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###
### Running command:
###
### chmod a+r Genominator -R && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data Genominator
###
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* checking for file 'Genominator/DESCRIPTION' ... OK
* preparing 'Genominator':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'Genominator.Rnw' using Sweave
Loading required package: RSQLite
Loading required package: DBI
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
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, colMeans, colSums, 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, rowMeans, rowSums,
rownames, sapply, setdiff, sort, table, tapply, union, unique,
unsplit, which, which.max, which.min
Loading required package: IRanges
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomeGraphs
Loading required package: biomaRt
Loading required package: grid
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
matplot: doing 1 plots with col= ("1") pch= ("1" "2" "3" "4" "5" "6" "7" "8" "9" "0" "a" "b" "c" "d" "e" "f" "g" "h" "i" "j" "k" "l" "m" "n" "o" "p" "q" "r" "s" "t" "u" "v" "w" "x" "y" "z" "A" "B" "C" "D" "E" "F" "G" "H" "I" "J" "K" "L" "M" "N" "O" "P" "Q" "R" "S" "T" "U" "V" "W" "X" "Y" "Z") ...
--- finished re-building 'Genominator.Rnw'
--- re-building 'plotting.Rnw' using Sweave
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Error: processing vignette 'plotting.Rnw' failed with diagnostics:
chunk 7
Error in bmAttrFilt("attributes", mart, verbose = verbose) :
biomaRt error: looks like we're connecting to incompatible version of BioMart suite.
--- failed re-building 'plotting.Rnw'
--- re-building 'withShortRead.Rnw' using Sweave
Loading required package: ShortRead
Loading required package: BiocParallel
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: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: GenomicAlignments
Loading required package: SummarizedExperiment
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: DelayedArray
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following object is masked from 'package:Biostrings':
type
The following objects are masked from 'package:base':
aperm, apply, rowsum
Loading required package: yeastRNASeq
Warning in result_fetch(res@ptr, n = n) :
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Warning in result_fetch(res@ptr, n = n) :
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Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
--- finished re-building 'withShortRead.Rnw'
Warning in file.remove(f) :
cannot remove file 'my.db', reason 'Permission denied'
Warning in file.remove(f) :
cannot remove file 'pmy.db', reason 'Permission denied'
SUMMARY: processing the following file failed:
'plotting.Rnw'
Error: Vignette re-building failed.
Execution halted
