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### Running command:
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### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data qpgraph
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* checking for file ‘qpgraph/DESCRIPTION’ ... OK
* preparing ‘qpgraph’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* running ‘cleanup’
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘eQTLnetworks.Rnw’ using Sweave
Loading required package: BiocGenerics
Loading required package: generics
Attaching package: ‘generics’
The following objects are masked from ‘package:base’:
as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
setequal, union
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, is.unsorted, lapply,
mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
unsplit, which.max, which.min
Loading required package: S4Vectors
Loading required package: stats4
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: IRanges
Attaching package: ‘qpgraph’
The following object is masked from ‘package:qtl’:
sim.cross
Calculating pairwise (conditional) independence tests
Estimating non-rejection rates with q=3
Using exact likelihood ratio tests.
--- finished re-building ‘eQTLnetworks.Rnw’
--- re-building ‘qpTxRegNet.Rnw’ using Sweave
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: AnnotationDbi
Loading required package: XML
Attaching package: ‘XML’
The following object is masked from ‘package:graph’:
addNode
Using t tests for zero partial regression coefficients.
Warning in .qpNrr(X, q, I, restrict.Q, fix.Q, nTests, alpha, pairup.i, pairup.j, :
With p=100 and q=11 the estimated fraction of valid Q sets is 0.79. Increasing nTests from 100 to 126 in order to achieve the desired precision
Using t tests for zero partial regression coefficients.
Warning in .qpNrr(X, q, I, restrict.Q, fix.Q, nTests, alpha, pairup.i, pairup.j, :
With p=100 and q=21 the estimated fraction of valid Q sets is 0.62. Increasing nTests from 100 to 160 in order to achieve the desired precision
Using t tests for zero partial regression coefficients.
Warning in .qpNrr(X, q, I, restrict.Q, fix.Q, nTests, alpha, pairup.i, pairup.j, :
With p=100 and q=31 the estimated fraction of valid Q sets is 0.47. Increasing nTests from 100 to 210 in order to achieve the desired precision
Using t tests for zero partial regression coefficients.
Warning in .old_qpGraph(nrrMatrix, ...) :
The function call 'qpGraph()' using arguments 'threshold' or 'return.type' is being deprecated and will dissapear in the next release version. Please consult the help page of qpGraph().
Attaching package: ‘Rgraphviz’
The following object is masked from ‘package:annotate’:
toFile
The following objects are masked from ‘package:IRanges’:
from, to
The following objects are masked from ‘package:S4Vectors’:
from, to
--- finished re-building ‘qpTxRegNet.Rnw’
--- re-building ‘qpgraphSimulate.Rnw’ using Sweave
*** buffer overflow detected ***: terminated
Aborted (core dumped)
