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### Running command:
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### /home/biocbuild/R/R-4.3.0/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, aperm, 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 object is masked from ‘package:utils’:
findMatches
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().
( 1667 GO terms found. )
Build GO DAG topology ..........
( 4334 GO terms and 9615 relations. )
Annotating nodes ...............
( 315 genes annotated to the GO terms. )
-- Classic Algorithm --
the algorithm is scoring 890 nontrivial nodes
parameters:
test statistic: fisher
-- Classic Algorithm --
the algorithm is scoring 978 nontrivial nodes
parameters:
test statistic: ks
score order: increasing
-- Elim Algorithm --
the algorithm is scoring 978 nontrivial nodes
parameters:
test statistic: ks
cutOff: 0.01
score order: increasing
Level 15: 1 nodes to be scored (0 eliminated genes)
Level 14: 1 nodes to be scored (0 eliminated genes)
Level 13: 6 nodes to be scored (0 eliminated genes)
Level 12: 15 nodes to be scored (25 eliminated genes)
Level 11: 30 nodes to be scored (25 eliminated genes)
Level 10: 57 nodes to be scored (36 eliminated genes)
Level 9: 87 nodes to be scored (55 eliminated genes)
Level 8: 125 nodes to be scored (107 eliminated genes)
Level 7: 158 nodes to be scored (131 eliminated genes)
Level 6: 168 nodes to be scored (157 eliminated genes)
Level 5: 158 nodes to be scored (166 eliminated genes)
Level 4: 104 nodes to be scored (200 eliminated genes)
Level 3: 51 nodes to be scored (200 eliminated genes)
Level 2: 16 nodes to be scored (225 eliminated genes)
Level 1: 1 nodes to be scored (225 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
Building most specific GOs .....
( 109 GO terms found. )
Build GO DAG topology ..........
( 226 GO terms and 298 relations. )
Annotating nodes ...............
( 86 genes annotated to the GO terms. )
Loading required package: multtest
Building most specific GOs .....
( 7680 GO terms found. )
Build GO DAG topology ..........
( 11520 GO terms and 25882 relations. )
Annotating nodes ...............
( 3884 genes annotated to the GO terms. )
-- Classic Algorithm --
the algorithm is scoring 4023 nontrivial nodes
parameters:
test statistic: Fisher test
-- Classic Algorithm --
the algorithm is scoring 5813 nontrivial nodes
parameters:
test statistic: KS tests
score order: increasing
-- Weight Algorithm --
The algorithm is scoring 4023 nontrivial nodes
parameters:
test statistic: Fisher test : ratio
Level 17: 1 nodes to be scored.
Level 16: 7 nodes to be scored.
Level 15: 24 nodes to be scored.
Level 14: 39 nodes to be scored.
Level 13: 86 nodes to be scored.
Level 12: 138 nodes to be scored.
Level 11: 253 nodes to be scored.
Level 10: 404 nodes to be scored.
Level 9: 549 nodes to be scored.
Level 8: 602 nodes to be scored.
Level 7: 658 nodes to be scored.
Level 6: 580 nodes to be scored.
Level 5: 366 nodes to be scored.
Level 4: 214 nodes to be scored.
Level 3: 84 nodes to be scored.
Level 2: 17 nodes to be scored.
Level 1: 1 nodes to be scored.
-- Classic Algorithm --
the algorithm is scoring 4023 nontrivial nodes
parameters:
test statistic: fisher
Error: processing vignette 'topGO.Rnw' failed with diagnostics:
unable to run pdflatex on 'topGO.tex'
LaTeX errors:
! LaTeX Error: File `sectsty.sty' not found.
Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)
! Emergency stop.
<read *>
l.11 \usepackage
{caption}^^M
! ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘topGO.Rnw’
SUMMARY: processing the following file failed:
‘topGO.Rnw’
Error: Vignette re-building failed.
Execution halted