* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘rliger’ ...
** package ‘rliger’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-14 (Debian 14.2.0-8) 14.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpMNwv63/R.INSTALL386d8127622b37/rliger/src'
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppProgress/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -DARMA_DONT_USE_OPENMP -fpic -g -O2 -Wall -pedantic -mtune=native -c ModularityOptimizer.cpp -o ModularityOptimizer.o
ModularityOptimizer.cpp: In constructor ‘ModularityOptimizer::Network::Network(int, DVector*, std::vector<std::vector<int> >&, DVector*)’:
ModularityOptimizer.cpp:206:3: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
206 | for (size_t j = 0; j < edge[0].size(); j++)
| ^~~
ModularityOptimizer.cpp:218:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
218 | for (; i <= nNodes; i++)
| ^~~
ModularityOptimizer.cpp: In member function ‘ModularityOptimizer::Clustering ModularityOptimizer::Network::identifyComponents()’:
ModularityOptimizer.cpp:389:9: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
389 | for (int l = firstNeighborIndex[node[k]]; l < firstNeighborIndex[node[k] + 1]; l++)
| ^~~
ModularityOptimizer.cpp:397:11: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
397 | k++;
| ^
ModularityOptimizer.cpp:379:3: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
379 | for (int i = 0; i < nNodes; i++)
| ^~~
ModularityOptimizer.cpp:401:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
401 | clustering.orderClustersByNNodes();
| ^~~~~~~~~~
ModularityOptimizer.cpp: In member function ‘ModularityOptimizer::Network ModularityOptimizer::Network::createSubnetwork(const ModularityOptimizer::Clustering&, int, IVector&, IVector&, IVector&, DVector&) const’:
ModularityOptimizer.cpp:431:7: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
431 | for (int k = firstNeighborIndex[j]; k < firstNeighborIndex[j + 1]; k++)
| ^~~
ModularityOptimizer.cpp:438:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
438 | subnetwork.firstNeighborIndex[i + 1] = subnetwork.nEdges;
| ^~~~~~~~~~
ModularityOptimizer.cpp: In member function ‘bool ModularityOptimizer::VOSClusteringTechnique::runLocalMovingAlgorithm(ModularityOptimizer::JavaRandom&)’:
ModularityOptimizer.cpp:571:3: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
571 | for (i = 0; i < network->nNodes; i++)
| ^~~
ModularityOptimizer.cpp:577:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
577 | for (i = 0; i < network->nNodes; i++)
| ^~~
ModularityOptimizer.cpp: In member function ‘int ModularityOptimizer::VOSClusteringTechnique::removeCluster(int)’:
ModularityOptimizer.cpp:709:3: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
709 | for (int j = 0; j < clustering->nClusters; j++)
| ^~~
ModularityOptimizer.cpp:720:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
720 | if (i >= 0)
| ^~
ModularityOptimizer.cpp:722:7: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
722 | for (int j = 0; j < network->nNodes; j++)
| ^~~
ModularityOptimizer.cpp:725:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
725 | if (cluster == clustering->nClusters - 1)
| ^~
ModularityOptimizer.cpp: In member function ‘void ModularityOptimizer::VOSClusteringTechnique::removeSmallClusters(int)’:
ModularityOptimizer.cpp:739:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
739 | for (int k = 0; k < vosClusteringTechnique.clustering->nClusters; k++)
| ^~~
ModularityOptimizer.cpp:746:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
746 | if (i >= 0)
| ^~
ModularityOptimizer.cpp: In function ‘std::shared_ptr<ModularityOptimizer::Network> ModularityOptimizer::matrixToNetwork(IVector&, IVector&, DVector&, int)’:
ModularityOptimizer.cpp:764:3: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
764 | for (size_t i = 0; i < node1.size(); i++)
| ^~~
ModularityOptimizer.cpp:771:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
771 | IVector firstNeighborIndex(nNodes + 1);
| ^~~~~~~
ModularityOptimizer.cpp:783:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
783 | for (size_t i = 0; i < node1.size(); i++)
| ^~~
ModularityOptimizer.cpp:796:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
796 | if (modularityFunction == 1)
| ^~
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppProgress/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -DARMA_DONT_USE_OPENMP -fpic -g -O2 -Wall -pedantic -mtune=native -c RModularityOptimizer.cpp -o RModularityOptimizer.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppProgress/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -DARMA_DONT_USE_OPENMP -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppProgress/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -DARMA_DONT_USE_OPENMP -fpic -g -O2 -Wall -pedantic -mtune=native -c centoidAlign.cpp -o centoidAlign.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppProgress/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -DARMA_DONT_USE_OPENMP -fpic -g -O2 -Wall -pedantic -mtune=native -c data_processing.cpp -o data_processing.o
data_processing.cpp: In function ‘arma::mat colNormalize_dense_cpp(arma::mat&, arma::uword)’:
data_processing.cpp:27:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
27 | for (int j = 0; j < x.n_cols; ++j) {
| ~~^~~~~~~~~~
data_processing.cpp:32:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
32 | for (int i = 0; i < x.n_rows; ++i) {
| ~~^~~~~~~~~~
data_processing.cpp: In function ‘Rcpp::NumericVector SparseRowVarStd(arma::sp_mat, Rcpp::NumericVector, Rcpp::NumericVector, double)’:
data_processing.cpp:254:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
254 | for (int k=0; k<x.n_cols; ++k) {
| ~^~~~~~~~~
data_processing.cpp: In function ‘arma::mat colAggregateMedian_dense_cpp(const arma::mat&, const arma::uvec&, arma::uword)’:
data_processing.cpp:290:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
290 | for (int i = 0; i < n; ++i) {
| ~~^~~
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppProgress/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -DARMA_DONT_USE_OPENMP -fpic -g -O2 -Wall -pedantic -mtune=native -c feature_mat.cpp -o feature_mat.o
feature_mat.cpp: In function ‘Rcpp::NumericMatrix makeFeatureMatrix(Rcpp::DataFrame&, Rcpp::StringVector&)’:
feature_mat.cpp:29:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
29 | for(int i = 0; i < barcodes_v.size(); ++i){
| ~~^~~~~~~~~~~~~~~~~~~
feature_mat.cpp:41:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
41 | for(int j=0; j < associated_barcodes.size(); ++j){
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppProgress/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -DARMA_DONT_USE_OPENMP -fpic -g -O2 -Wall -pedantic -mtune=native -c quantile_norm.cpp -o quantile_norm.o
quantile_norm.cpp: In function ‘Rcpp::IntegerVector cluster_vote_rcpp(const arma::mat&, Rcpp::IntegerVector)’:
quantile_norm.cpp:12:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
12 | for(int j=0; j<k; ++j) {
| ~^~
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppProgress/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -DARMA_DONT_USE_OPENMP -fpic -g -O2 -Wall -pedantic -mtune=native -c snn.cpp -o snn.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppProgress/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -DARMA_DONT_USE_OPENMP -fpic -g -O2 -Wall -pedantic -mtune=native -c wilcoxon.cpp -o wilcoxon.o
wilcoxon.cpp: In function ‘std::__cxx11::list<float> cpp_in_place_rank_mean(arma::vec&, int, int)’:
wilcoxon.cpp:19:34: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
19 | for (size_t i = idx_begin; i <= idx_end; i++) {
| ~~^~~~~~~~~~
g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o rliger.so ModularityOptimizer.o RModularityOptimizer.o RcppExports.o centoidAlign.o data_processing.o feature_mat.o quantile_norm.o snn.o wilcoxon.o -llapack -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpMNwv63/R.INSTALL386d8127622b37/rliger/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpMNwv63/R.INSTALL386d8127622b37/rliger/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpMNwv63/R.INSTALL386d8127622b37/rliger/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-rliger/00new/rliger/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘rliger’
finding HTML links ... done
H5Apply html
alignFactors html
as.liger html
as.ligerDataset html
bmmc html
calcARI html
calcAgreement html
calcAlignment html
calcDatasetSpecificity html
calcNMI html
calcPurity html
centroidAlign html
closeAllH5 html
commandDiff html
convertOldLiger html
coordinate html
createH5LigerDataset html
createLiger html
createLigerDataset html
deg.marker html
deg.pw html
dot-complexHeatmapDotPlot html
dot-ggCellViolin html
dot-ggScatter html
dot-ggplotLigerTheme html
dot-plotHeatmap html
downsample html
exportInteractTrack html
getFactorMarkers html
getProportionMito html
importVignetteData html
imputeKNN html
is.newLiger html
isH5Liger html
liger-DEG html
liger-class html
ligerATACDataset-class html
ligerCommand-class html
ligerDataset-class html
ligerMethDataset-class html
ligerRNADataset-class html
ligerSpatialDataset-class html
ligerToSeurat html
linkGenesAndPeaks html
louvainCluster-deprecated html
makeFeatureMatrix html
makeInteractTrack-deprecated html
makeRiverplot-deprecated html
mapCellMeta html
mergeH5 html
mergeSparseAll html
modalOf html
normalize html
online_iNMF-deprecated html
optimizeALS-deprecated html
optimizeNewData html
optimizeNewK html
optimizeNewLambda html
optimizeSubset html
pbmc html
pbmcPlot html
peak html
plotBarcodeRank html
plotCellViolin html
plotClusterFactorDot html
plotClusterGeneDot html
plotClusterGeneViolin html
plotDensityDimRed html
plotDimRed html
plotEnhancedVolcano html
plotGODot html
plotGeneLoadings html
plotGroupClusterDimRed html
plotHeatmap html
plotMarkerHeatmap html
plotPairwiseDEGHeatmap html
plotProportion html
plotProportionBox html
plotSankey html
plotSpatial html
plotVarFeatures html
plotViolin html
plotVolcano html
quantileAlignSNF html
quantileNorm html
quantile_norm-deprecated html
read10X html
read10XFiles html
readLiger html
readSubset html
reexports html
removeMissing html
restoreH5Liger html
retrieveCellFeature html
reverseMethData html
rliger-deprecated html
rliger-package html
runCINMF html
runCluster html
runDoubletFinder html
runGOEnrich html
runGSEA html
runGeneralQC html
runINMF html
runIntegration html
runOnlineINMF html
runTSNE html
runUINMF html
runUMAP html
scaleNotCenter html
selectGenes html
selectGenesVST html
sub-liger html
sub-ligerDataset html
sub-sub-liger html
subsetLiger html
subsetLigerDataset html
updateLigerObject html
writeH5 html
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (rliger)