flowWorkspace 3.31.15
Greg Finak ,Mike Jiang
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/flowWorkspace |
| Branch: master |
| Last Commit: 6803ddb |
| Last Changed Date: 2019-04-08 14:02:14 -0400 (Mon, 08 Apr 2019) |
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | [ OK ] | OK | OK | OK | |
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/flowWorkspace_3.31.15.tar.gz && rm -rf flowWorkspace.buildbin-libdir && mkdir flowWorkspace.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=flowWorkspace.buildbin-libdir flowWorkspace_3.31.15.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL flowWorkspace_3.31.15.zip && rm flowWorkspace_3.31.15.tar.gz flowWorkspace_3.31.15.zip
###
##############################################################################
##############################################################################
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 2634k 100 2634k 0 0 29.9M 0 --:--:-- --:--:-- --:--:-- 32.5M
install for i386
* installing *source* package 'flowWorkspace' ...
** libs
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -DROUT -DRCPP_PARALLEL_USE_TBB=1 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/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-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
from R_API.cpp:9:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.9-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-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.9-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˜1.9-B/R/include" -DNDEBUG -DROUT -DRCPP_PARALLEL_USE_TBB=1 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/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-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
from R_GatingHierarchy.cpp:17:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.9-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-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.9-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˜1.9-B/R/include" -DNDEBUG -DROUT -DRCPP_PARALLEL_USE_TBB=1 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c R_GatingSet.cpp -o R_GatingSet.o
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
from R_GatingSet.cpp:10:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.9-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-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.9-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˜1.9-B/R/include" -DNDEBUG -DROUT -DRCPP_PARALLEL_USE_TBB=1 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c RcppExports.cpp -o RcppExports.o
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
from ../inst/include/flowWorkspace.h:5,
from RcppExports.cpp:4:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.9-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-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.9-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˜1.9-B/R/include" -DNDEBUG -DROUT -DRCPP_PARALLEL_USE_TBB=1 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c getDescendants.cpp -o getDescendants.o
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
from getDescendants.cpp:1:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.9-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-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.9-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˜1.9-B/R/include" -DNDEBUG -DROUT -DRCPP_PARALLEL_USE_TBB=1 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c getPopStats.cpp -o getPopStats.o
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
from getPopStats.cpp:1:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.9-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-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.9-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˜1.9-B/R/include" -DNDEBUG -DROUT -DRCPP_PARALLEL_USE_TBB=1 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c getSingleCellExpression.cpp -o getSingleCellExpression.o
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
from getSingleCellExpression.cpp:1:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.9-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-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.9-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˜1.9-B/R/include" -DNDEBUG -DROUT -DRCPP_PARALLEL_USE_TBB=1 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c setCounts.cpp -o setCounts.o
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
from setCounts.cpp:1:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.9-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-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.9-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-3.9-bioc/meat/flowWorkspace.buildbin-libdir/00LOCK-flowWorkspace/00new/flowWorkspace/lib/i386"
C:/Rtools/mingw_32/bin/ar rs "C:/Users/biocbuild/bbs-3.9-bioc/meat/flowWorkspace.buildbin-libdir/00LOCK-flowWorkspace/00new/flowWorkspace/lib/i386/libflowWorkspace.a" R_API.o R_GatingHierarchy.o R_GatingSet.o RcppExports.o getDescendants.o getPopStats.o getSingleCellExpression.o setCounts.o
C:\Rtools\mingw_32\bin\ar.exe: creating C:/Users/biocbuild/bbs-3.9-bioc/meat/flowWorkspace.buildbin-libdir/00LOCK-flowWorkspace/00new/flowWorkspace/lib/i386/libflowWorkspace.a
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o flowWorkspace.dll tmp.def R_API.o R_GatingHierarchy.o R_GatingSet.o RcppExports.o getDescendants.o getPopStats.o getSingleCellExpression.o setCounts.o C:/Users/biocbuild/bbs-3.9-bioc/R/library/RProtoBufLib/lib/i386/GatingSet.pb.o C:/Users/biocbuild/bbs-3.9-bioc/R/library/RProtoBufLib/lib/i386/libprotobuf.a -LC:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/lib/i386 -ltbb -ltbbmalloc -lws2_32 -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/flowWorkspace.buildbin-libdir/00LOCK-flowWorkspace/00new/flowWorkspace/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'flowWorkspace'
finding HTML links ... done
GatingHierarchy-class html
GatingSet-class html
GatingSet-methods html
GatingSetList-class html
add html
asinh_Gml2 html
asinhtGml2_trans html
booleanFilter-class html
finding level-2 HTML links ... done
checkRedundantNodes html
clone html
compensate html
compute_timestep html
copyNode html
dropRedundantChannels html
dropRedundantNodes html
estimateLogicle.GatingHierarchy html
extract_cluster_pop_name_from_node html
filterObject html
fix_channel_slash html
flowData html
flowJo.fasinh html
flowJo.flog html
flowJoTrans 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
getFullNodePath html
getGate html
getIndiceMat html
getIndices-GatingSet-name-method html
getIndices html
getMergedStats html
getNodes html
getParent html
getPopStats html
getSingleCellExpression html
getStats html
getTransformations html
get_leaf_nodes 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
plot-methods html
plotGate-methods html
plotPopCV html
plot_diff_tree html
prettyAxis html
recompute html
rotate_gate html
sampleNames html
save_gs html
scale_gate html
set.count.xml html
setGate html
setNode-methods html
shift_gate html
standardize-GatingSet html
stats.fun html
subset html
swap_data_cols html
transform html
transform_gate html
transformerList html
updateChannels html
updateIndices-GatingHierarchy-character-logical-method
html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'flowWorkspace' ...
** libs
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -DROUT -DRCPP_PARALLEL_USE_TBB=1 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/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-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
from R_API.cpp:9:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.9-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-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.9-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˜1.9-B/R/include" -DNDEBUG -DROUT -DRCPP_PARALLEL_USE_TBB=1 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/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-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
from R_GatingHierarchy.cpp:17:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.9-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-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.9-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˜1.9-B/R/include" -DNDEBUG -DROUT -DRCPP_PARALLEL_USE_TBB=1 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c R_GatingSet.cpp -o R_GatingSet.o
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
from R_GatingSet.cpp:10:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.9-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-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.9-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˜1.9-B/R/include" -DNDEBUG -DROUT -DRCPP_PARALLEL_USE_TBB=1 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c RcppExports.cpp -o RcppExports.o
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
from ../inst/include/flowWorkspace.h:5,
from RcppExports.cpp:4:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.9-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-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.9-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˜1.9-B/R/include" -DNDEBUG -DROUT -DRCPP_PARALLEL_USE_TBB=1 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c getDescendants.cpp -o getDescendants.o
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
from getDescendants.cpp:1:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.9-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-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.9-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˜1.9-B/R/include" -DNDEBUG -DROUT -DRCPP_PARALLEL_USE_TBB=1 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c getPopStats.cpp -o getPopStats.o
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
from getPopStats.cpp:1:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.9-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-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.9-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˜1.9-B/R/include" -DNDEBUG -DROUT -DRCPP_PARALLEL_USE_TBB=1 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c getSingleCellExpression.cpp -o getSingleCellExpression.o
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
from getSingleCellExpression.cpp:1:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.9-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-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.9-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˜1.9-B/R/include" -DNDEBUG -DROUT -DRCPP_PARALLEL_USE_TBB=1 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c setCounts.cpp -o setCounts.o
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
from setCounts.cpp:1:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.9-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-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.9-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-3.9-bioc/meat/flowWorkspace.buildbin-libdir/flowWorkspace/lib/x64"
C:/Rtools/mingw_64/bin/ar rs "C:/Users/biocbuild/bbs-3.9-bioc/meat/flowWorkspace.buildbin-libdir/flowWorkspace/lib/x64/libflowWorkspace.a" R_API.o R_GatingHierarchy.o R_GatingSet.o RcppExports.o getDescendants.o getPopStats.o getSingleCellExpression.o setCounts.o
C:\Rtools\mingw_64\bin\ar.exe: creating C:/Users/biocbuild/bbs-3.9-bioc/meat/flowWorkspace.buildbin-libdir/flowWorkspace/lib/x64/libflowWorkspace.a
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o flowWorkspace.dll tmp.def R_API.o R_GatingHierarchy.o R_GatingSet.o RcppExports.o getDescendants.o getPopStats.o getSingleCellExpression.o setCounts.o C:/Users/biocbuild/bbs-3.9-bioc/R/library/RProtoBufLib/lib/x64/GatingSet.pb.o C:/Users/biocbuild/bbs-3.9-bioc/R/library/RProtoBufLib/lib/x64/libprotobuf.a -LC:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/lib/x64 -ltbb -ltbbmalloc -lws2_32 -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/flowWorkspace.buildbin-libdir/flowWorkspace/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'flowWorkspace' as flowWorkspace_3.31.15.zip
* DONE (flowWorkspace)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'flowWorkspace' successfully unpacked and MD5 sums checked