############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data cellTree ### ############################################################################## ############################################################################## * checking for file ‘cellTree/DESCRIPTION’ ... OK * preparing ‘cellTree’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘cellTree-vignette.Rnw’ using knitr Loading required package: topGO Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: graph Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: GO.db Loading required package: AnnotationDbi Loading required package: stats4 Loading required package: IRanges Loading required package: S4Vectors Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: SparseM Attaching package: 'SparseM' The following object is masked from 'package:base': backsolve groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built. Attaching package: 'topGO' The following object is masked from 'package:IRanges': members Loading required namespace: maptpx Building most specific GOs ..... ( 1580 GO terms found. ) Build GO DAG topology .......... ( 1799 GO terms and 3022 relations. ) Annotating nodes ............... ( 9903 genes annotated to the GO terms. ) -- Weight01 Algorithm -- the algorithm is scoring 794 nontrivial nodes parameters: test statistic: KS score order: decreasing Level 13: 1 nodes to be scored (0 eliminated genes) Level 12: 5 nodes to be scored (0 eliminated genes) Level 11: 41 nodes to be scored (13 eliminated genes) Level 10: 100 nodes to be scored (61 eliminated genes) Level 9: 127 nodes to be scored (793 eliminated genes) Level 8: 112 nodes to be scored (2317 eliminated genes) Level 7: 105 nodes to be scored (4010 eliminated genes) Level 6: 104 nodes to be scored (6540 eliminated genes) Level 5: 86 nodes to be scored (7569 eliminated genes) Level 4: 58 nodes to be scored (8915 eliminated genes) Level 3: 52 nodes to be scored (9580 eliminated genes) Level 2: 2 nodes to be scored (9806 eliminated genes) Level 1: 1 nodes to be scored (9860 eliminated genes) Building most specific GOs ..... ( 1580 GO terms found. ) Build GO DAG topology .......... ( 1799 GO terms and 3022 relations. ) Annotating nodes ............... ( 9903 genes annotated to the GO terms. ) -- Weight01 Algorithm -- the algorithm is scoring 794 nontrivial nodes parameters: test statistic: KS score order: decreasing Level 13: 1 nodes to be scored (0 eliminated genes) Level 12: 5 nodes to be scored (0 eliminated genes) Level 11: 41 nodes to be scored (13 eliminated genes) Level 10: 100 nodes to be scored (61 eliminated genes) Level 9: 127 nodes to be scored (793 eliminated genes) Level 8: 112 nodes to be scored (2317 eliminated genes) Level 7: 105 nodes to be scored (4010 eliminated genes) Level 6: 104 nodes to be scored (6540 eliminated genes) Level 5: 86 nodes to be scored (7569 eliminated genes) Level 4: 58 nodes to be scored (8915 eliminated genes) Level 3: 52 nodes to be scored (9580 eliminated genes) Level 2: 2 nodes to be scored (9806 eliminated genes) Level 1: 1 nodes to be scored (9860 eliminated genes) Building most specific GOs ..... ( 1580 GO terms found. ) Build GO DAG topology .......... ( 1799 GO terms and 3022 relations. ) Annotating nodes ............... ( 9903 genes annotated to the GO terms. ) -- Weight01 Algorithm -- the algorithm is scoring 794 nontrivial nodes parameters: test statistic: KS score order: decreasing Level 13: 1 nodes to be scored (0 eliminated genes) Level 12: 5 nodes to be scored (0 eliminated genes) Level 11: 41 nodes to be scored (13 eliminated genes) Level 10: 100 nodes to be scored (61 eliminated genes) Level 9: 127 nodes to be scored (793 eliminated genes) Level 8: 112 nodes to be scored (2317 eliminated genes) Level 7: 105 nodes to be scored (4010 eliminated genes) Level 6: 104 nodes to be scored (6540 eliminated genes) Level 5: 86 nodes to be scored (7569 eliminated genes) Level 4: 58 nodes to be scored (8915 eliminated genes) Level 3: 52 nodes to be scored (9580 eliminated genes) Level 2: 2 nodes to be scored (9806 eliminated genes) Level 1: 1 nodes to be scored (9860 eliminated genes) Building most specific GOs ..... ( 1580 GO terms found. ) Build GO DAG topology .......... ( 1799 GO terms and 3022 relations. ) Annotating nodes ............... ( 9903 genes annotated to the GO terms. ) -- Weight01 Algorithm -- the algorithm is scoring 794 nontrivial nodes parameters: test statistic: KS score order: decreasing Level 13: 1 nodes to be scored (0 eliminated genes) Level 12: 5 nodes to be scored (0 eliminated genes) Level 11: 41 nodes to be scored (13 eliminated genes) Level 10: 100 nodes to be scored (61 eliminated genes) Level 9: 127 nodes to be scored (793 eliminated genes) Level 8: 112 nodes to be scored (2317 eliminated genes) Level 7: 105 nodes to be scored (4010 eliminated genes) Level 6: 104 nodes to be scored (6540 eliminated genes) Level 5: 86 nodes to be scored (7569 eliminated genes) Level 4: 58 nodes to be scored (8915 eliminated genes) Level 3: 52 nodes to be scored (9580 eliminated genes) Level 2: 2 nodes to be scored (9806 eliminated genes) Level 1: 1 nodes to be scored (9860 eliminated genes) Building most specific GOs ..... ( 1580 GO terms found. ) Build GO DAG topology .......... ( 1799 GO terms and 3022 relations. ) Annotating nodes ............... ( 9903 genes annotated to the GO terms. ) -- Weight01 Algorithm -- the algorithm is scoring 794 nontrivial nodes parameters: test statistic: KS score order: decreasing Level 13: 1 nodes to be scored (0 eliminated genes) Level 12: 5 nodes to be scored (0 eliminated genes) Level 11: 41 nodes to be scored (13 eliminated genes) Level 10: 100 nodes to be scored (61 eliminated genes) Level 9: 127 nodes to be scored (793 eliminated genes) Level 8: 112 nodes to be scored (2317 eliminated genes) Level 7: 105 nodes to be scored (4010 eliminated genes) Level 6: 104 nodes to be scored (6540 eliminated genes) Level 5: 86 nodes to be scored (7569 eliminated genes) Level 4: 58 nodes to be scored (8915 eliminated genes) Level 3: 52 nodes to be scored (9580 eliminated genes) Level 2: 2 nodes to be scored (9806 eliminated genes) Level 1: 1 nodes to be scored (9860 eliminated genes) Quitting from lines 348-352 (cellTree-vignette.Rnw) Error: processing vignette 'cellTree-vignette.Rnw' failed with diagnostics: At core/layout/fruchterman_reingold.c:401 : Weights must be positive for Fruchterman-Reingold layout. Invalid value --- failed re-building ‘cellTree-vignette.Rnw’ SUMMARY: processing the following file failed: ‘cellTree-vignette.Rnw’ Error: Vignette re-building failed. Execution halted