* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘WGCNA’ ...
** package ‘WGCNA’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-13 (Debian 13.2.0-13) 13.2.0’
using C++ compiler: ‘g++-13 (Debian 13.2.0-13) 13.2.0’
make[1]: Entering directory '/tmp/RtmpDUXjXx/R.INSTALL3b90d32e2b6aac/WGCNA/src'
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DWITH_THREADS -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c corFunctions-utils.c -o corFunctions-utils.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DWITH_THREADS -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c corFunctions.c -o corFunctions.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DWITH_THREADS -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c myMatrixMultiplication.c -o myMatrixMultiplication.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DWITH_THREADS -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c networkFunctions.c -o networkFunctions.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DWITH_THREADS -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c parallelQuantile.cc -o parallelQuantile.o
parallelQuantile.cc: In function ‘SEXPREC* parallelMean(SEXP, SEXP)’:
parallelQuantile.cc:81:12: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
81 | if (nSets!=weight.length())
| ~~~~~^~~~~~~~~~~~~~~~~
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DWITH_THREADS -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c pivot.c -o pivot.o
g++-13 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o WGCNA.so corFunctions-utils.o corFunctions.o myMatrixMultiplication.o networkFunctions.o parallelQuantile.o pivot.o -lpthread -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/tmp/RtmpDUXjXx/R.INSTALL3b90d32e2b6aac/WGCNA/src'
make[1]: Entering directory '/tmp/RtmpDUXjXx/R.INSTALL3b90d32e2b6aac/WGCNA/src'
make[1]: Leaving directory '/tmp/RtmpDUXjXx/R.INSTALL3b90d32e2b6aac/WGCNA/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-WGCNA/00new/WGCNA/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘WGCNA’
finding HTML links ... done
AFcorMI html
BD.getData html
BloodLists html
BrainLists html
BrainRegionMarkers html
GOenrichmentAnalysis html
GTOMdist html
ImmunePathwayLists html
PWLists html
SCsLists html
TOMplot html
TOMsimilarity html
TOMsimilarityFromExpr html
TrueTrait html
accuracyMeasures html
addErrorBars html
addGrid html
addGuideLines html
addTraitToMEs html
adjacency html
adjacency.polyReg html
adjacency.splineReg html
alignExpr html
allocateJobs html
allowWGCNAThreads html
automaticNetworkScreening html
automaticNetworkScreeningGS html
bicor html
bicorAndPvalue html
bicovWeights html
binarizeCategoricalColumns html
binarizeCategoricalVariable html
blockSize html
blockwiseConsensusModules html
blockwiseIndividualTOMs html
blockwiseModules html
blueWhiteRed html
branchEigengeneDissim html
branchSplit html
branchSplit.dissim html
branchSplitFromStabilityLabels html
checkAdjMat html
checkSets html
chooseOneHubInEachModule html
chooseTopHubInEachModule html
clusterCoef html
coClustering html
coClustering.permutationTest html
colQuantileC html
collapseRows html
collapseRowsUsingKME html
collectGarbage html
conformityBasedNetworkConcepts html
conformityDecomposition html
consensusCalculation html
finding level-2 HTML links ... done
consensusDissTOMandTree html
consensusKME html
consensusMEDissimilarity html
consensusOrderMEs html
consensusProjectiveKMeans html
consensusRepresentatives html
consensusTOM html
consensusTreeInputs html
convertNumericColumnsToNumeric html
cor html
corAndPvalue html
corPredictionSuccess html
corPvalueFisher html
corPvalueStudent html
correlationPreservation html
coxRegressionResiduals html
cutreeStatic html
cutreeStaticColor html
displayColors html
dynamicMergeCut html
empiricalBayesLM html
exportNetworkToCytoscape html
exportNetworkToVisANT html
factorizeNonNumericColumns html
fixDataStructure html
formatLabels html
fundamentalNetworkConcepts html
goodGenes html
goodGenesMS html
goodSamples html
goodSamplesGenes html
goodSamplesGenesMS html
goodSamplesMS html
greenBlackRed html
greenWhiteRed html
hierarchicalConsensusCalculation html
hierarchicalConsensusKME html
hierarchicalConsensusMEDissimilarity html
hierarchicalConsensusModules html
hierarchicalConsensusTOM html
hierarchicalMergeCloseModules html
hubGeneSignificance html
imputeByModule html
individualTOMs html
initProgInd html
intramodularConnectivity html
isMultiData html
kMEcomparisonScatterplot html
keepCommonProbes html
labelPoints html
labeledBarplot html
labeledHeatmap html
labeledHeatmap.multiPage html
labels2colors html
list2multiData html
lowerTri2matrix html
matchLabels html
matrixToNetwork html
mergeCloseModules html
metaAnalysis html
metaZfunction html
minWhichMin html
moduleColor.getMEprefix html
moduleEigengenes html
moduleMergeUsingKME html
moduleNumber html
modulePreservation html
mtd.apply html
mtd.mapply html
mtd.rbindSelf html
mtd.setAttr html
mtd.setColnames html
mtd.simplify html
mtd.subset html
multiData html
multiData.eigengeneSignificance html
multiGSub html
multiSetMEs html
multiUnion html
mutualInfoAdjacency html
nPresent html
nSets html
nearestCentroidPredictor html
nearestNeighborConnectivity html
nearestNeighborConnectivityMS html
networkConcepts html
networkScreening html
networkScreeningGS html
newBlockInformation html
newBlockwiseData html
newConsensusOptions html
newConsensusTree html
newCorrelationOptions html
newNetworkOptions html
normalizeLabels html
numbers2colors html
orderBranchesUsingHubGenes html
orderMEs html
orderMEsByHierarchicalConsensus html
overlapTable html
overlapTableUsingKME html
pickHardThreshold html
pickSoftThreshold html
plotClusterTreeSamples html
plotColorUnderTree html
plotCor html
plotDendroAndColors html
plotEigengeneNetworks html
plotMEpairs html
plotMat html
plotModuleSignificance html
plotMultiHist html
plotNetworkHeatmap html
populationMeansInAdmixture html
pquantile html
prepComma html
prependZeros html
preservationNetworkConnectivity html
projectiveKMeans html
propVarExplained html
proportionsInAdmixture html
pruneAndMergeConsensusModules html
pruneConsensusModules html
qvalue html
qvalue.restricted html
randIndex html
rankPvalue html
recutBlockwiseTrees html
recutConsensusTrees html
redWhiteGreen html
relativeCorPredictionSuccess html
removeGreyME html
removePrincipalComponents html
replaceMissing html
returnGeneSetsAsList html
rgcolors.func html
sampledBlockwiseModules html
sampledHierarchicalConsensusModules html
scaleFreeFitIndex html
scaleFreePlot html
selectFewestConsensusMissing html
setCorrelationPreservation html
shortenStrings html
sigmoidAdjacencyFunction html
signedKME html
signifNumeric html
signumAdjacencyFunction html
simpleConsensusCalculation html
simpleHierarchicalConsensusCalculation
html
simulateDatExpr html
simulateDatExpr5Modules html
simulateEigengeneNetwork html
simulateModule html
simulateMultiExpr html
simulateSmallLayer html
sizeGrWindow html
sizeRestrictedClusterMerge html
softConnectivity html
spaste html
standardColors html
standardScreeningBinaryTrait html
standardScreeningCensoredTime html
standardScreeningNumericTrait html
stdErr html
stratifiedBarplot html
subsetTOM html
swapTwoBranches html
transposeBigData html
unsignedAdjacency html
userListEnrichment html
vectorTOM html
vectorizeMatrix html
verboseBarplot html
verboseBoxplot html
verboseIplot html
verboseScatterplot html
votingLinearPredictor html
** building package indices
** 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 (WGCNA)