flowWorkspace 3.30.2
Greg Finak ,Mike Jiang
| Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019) |
| URL: https://git.bioconductor.org/packages/flowWorkspace |
| Branch: RELEASE_3_8 |
| Last Commit: eac7b2d |
| Last Changed Date: 2019-01-04 13:33:27 -0400 (Fri, 04 Jan 2019) |
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | WARNINGS | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | [ OK ] | OK | WARNINGS | OK | |
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
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### Running command:
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### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/flowWorkspace_3.30.2.tar.gz && rm -rf flowWorkspace.buildbin-libdir && mkdir flowWorkspace.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=flowWorkspace.buildbin-libdir flowWorkspace_3.30.2.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL flowWorkspace_3.30.2.zip && rm flowWorkspace_3.30.2.tar.gz flowWorkspace_3.30.2.zip
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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˜1.8-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -IC:/libxml2//i386/include/libxml2 -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.8-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-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
from C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
from C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
from C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
from R_API.cpp:9:
C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.8-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-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -IC:/libxml2//i386/include/libxml2 -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.8-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-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
from C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
from C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
from R_GatingHierarchy.cpp:17:
C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.8-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-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -IC:/libxml2//i386/include/libxml2 -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.8-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-3.8-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-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.8-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-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.8-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:802:12: warning: unused variable 'minRange' [-Wunused-variable]
double minRange=atof(transNode.getProperty("minRange").c_str());
^
In file included from C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15:0,
from C:/Users/biocbuild/bbs-3.8-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-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp: In member function 'CurlyGuadGate* winFlowJoWorkspace::getGate(wsCurlyQuadGateNode&)':
C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:1314:94: 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˜1.8-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -IC:/libxml2//i386/include/libxml2 -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.8-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-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
from C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
from C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
from C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
from ../inst/include/flowWorkspace.h:5,
from RcppExports.cpp:4:
C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.8-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-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -IC:/libxml2//i386/include/libxml2 -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.8-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-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
from C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
from C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
from C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
from getDescendants.cpp:2:
C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.8-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-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -IC:/libxml2//i386/include/libxml2 -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.8-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-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
from C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
from C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
from getSingleCellExpression.cpp:2:
C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.8-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-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -IC:/libxml2//i386/include/libxml2 -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.8-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-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
from C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
from C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
from C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
from setCounts.cpp:2:
C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.8-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-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.8-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-3.8-bioc/meat/flowWorkspace.buildbin-libdir/flowWorkspace/lib/i386"
C:/Rtools/mingw_32/bin/ar rs "C:/Users/biocbuild/bbs-3.8-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-3.8-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-3.8-bioc/R/library/RProtoBufLib/lib/i386/GatingSet.pb.o C:/Users/biocbuild/bbs-3.8-bioc/R/library/RProtoBufLib/lib/i386/libprotobuf.a -lws2_32 -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.8-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
compute_timestep html
dropRedundantChannels html
dropRedundantNodes html
estimateLogicle.GatingHierarchy html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOgG1q4/R.INSTALL1bf4598c1d9c/flowWorkspace/man/estimateLogicle.GatingHierarchy.Rd:20: file link 'estimateLogicle' in package 'flowCore' does not exist and so has been treated as a topic
extract_cluster_pop_name_from_node html
filterObject html
fix_channel_slash 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
getCompensationObj 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
gh_check_cluster_node html
gh_get_cluster_labels 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
nodeflags html
openWorkspace html
pData-methods html
parseWorkspace html
plot-methods html
plotGate-methods html
plotPopCV html
plot_diff_tree 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˜1.8-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -IC:/libxml2//x64/include/libxml2 -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.8-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-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
from C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
from C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
from C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
from R_API.cpp:9:
C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.8-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-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -IC:/libxml2//x64/include/libxml2 -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.8-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-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
from C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
from C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
from R_GatingHierarchy.cpp:17:
C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.8-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-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -IC:/libxml2//x64/include/libxml2 -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.8-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-3.8-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-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.8-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-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.8-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:802:12: warning: unused variable 'minRange' [-Wunused-variable]
double minRange=atof(transNode.getProperty("minRange").c_str());
^
In file included from C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15:0,
from C:/Users/biocbuild/bbs-3.8-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-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp: In member function 'CurlyGuadGate* winFlowJoWorkspace::getGate(wsCurlyQuadGateNode&)':
C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:1314:94: 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˜1.8-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -IC:/libxml2//x64/include/libxml2 -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.8-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-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
from C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
from C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
from C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
from ../inst/include/flowWorkspace.h:5,
from RcppExports.cpp:4:
C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.8-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-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -IC:/libxml2//x64/include/libxml2 -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.8-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-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
from C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
from C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
from C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
from getDescendants.cpp:2:
C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.8-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-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -IC:/libxml2//x64/include/libxml2 -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.8-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-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
from C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
from C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
from getSingleCellExpression.cpp:2:
C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.8-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-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -IC:/libxml2//x64/include/libxml2 -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.8-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-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
from C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
from C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
from C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
from setCounts.cpp:2:
C:/Users/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.8-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-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.8-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-3.8-bioc/meat/flowWorkspace.buildbin-libdir/flowWorkspace/lib/x64"
C:/Rtools/mingw_64/bin/ar rs "C:/Users/biocbuild/bbs-3.8-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-3.8-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-3.8-bioc/R/library/RProtoBufLib/lib/x64/GatingSet.pb.o C:/Users/biocbuild/bbs-3.8-bioc/R/library/RProtoBufLib/lib/x64/libprotobuf.a -lws2_32 -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/flowWorkspace.buildbin-libdir/flowWorkspace/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'flowWorkspace' as flowWorkspace_3.30.2.zip
* DONE (flowWorkspace)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'flowWorkspace' successfully unpacked and MD5 sums checked
In R CMD INSTALL