Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:20:52 -0400 (Thu, 12 Apr 2018).
Package 500/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
flowWorkspace 3.26.9 Greg Finak
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | [ OK ] | OK | WARNINGS | OK | ![]() | ||||||
veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | ![]() |
Package: flowWorkspace |
Version: 3.26.9 |
Command: rm -rf flowWorkspace.buildbin-libdir && mkdir flowWorkspace.buildbin-libdir && C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.6/bioc/src/contrib/flowWorkspace_3.26.9.tar.gz && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --library=flowWorkspace.buildbin-libdir --merge-multiarch flowWorkspace_3.26.9.tar.gz && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL flowWorkspace_3.26.9.zip && rm flowWorkspace_3.26.9.tar.gz flowWorkspace_3.26.9.zip |
StartedAt: 2018-04-11 18:40:47 -0400 (Wed, 11 Apr 2018) |
EndedAt: 2018-04-11 18:47:20 -0400 (Wed, 11 Apr 2018) |
EllapsedTime: 393.1 seconds |
RetCode: 0 |
Status: OK |
############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf flowWorkspace.buildbin-libdir && mkdir flowWorkspace.buildbin-libdir && C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.6/bioc/src/contrib/flowWorkspace_3.26.9.tar.gz && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --library=flowWorkspace.buildbin-libdir --merge-multiarch flowWorkspace_3.26.9.tar.gz && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL flowWorkspace_3.26.9.zip && rm flowWorkspace_3.26.9.tar.gz flowWorkspace_3.26.9.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 30 2823k 30 864k 0 0 7120k 0 --:--:-- --:--:-- --:--:-- 7260k 100 2823k 100 2823k 0 0 10.1M 0 --:--:-- --:--:-- --:--:-- 10.2M 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˜1.6-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -IC:/libxml2//i386/include/libxml2 -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/cytolib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c R_API.cpp -o R_API.o C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -IC:/libxml2//i386/include/libxml2 -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/cytolib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c R_GatingHierarchy.cpp -o R_GatingHierarchy.o C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -IC:/libxml2//i386/include/libxml2 -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/cytolib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c R_GatingSet.cpp -o R_GatingSet.o C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -IC:/libxml2//i386/include/libxml2 -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/cytolib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c RcppExports.cpp -o RcppExports.o C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -IC:/libxml2//i386/include/libxml2 -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/cytolib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c flowJoWorkspace.cpp -o flowJoWorkspace.o C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -IC:/libxml2//i386/include/libxml2 -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/cytolib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c getSingleCellExpression.cpp -o getSingleCellExpression.o 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˜1.6-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -IC:/libxml2//i386/include/libxml2 -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/cytolib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c macFlowJoWorkspace.cpp -o macFlowJoWorkspace.o C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -IC:/libxml2//i386/include/libxml2 -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/cytolib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c setCounts.cpp -o setCounts.o C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -IC:/libxml2//i386/include/libxml2 -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/cytolib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c winFlowJoWorkspace.cpp -o winFlowJoWorkspace.o winFlowJoWorkspace.cpp:562:27: warning: "/*" within comment [-Wcomment] * "*[local-name()='edge']/*[local-name()='vertex']" is for ellipsoidGate ^ winFlowJoWorkspace.cpp: In member function 'virtual trans_local xFlowJoWorkspace::getTransformation(wsRootNode, const compensation&, PARAM_VEC&, trans_global_vec*, biexpTrans*, linTrans*, bool)': winFlowJoWorkspace.cpp:113:11: warning: unused variable 'minRange' [-Wunused-variable] double minRange=atof(transNode.getProperty("minRange").c_str()); ^ In file included from C:/Users/biocbuild/bbs-3.6-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15:0, from C:/Users/biocbuild/bbs-3.6-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/winFlowJoWorkspace.hpp:10, from winFlowJoWorkspace.cpp:8: C:/Users/biocbuild/bbs-3.6-bioc/R/library/cytolib/include/cytolib/gate.hpp: In member function 'CurlyGuadGate* winFlowJoWorkspace::getGate(wsCurlyQuadGateNode&)': C:/Users/biocbuild/bbs-3.6-bioc/R/library/cytolib/include/cytolib/gate.hpp:440:94: warning: 'quad' may be used uninitialized in this function [-Wmaybe-uninitialized] CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),interpolated(false),quadrant(_quad){ ^ winFlowJoWorkspace.cpp:539:7: note: 'quad' was declared here QUAD quad; ^ C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -IC:/libxml2//i386/include/libxml2 -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/cytolib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c workspace.cpp -o workspace.o C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -IC:/libxml2//i386/include/libxml2 -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/cytolib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c ws2gh.cpp -o ws2gh.o C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -IC:/libxml2//i386/include/libxml2 -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/cytolib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c ws2gs.cpp -o ws2gs.o C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -IC:/libxml2//i386/include/libxml2 -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/cytolib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c wsNode.cpp -o wsNode.o mkdir -p "C:/Users/biocbuild/bbs-3.6-bioc/meat/flowWorkspace.buildbin-libdir/flowWorkspace/lib/i386" C:/Rtools/mingw_32/bin/ar rs "C:/Users/biocbuild/bbs-3.6-bioc/meat/flowWorkspace.buildbin-libdir/flowWorkspace/lib/i386/libflowWorkspace.a" R_API.o R_GatingHierarchy.o R_GatingSet.o RcppExports.o flowJoWorkspace.o getSingleCellExpression.o macFlowJoWorkspace.o setCounts.o winFlowJoWorkspace.o workspace.o ws2gh.o ws2gs.o wsNode.o C:\Rtools\mingw_32\bin\ar.exe: creating C:/Users/biocbuild/bbs-3.6-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 flowJoWorkspace.o getSingleCellExpression.o macFlowJoWorkspace.o setCounts.o winFlowJoWorkspace.o workspace.o ws2gh.o ws2gs.o wsNode.o C:/libxml2//i386/lib/libxml2.a C:/Users/biocbuild/bbs-3.6-bioc/R/library/cytolib/lib/i386/libcytolib.a C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/lib/i386/libprotobuf.a -lws2_32 -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lR installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/flowWorkspace.buildbin-libdir/flowWorkspace/libs/i386 ** R ** inst ** preparing 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-3.6-bioc/tmpdir/RtmpKE1vM1/R.INSTALLd14554a6d3c/flowWorkspace/man/estimateLogicle.GatingHierarchy.Rd:20: missing file link 'estimateLogicle' filterObject html flowData html flowJo.fasinh 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 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 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 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 subset html transform html transformerList html updateChannels 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˜1.6-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -IC:/libxml2//x64/include/libxml2 -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/cytolib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c R_API.cpp -o R_API.o C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -IC:/libxml2//x64/include/libxml2 -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/cytolib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c R_GatingHierarchy.cpp -o R_GatingHierarchy.o C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -IC:/libxml2//x64/include/libxml2 -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/cytolib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c R_GatingSet.cpp -o R_GatingSet.o C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -IC:/libxml2//x64/include/libxml2 -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/cytolib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c RcppExports.cpp -o RcppExports.o C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -IC:/libxml2//x64/include/libxml2 -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/cytolib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c flowJoWorkspace.cpp -o flowJoWorkspace.o C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -IC:/libxml2//x64/include/libxml2 -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/cytolib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c getSingleCellExpression.cpp -o getSingleCellExpression.o C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -IC:/libxml2//x64/include/libxml2 -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/cytolib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c macFlowJoWorkspace.cpp -o macFlowJoWorkspace.o C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -IC:/libxml2//x64/include/libxml2 -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/cytolib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c setCounts.cpp -o setCounts.o C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -IC:/libxml2//x64/include/libxml2 -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/cytolib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c winFlowJoWorkspace.cpp -o winFlowJoWorkspace.o winFlowJoWorkspace.cpp:562:27: warning: "/*" within comment [-Wcomment] * "*[local-name()='edge']/*[local-name()='vertex']" is for ellipsoidGate ^ winFlowJoWorkspace.cpp: In member function 'virtual trans_local xFlowJoWorkspace::getTransformation(wsRootNode, const compensation&, PARAM_VEC&, trans_global_vec*, biexpTrans*, linTrans*, bool)': winFlowJoWorkspace.cpp:113:11: warning: unused variable 'minRange' [-Wunused-variable] double minRange=atof(transNode.getProperty("minRange").c_str()); ^ In file included from C:/Users/biocbuild/bbs-3.6-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15:0, from C:/Users/biocbuild/bbs-3.6-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/winFlowJoWorkspace.hpp:10, from winFlowJoWorkspace.cpp:8: C:/Users/biocbuild/bbs-3.6-bioc/R/library/cytolib/include/cytolib/gate.hpp: In member function 'CurlyGuadGate* winFlowJoWorkspace::getGate(wsCurlyQuadGateNode&)': C:/Users/biocbuild/bbs-3.6-bioc/R/library/cytolib/include/cytolib/gate.hpp:440:94: warning: 'quad' may be used uninitialized in this function [-Wmaybe-uninitialized] CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),interpolated(false),quadrant(_quad){ ^ winFlowJoWorkspace.cpp:539:7: note: 'quad' was declared here QUAD quad; ^ C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -IC:/libxml2//x64/include/libxml2 -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/cytolib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c workspace.cpp -o workspace.o C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -IC:/libxml2//x64/include/libxml2 -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/cytolib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c ws2gh.cpp -o ws2gh.o C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -IC:/libxml2//x64/include/libxml2 -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/cytolib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c ws2gs.cpp -o ws2gs.o C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -IC:/libxml2//x64/include/libxml2 -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/cytolib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c wsNode.cpp -o wsNode.o mkdir -p "C:/Users/biocbuild/bbs-3.6-bioc/meat/flowWorkspace.buildbin-libdir/flowWorkspace/lib/x64" C:/Rtools/mingw_64/bin/ar rs "C:/Users/biocbuild/bbs-3.6-bioc/meat/flowWorkspace.buildbin-libdir/flowWorkspace/lib/x64/libflowWorkspace.a" R_API.o R_GatingHierarchy.o R_GatingSet.o RcppExports.o flowJoWorkspace.o getSingleCellExpression.o macFlowJoWorkspace.o setCounts.o winFlowJoWorkspace.o workspace.o ws2gh.o ws2gs.o wsNode.o C:\Rtools\mingw_64\bin\ar.exe: creating C:/Users/biocbuild/bbs-3.6-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 flowJoWorkspace.o getSingleCellExpression.o macFlowJoWorkspace.o setCounts.o winFlowJoWorkspace.o workspace.o ws2gh.o ws2gs.o wsNode.o C:/libxml2//x64/lib/libxml2.a C:/Users/biocbuild/bbs-3.6-bioc/R/library/cytolib/lib/x64/libcytolib.a C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/lib/x64/libprotobuf.a -lws2_32 -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/flowWorkspace.buildbin-libdir/flowWorkspace/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'flowWorkspace' as flowWorkspace_3.26.9.zip * DONE (flowWorkspace) In R CMD INSTALL In R CMD INSTALL * installing to library 'C:/Users/biocbuild/bbs-3.6-bioc/R/library' package 'flowWorkspace' successfully unpacked and MD5 sums checked In R CMD INSTALL