size is 15.2Mb
sub-directories of 1Mb or more:
lib 7.0Mb
libs 6.5Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Versioned 'LinkingTo' values for
'BH' 'cytolib'
are only usable in R >= 3.0.2
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
'RBGL' 'grDevices' 'graphics'
All declared Imports should be used.
Unexported objects imported by ':::' calls:
'flowCore:::.estimateLogicle' 'flowCore:::checkClass'
'flowCore:::copyFlowSet' 'flowCore:::guid'
'flowCore:::logicle_transform' 'flowCore:::updateTransformKeywords'
'graph:::.makeEdgeKeys' 'lattice:::updateList'
'ncdfFlow:::.isValidSamples' 'stats:::.splinefun'
See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
'.cpp_setIndices' '.getNodeInd'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
getGate,GatingSetList-character: warning in unlist(res, recur = FALSE):
partial argument match of 'recur' to 'recursive'
.addGatingHierarchies: no visible global function definition for 'is'
.computeCV : <anonymous>: no visible binding for global variable
'xml.count'
.computeCV : <anonymous>: no visible binding for global variable
'openCyto.count'
.computeCV : <anonymous> : <anonymous>: no visible global function
definition for 'IQR'
.computeCV : <anonymous> : <anonymous>: no visible global function
definition for 'median'
.computeCV_gh : <anonymous>: no visible global function definition for
'IQR'
.computeCV_gh : <anonymous>: no visible global function definition for
'median'
.dropRedundantNodes : <anonymous>: no visible global function
definition for 'is'
.getSingleCellExpression: no visible binding for global variable
'parallel'
.graph_handler : asGraphNEL: no visible global function definition for
'new'
.graph_handler : asGraphNEL: no visible global function definition for
'validObject'
.load_gs: no visible global function definition for 'new'
.load_gs: no visible global function definition for '.hasSlot'
.load_gs: no visible global function definition for 'slot'
.load_gs: no visible global function definition for 'is'
.mergeGates : <anonymous>: no visible global function definition for
'extends'
.parse.pData: no visible binding for global variable '.'
.plotGate: no visible global function definition for 'new'
.plotGate: no visible global function definition for 'as.formula'
.preplot: no visible global function definition for 'as'
.preprocessMap: no visible binding for global variable 'old'
.preprocessMap: no visible binding for global variable '.'
.preprocessor: no visible binding for global variable 'groupName'
GatingSetList: no visible global function definition for 'as'
GatingSetList: no visible global function definition for 'validObject'
booleanFilter: no visible global function definition for 'new'
booleanFilter: no visible global function definition for 'is'
char2booleanFilter: no visible global function definition for 'new'
dropRedundantNodes : <anonymous>: no visible global function definition
for 'is'
flowWorkspace.par.init: no visible global function definition for
'gray'
getMergedStats: no visible binding for global variable 'sampleName'
mkformula: no visible global function definition for 'as.formula'
pop.MFI: no visible binding for global variable 'desc'
save_gslist: no visible binding for global variable 'slot'
transformerList: no visible global function definition for 'is'
transformerList: no visible binding for global variable 'is'
GatingSet,GatingHierarchy-character: no visible global function
definition for 'new'
GatingSet,character-character: no visible global function definition
for 'new'
GatingSet,flowSet-ANY: no visible global function definition for 'new'
Rm,character-GatingSetList-character: no visible global function
definition for 'selectMethod'
[,GatingSet-ANY: no visible global function definition for 'extends'
[,GatingSetList-ANY: no visible global function definition for
'callNextMethod'
[,GatingSetList-ANY: no visible global function definition for 'as'
[[,GatingSet-character: no visible global function definition for 'new'
add,GatingHierarchy-logicalFilterResult: no visible global function
definition for 'selectMethod'
add,GatingSet-filtersList: no visible global function definition for
'selectMethod'
add,GatingSet-list: no visible global function definition for
'selectMethod'
add,GatingSetList-filter: no visible global function definition for
'selectMethod'
add,GatingSetList-filterList: no visible global function definition for
'selectMethod'
add,GatingSetList-filters: no visible global function definition for
'selectMethod'
add,GatingSetList-filtersList: no visible global function definition
for 'selectMethod'
add,GatingSetList-list: no visible global function definition for
'selectMethod'
getPopStats,GatingHierarchy: no visible binding for global variable
'node'
keyword,GatingSetList-character: no visible global function definition
for 'selectMethod'
keyword,GatingSetList-missing: no visible global function definition
for 'selectMethod'
openWorkspace,character: no visible global function definition for
'new'
pData<-,GatingSetList-data.frame: no visible global function definition
for 'callNextMethod'
pData<-,GatingSetList-data.frame: no visible global function definition
for 'as'
plotGate,GatingSetList-character: no visible global function definition
for 'selectMethod'
rbind2,GatingSetList-missing: no visible global function definition for
'new'
rbind2,GatingSetList-missing: no visible binding for global variable
'slot'
recompute,GatingSetList: no visible global function definition for
'selectMethod'
show,flowJoWorkspace: no visible global function definition for '.'
show,flowJoWorkspace: no visible binding for global variable
'groupName'
transform,GatingSet: no visible global function definition for 'is'
transform,GatingSet : <anonymous>: no visible global function
definition for 'is'
Undefined global functions or variables:
. .hasSlot IQR as as.formula callNextMethod desc extends gray
groupName is median new node old openCyto.count parallel sampleName
selectMethod slot validObject xml.count
Consider adding
importFrom("grDevices", "gray")
importFrom("methods", ".hasSlot", "as", "callNextMethod", "extends",
"is", "new", "selectMethod", "slot", "validObject")
importFrom("stats", "IQR", "as.formula", "median")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.7-bioc/R/library/flowWorkspace/libs/i386/flowWorkspace.dll':
Found '_exit', possibly from '_exit' (C)
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
Found 'puts', possibly from 'printf' (C), 'puts' (C)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
Running 'testthat.R'
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 6 NOTEs
See
'C:/Users/biocbuild/bbs-3.7-bioc/meat/flowWorkspace.Rcheck/00check.log'
for details.
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/flowWorkspace_3.28.2.tar.gz && rm -rf flowWorkspace.buildbin-libdir && mkdir flowWorkspace.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=flowWorkspace.buildbin-libdir flowWorkspace_3.28.2.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL flowWorkspace_3.28.2.zip && rm flowWorkspace_3.28.2.tar.gz flowWorkspace_3.28.2.zip
###
##############################################################################
##############################################################################
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 2825k 100 2825k 0 0 24.3M 0 --:--:-- --:--:-- --:--:-- 25.7M
install for i386
* installing *source* package 'flowWorkspace' ...
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -Ic:/libxml2//i386/include/libxml2 -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c R_API.cpp -o R_API.o
In file included from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
from R_API.cpp:9:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.7-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-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.7-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˜1.7-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -Ic:/libxml2//i386/include/libxml2 -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c R_GatingHierarchy.cpp -o R_GatingHierarchy.o
In file included from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
from R_GatingHierarchy.cpp:17:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.7-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-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.7-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˜1.7-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -Ic:/libxml2//i386/include/libxml2 -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c R_GatingSet.cpp -o R_GatingSet.o
In file included from ../inst/include/flowWorkspace/openWorkspace.hpp:12:0,
from R_GatingSet.cpp:10:
../inst/include/flowWorkspace/winFlowJoWorkspace.hpp:433:30: warning: "/*" within comment [-Wcomment]
* "*[local-name()='edge']/*[local-name()='vertex']" is for ellipsoidGate
^
In file included from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
from ../inst/include/flowWorkspace/wsNode.hpp:10,
from ../inst/include/flowWorkspace/workspace.hpp:14,
from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
from R_GatingSet.cpp:10:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.7-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-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:228:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(auto i = 0; i < nEvents; i++)
^
In file included from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11:0,
from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
from R_GatingSet.cpp:10:
../inst/include/flowWorkspace/workspace.hpp: In member function 'void workspace::toArray(std::string, std::vector<double>&, std::vector<double>&)':
../inst/include/flowWorkspace/workspace.hpp:108:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(unsigned i=0;i<nLen;i++)
^
In file included from ../inst/include/flowWorkspace/openWorkspace.hpp:12:0,
from R_GatingSet.cpp:10:
../inst/include/flowWorkspace/winFlowJoWorkspace.hpp: In member function 'virtual trans_local xFlowJoWorkspace::getTransformation(wsRootNode, const compensation&, PARAM_VEC&, trans_global_vec*, biexpTrans*, linTrans*, bool)':
../inst/include/flowWorkspace/winFlowJoWorkspace.hpp:779:12: warning: unused variable 'minRange' [-Wunused-variable]
double minRange=atof(transNode.getProperty("minRange").c_str());
^
In file included from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15:0,
from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
from ../inst/include/flowWorkspace/wsNode.hpp:10,
from ../inst/include/flowWorkspace/workspace.hpp:14,
from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
from R_GatingSet.cpp:10:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp: In member function 'CurlyGuadGate* winFlowJoWorkspace::getGate(wsCurlyQuadGateNode&)':
C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:1291:94: warning: 'quad' may be used uninitialized in this function [-Wmaybe-uninitialized]
CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),interpolated(false),quadrant(_quad){
^
In file included from ../inst/include/flowWorkspace/openWorkspace.hpp:12:0,
from R_GatingSet.cpp:10:
../inst/include/flowWorkspace/winFlowJoWorkspace.hpp:410:10: note: 'quad' was declared here
QUAD quad;
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -Ic:/libxml2//i386/include/libxml2 -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c RcppExports.cpp -o RcppExports.o
In file included from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
from ../inst/include/flowWorkspace.h:5,
from RcppExports.cpp:4:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.7-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-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.7-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˜1.7-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -Ic:/libxml2//i386/include/libxml2 -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c getDescendants.cpp -o getDescendants.o
In file included from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
from getDescendants.cpp:2:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.7-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-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.7-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˜1.7-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -Ic:/libxml2//i386/include/libxml2 -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c getSingleCellExpression.cpp -o getSingleCellExpression.o
In file included from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
from getSingleCellExpression.cpp:2:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.7-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-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.7-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˜1.7-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -Ic:/libxml2//i386/include/libxml2 -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c setCounts.cpp -o setCounts.o
In file included from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
from setCounts.cpp:2:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.7-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-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.7-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-3.7-bioc/meat/flowWorkspace.buildbin-libdir/flowWorkspace/lib/i386"
C:/Rtools/mingw_32/bin/ar rs "C:/Users/biocbuild/bbs-3.7-bioc/meat/flowWorkspace.buildbin-libdir/flowWorkspace/lib/i386/libflowWorkspace.a" R_API.o R_GatingHierarchy.o R_GatingSet.o RcppExports.o getDescendants.o getSingleCellExpression.o setCounts.o
C:\Rtools\mingw_32\bin\ar.exe: creating C:/Users/biocbuild/bbs-3.7-bioc/meat/flowWorkspace.buildbin-libdir/flowWorkspace/lib/i386/libflowWorkspace.a
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o flowWorkspace.dll tmp.def R_API.o R_GatingHierarchy.o R_GatingSet.o RcppExports.o getDescendants.o getSingleCellExpression.o setCounts.o c:/libxml2//i386/lib/libxml2.a C:/Users/biocbuild/bbs-3.7-bioc/R/library/RProtoBufLib/lib/i386/GatingSet.pb.o C:/Users/biocbuild/bbs-3.7-bioc/R/library/RProtoBufLib/lib/i386/libprotobuf.a -lws2_32 -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/flowWorkspace.buildbin-libdir/flowWorkspace/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'flowWorkspace'
finding HTML links ... done
GatingHierarchy-class html
GatingSet-class html
GatingSet-methods html
finding level-2 HTML links ... done
GatingSetList-class html
add html
asinh_Gml2 html
asinhtGml2_trans html
booleanFilter-class html
checkRedundantNodes html
clone html
compensate html
dropRedundantChannels html
dropRedundantNodes html
estimateLogicle.GatingHierarchy html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpeKdHJV/R.INSTALLf101cdf7f8a/flowWorkspace/man/estimateLogicle.GatingHierarchy.Rd:20: file link 'estimateLogicle' in package 'flowCore' does not exist and so has been treated as a topic
filterObject html
flowData html
flowJo.fasinh html
flowJo.flog html
flowJoTrans html
flowJoWorkspace-class html
flowJo_biexp_trans html
flowJo_fasinh_trans html
flowWorkspace-package html
flowWorkspace.par.get html
flowWorkspace.par.init html
flow_breaks html
flow_trans html
getCompensationMatrices html
getData-methods html
getDescendants html
getFJWSubsetIndices html
getGate html
getIndiceMat html
getIndices-GatingSet-name-method html
getIndices html
getKeywords html
getMergedStats html
getNodes html
getParent html
getPopStats html
getSampleGroups html
getSamples html
getSingleCellExpression html
getStats html
getTransformations html
groupByChannels html
groupByTree html
insertGate html
isNcdf html
keyword html
lapply-methods html
length html
logicleGml2_trans html
logicle_trans html
loglevel html
logtGml2_trans html
markernames html
mkformula html
moveNode html
ncFlowSet-methods html
openWorkspace html
pData-methods html
parseWorkspace html
plot-methods html
plotGate-methods html
plotPopCV html
prettyAxis html
recompute html
sampleNames html
save_gs html
set.count.xml html
setGate html
setNode-methods html
standardize-GatingSet html
stats.fun html
subset html
transform html
transformerList html
updateChannels html
updateIndices-GatingHierarchy-character-logical-method
html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'flowWorkspace' ...
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -Ic:/libxml2//x64/include/libxml2 -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c R_API.cpp -o R_API.o
In file included from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
from R_API.cpp:9:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.7-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-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.7-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˜1.7-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -Ic:/libxml2//x64/include/libxml2 -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c R_GatingHierarchy.cpp -o R_GatingHierarchy.o
In file included from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
from R_GatingHierarchy.cpp:17:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.7-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-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.7-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˜1.7-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -Ic:/libxml2//x64/include/libxml2 -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c R_GatingSet.cpp -o R_GatingSet.o
In file included from ../inst/include/flowWorkspace/openWorkspace.hpp:12:0,
from R_GatingSet.cpp:10:
../inst/include/flowWorkspace/winFlowJoWorkspace.hpp:433:30: warning: "/*" within comment [-Wcomment]
* "*[local-name()='edge']/*[local-name()='vertex']" is for ellipsoidGate
^
In file included from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
from ../inst/include/flowWorkspace/wsNode.hpp:10,
from ../inst/include/flowWorkspace/workspace.hpp:14,
from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
from R_GatingSet.cpp:10:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.7-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-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:228:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(auto i = 0; i < nEvents; i++)
^
In file included from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11:0,
from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
from R_GatingSet.cpp:10:
../inst/include/flowWorkspace/workspace.hpp: In member function 'void workspace::toArray(std::string, std::vector<double>&, std::vector<double>&)':
../inst/include/flowWorkspace/workspace.hpp:108:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(unsigned i=0;i<nLen;i++)
^
In file included from ../inst/include/flowWorkspace/openWorkspace.hpp:12:0,
from R_GatingSet.cpp:10:
../inst/include/flowWorkspace/winFlowJoWorkspace.hpp: In member function 'virtual trans_local xFlowJoWorkspace::getTransformation(wsRootNode, const compensation&, PARAM_VEC&, trans_global_vec*, biexpTrans*, linTrans*, bool)':
../inst/include/flowWorkspace/winFlowJoWorkspace.hpp:779:12: warning: unused variable 'minRange' [-Wunused-variable]
double minRange=atof(transNode.getProperty("minRange").c_str());
^
In file included from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15:0,
from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
from ../inst/include/flowWorkspace/wsNode.hpp:10,
from ../inst/include/flowWorkspace/workspace.hpp:14,
from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
from R_GatingSet.cpp:10:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp: In member function 'CurlyGuadGate* winFlowJoWorkspace::getGate(wsCurlyQuadGateNode&)':
C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:1291:94: warning: 'quad' may be used uninitialized in this function [-Wmaybe-uninitialized]
CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),interpolated(false),quadrant(_quad){
^
In file included from ../inst/include/flowWorkspace/openWorkspace.hpp:12:0,
from R_GatingSet.cpp:10:
../inst/include/flowWorkspace/winFlowJoWorkspace.hpp:410:10: note: 'quad' was declared here
QUAD quad;
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -Ic:/libxml2//x64/include/libxml2 -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c RcppExports.cpp -o RcppExports.o
In file included from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
from ../inst/include/flowWorkspace.h:5,
from RcppExports.cpp:4:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.7-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-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.7-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˜1.7-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -Ic:/libxml2//x64/include/libxml2 -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c getDescendants.cpp -o getDescendants.o
In file included from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
from getDescendants.cpp:2:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.7-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-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.7-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˜1.7-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -Ic:/libxml2//x64/include/libxml2 -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c getSingleCellExpression.cpp -o getSingleCellExpression.o
In file included from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
from getSingleCellExpression.cpp:2:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.7-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-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.7-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˜1.7-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -Ic:/libxml2//x64/include/libxml2 -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c setCounts.cpp -o setCounts.o
In file included from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
from setCounts.cpp:2:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.7-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-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.7-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-3.7-bioc/meat/flowWorkspace.buildbin-libdir/flowWorkspace/lib/x64"
C:/Rtools/mingw_64/bin/ar rs "C:/Users/biocbuild/bbs-3.7-bioc/meat/flowWorkspace.buildbin-libdir/flowWorkspace/lib/x64/libflowWorkspace.a" R_API.o R_GatingHierarchy.o R_GatingSet.o RcppExports.o getDescendants.o getSingleCellExpression.o setCounts.o
C:\Rtools\mingw_64\bin\ar.exe: creating C:/Users/biocbuild/bbs-3.7-bioc/meat/flowWorkspace.buildbin-libdir/flowWorkspace/lib/x64/libflowWorkspace.a
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o flowWorkspace.dll tmp.def R_API.o R_GatingHierarchy.o R_GatingSet.o RcppExports.o getDescendants.o getSingleCellExpression.o setCounts.o c:/libxml2//x64/lib/libxml2.a C:/Users/biocbuild/bbs-3.7-bioc/R/library/RProtoBufLib/lib/x64/GatingSet.pb.o C:/Users/biocbuild/bbs-3.7-bioc/R/library/RProtoBufLib/lib/x64/libprotobuf.a -lws2_32 -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/flowWorkspace.buildbin-libdir/flowWorkspace/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'flowWorkspace' as flowWorkspace_3.28.2.zip
* DONE (flowWorkspace)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'flowWorkspace' successfully unpacked and MD5 sums checked
In R CMD INSTALL