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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data topGO
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* checking for file ‘topGO/DESCRIPTION’ ... OK
* preparing ‘topGO’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘topGO.Rnw’ using Sweave
Loading required package: xtable
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 package: org.Hs.eg.db
Building most specific GOs .....
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
( 1616 GO terms found. )
Build GO DAG topology ..........
( 4344 GO terms and 9738 relations. )
Annotating nodes ...............
( 315 genes annotated to the GO terms. )
-- Classic Algorithm --
the algorithm is scoring 892 nontrivial nodes
parameters:
test statistic: fisher
-- Classic Algorithm --
the algorithm is scoring 968 nontrivial nodes
parameters:
test statistic: ks
score order: increasing
-- Elim Algorithm --
the algorithm is scoring 968 nontrivial nodes
parameters:
test statistic: ks
cutOff: 0.01
score order: increasing
Level 15: 1 nodes to be scored (0 eliminated genes)
Level 14: 2 nodes to be scored (0 eliminated genes)
Level 13: 9 nodes to be scored (0 eliminated genes)
Level 12: 20 nodes to be scored (39 eliminated genes)
Level 11: 31 nodes to be scored (39 eliminated genes)
Level 10: 52 nodes to be scored (39 eliminated genes)
Level 9: 92 nodes to be scored (39 eliminated genes)
Level 8: 116 nodes to be scored (71 eliminated genes)
Level 7: 145 nodes to be scored (145 eliminated genes)
Level 6: 168 nodes to be scored (158 eliminated genes)
Level 5: 162 nodes to be scored (178 eliminated genes)
Level 4: 102 nodes to be scored (202 eliminated genes)
Level 3: 52 nodes to be scored (205 eliminated genes)
Level 2: 15 nodes to be scored (228 eliminated genes)
Level 1: 1 nodes to be scored (228 eliminated genes)
Loading required package: Rgraphviz
Loading required package: grid
Attaching package: ‘grid’
The following object is masked from ‘package:topGO’:
depth
Attaching package: ‘Rgraphviz’
The following objects are masked from ‘package:IRanges’:
from, to
The following objects are masked from ‘package:S4Vectors’:
from, to
Error: processing vignette 'topGO.Rnw' failed with diagnostics:
chunk 24
Error in library(genefilter) : there is no package called ‘genefilter’
--- failed re-building ‘topGO.Rnw’
SUMMARY: processing the following file failed:
‘topGO.Rnw’
Error: Vignette re-building failed.
Execution halted
