##############################################################################
##############################################################################
###
### Running command:
###
### chmod a+r groHMM -R && F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data groHMM
###
##############################################################################
##############################################################################
* checking for file 'groHMM/DESCRIPTION' ... OK
* preparing 'groHMM':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'groHMM.Rnw' using Sweave
Loading required package: MASS
Loading required package: parallel
Loading required package: S4Vectors
Loading required package: stats4
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, table, tapply,
union, unique, unsplit, which.max, which.min
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: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: GenomicAlignments
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
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")'.
Attaching package: 'Biobase'
The following object is masked from 'package:MatrixGenerics':
rowMedians
The following objects are masked from 'package:matrixStats':
anyMissing, rowMedians
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Loading required package: Rsamtools
Loading required package: rtracklayer
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
Attaching package: 'AnnotationDbi'
The following object is masked from 'package:MASS':
select
Warning in makeConsensusAnnotations(kgChr7, keytype = "gene_id", mc.cores = getOption("mc.cores")) :
562 ranges do not have gene_id and they are
dropped
Reduce isoforms(701) ... OK
Truncate overlapped ranges ... OK
'select()' returned 1:1 mapping between keys and columns
Calculate overlapping ... OK
Scale overlapping ... OK
Warning: file stem 'F:/biocbuild/bbs-3.20-bioc/tmpdir/Rtmp6huaWQ/Rbuild3a7c52dd6d4/groHMM/vignettes/groHMM-fig2' is not portable
Calculate overlapping ... OK
Scale overlapping ... OK
Loading required package: limma
Attaching package: 'limma'
The following object is masked from 'package:BiocGenerics':
plotMA
Error: processing vignette 'groHMM.Rnw' failed with diagnostics:
chunk 21 (label = DE for trascripts)
Error in decideTestsDGE(et, p = 0.001, adjust = "fdr") :
could not find function "decideTestsDGE"
--- failed re-building 'groHMM.Rnw'
SUMMARY: processing the following file failed:
'groHMM.Rnw'
Error: Vignette re-building failed.
Execution halted