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 | |
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### Running command:
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### 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
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% Total % Received % Xferd Average Speed Time Time Time Current
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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