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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 DiffBind
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* checking for file ‘DiffBind/DESCRIPTION’ ... OK
* preparing ‘DiffBind’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘DiffBind.Rnw’ using Sweave
Loading required package: GenomicRanges
Loading required package: stats4
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
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
Loading required package: Seqinfo
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: ‘MatrixGenerics’
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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
>>> DiffBind 3.21.0
BT4741 BT474 ER Resistant Full-Media 1 bed
BT4742 BT474 ER Resistant Full-Media 2 bed
MCF71 MCF7 ER Responsive Full-Media 1 bed
MCF72 MCF7 ER Responsive Full-Media 2 bed
MCF73 MCF7 ER Responsive Full-Media 3 bed
T47D1 T47D ER Responsive Full-Media 1 bed
T47D2 T47D ER Responsive Full-Media 2 bed
MCF7r1 MCF7 ER Resistant Full-Media 1 bed
MCF7r2 MCF7 ER Resistant Full-Media 2 bed
ZR751 ZR75 ER Responsive Full-Media 1 bed
ZR752 ZR75 ER Responsive Full-Media 2 bed
Computing results names...
Analyzing...
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
Generating report-based DBA object...
Replacing design and removing analysis.
Computing results names...
Analyzing...
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
Normalize edgeR with defaults...
Analyzing...
Analyze error: Error: Package edgeR not installed
Unable to complete analysis.
Generating report-based DBA object...
Error: processing vignette 'DiffBind.Rnw' failed with diagnostics:
chunk 49 (label = tamox_block_venn)
Error in dba.plotVenn(tamoxifen, contrast = 1, method = DBA_ALL_METHODS, :
Only one peakset meets specified criteria.
--- failed re-building ‘DiffBind.Rnw’
SUMMARY: processing the following file failed:
‘DiffBind.Rnw’
Error: Vignette re-building failed.
Execution halted