############################################################################## ############################################################################## ### ### Running command: ### ### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL LineagePulse ### ############################################################################## ############################################################################## * installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library' * installing *source* package 'LineagePulse' ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Note: possible error in 'evalLogLikGeneMM(vecCounts = vecCounts, ': unused arguments (matDispParam = matDispParam, matDropParam = matDropParam, matWeights = matWeights) Note: possible error in 'evalLogLikGeneMM(vecCounts = vecCounts, ': unused arguments (matDispParam = do.call(cbind, lapply(seq_len(ncol(matWeights)), function(m) vecDispParam)), matDropParam = do.call(cbind, lapply(seq_len(ncol(matWeights)), function(m) vecPiParam)), matWeights = matWeights) ** help *** installing help indices converting help for package 'LineagePulse' finding HTML links ... done LPsetters html LineagePulseObject-class html accessors html calcNormConst html calcPostDrop_Matrix html calcPostDrop_Vector html cash-LineagePulseObject-method html decompressDispByGene html decompressDispByGeneMM html decompressDropoutRateByCell html decompressDropoutRateByGene html decompressMeansByGene html decompressMuByGeneMM html evalDropoutModel html evalDropoutModel_comp html evalImpulseModel html evalImpulseModel_comp html evalLogLikGene html evalLogLikGeneMM html evalLogLikMatrix html evalLogLikMuDispGeneFit html evalLogLikMuDispGeneFit_comp html evalLogLikNB html evalLogLikNB_comp html evalLogLikPiZINB_ManyCells html evalLogLikPiZINB_ManyCells_comp html evalLogLikPiZINB_SingleCell html evalLogLikPiZINB_SingleCell_comp html evalLogLikZINB html evalLogLikZINB_comp html fitLPModels html fitModel html fitMuDisp html fitMuDispGene html fitMuDispGeneImpulse html fitMuDispGeneMM html fitPi html fitPi_ManyCells html fitPi_SingleCell html getFitsDispersion html getFitsDropout html getFitsMean html getNormData html getPostDrop html initDispModel html initDropModel html initMuModel html initialiseImpulseParameters html names-LineagePulseObject-method html plotCellDensity html plotGene html processSCData html runDEAnalysis html runLineagePulse html simulateContinuousDataSet html sortGeneTrajectories html sub-sub-LineagePulseObject-character-missing-method html testDropout html writeReport 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 * DONE (LineagePulse) Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") : DESCRIPTION file of package 'LRcell' is missing or broken done