Back to Books build report for BioC 3.13

BUILD report for csawBook on riesling1

This page was generated on 2021-01-15 16:45:06 -0500 (Fri, 15 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE csawBook PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1/3HostnameOS / ArchINSTALLBUILD
csawBook 0.99.3
Aaron Lun
Snapshot Date: 2021-01-15 09:00:02 -0500 (Fri, 15 Jan 2021)
URL: https://git.bioconductor.org/packages/csawBook
Branch: master
Last Commit: 22c5503
Last Changed Date: 2020-11-19 00:13:03 -0500 (Thu, 19 Nov 2020)
malbec2 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64  OK [ ERROR ]

Summary

Package: csawBook
Version: 0.99.3
Command: chmod a+r csawBook -R && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data csawBook
StartedAt: 2021-01-15 10:31:06 -0500 (Fri, 15 Jan 2021)
EndedAt: 2021-01-15 11:56:26 -0500 (Fri, 15 Jan 2021)
EllapsedTime: 5119.9 seconds
RetCode: 1
Status:  ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   chmod a+r csawBook -R && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data csawBook
###
##############################################################################
##############################################################################


* checking for file 'csawBook/DESCRIPTION' ... OK
* preparing 'csawBook':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'stub.Rmd' using rmarkdown
--- finished re-building 'stub.Rmd'

cd book && "D:/biocbuild/bbs-3.13-bioc/R/bin/R" -e "bookdown::render_book('index.Rmd')"

R Under development (unstable) (2020-12-30 r79736) -- "Unsuffered Consequences"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> bookdown::render_book('index.Rmd')


processing file: index.Rmd

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label: unnamed-chunk-1 (with options) 
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label: unnamed-chunk-2 (with options) 
List of 2
 $ echo   : logi FALSE
 $ results: chr "asis"


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label: unnamed-chunk-3
snapshotDate(): 2021-01-15
see ?chipseqDBData and browseVignettes('chipseqDBData') for documentation
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see ?chipseqDBData and browseVignettes('chipseqDBData') for documentation
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see ?chipseqDBData and browseVignettes('chipseqDBData') for documentation
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see ?chipseqDBData and browseVignettes('chipseqDBData') for documentation
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see ?chipseqDBData and browseVignettes('chipseqDBData') for documentation
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see ?chipseqDBData and browseVignettes('chipseqDBData') for documentation
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see ?chipseqDBData and browseVignettes('chipseqDBData') for documentation
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see ?chipseqDBData and browseVignettes('chipseqDBData') for documentation
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label: unnamed-chunk-4 (with options) 
List of 1
 $ indent: chr "    "

Loading required package: GenomicRanges
Loading required package: stats4
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, 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: S4Vectors

Attaching package: 'S4Vectors'

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: 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


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Loading required package: limma

Attaching package: 'limma'

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label: unnamed-chunk-9 (with options) 
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 $ echo   : logi FALSE
 $ results: chr "asis"


output file: index.knit.md



processing file: window-counts.Rmd

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label: unnamed-chunk-1 (with options) 
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 $ echo   : logi FALSE
 $ results: chr "asis"


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label: extension-schematic (with options) 
List of 4
 $ echo      : logi FALSE
 $ fig.width : num 8
 $ fig.height: num 5
 $ fig.cap   : chr "Schematic of the read extension process for single-end data. Reads are extended to the average fragment length "| __truncated__


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label: unnamed-chunk-2
snapshotDate(): 2021-01-15
see ?chipseqDBData and browseVignettes('chipseqDBData') for documentation
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see ?chipseqDBData and browseVignettes('chipseqDBData') for documentation
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see ?chipseqDBData and browseVignettes('chipseqDBData') for documentation
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see ?chipseqDBData and browseVignettes('chipseqDBData') for documentation
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label: unnamed-chunk-3
Loading required package: GenomicRanges
Loading required package: stats4
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, 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: S4Vectors

Attaching package: 'S4Vectors'

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: 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


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 $ fig.cap: chr "Cross-correlation plots for a variety of histone mark datasets."

snapshotDate(): 2021-01-15
see ?chipseqDBData and browseVignettes('chipseqDBData') for documentation
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see ?chipseqDBData and browseVignettes('chipseqDBData') for documentation
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see ?chipseqDBData and browseVignettes('chipseqDBData') for documentation
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snapshotDate(): 2021-01-15
see ?chipseqDBData and browseVignettes('chipseqDBData') for documentation
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see ?chipseqDBData and browseVignettes('chipseqDBData') for documentation
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see ?chipseqDBData and browseVignettes('chipseqDBData') for documentation
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see ?chipseqDBData and browseVignettes('chipseqDBData') for documentation
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see ?chipseqDBData and browseVignettes('chipseqDBData') for documentation
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see ?chipseqDBData and browseVignettes('chipseqDBData') for documentation
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see ?chipseqDBData and browseVignettes('chipseqDBData') for documentation
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[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
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[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
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  66 genes were dropped because they have exons located on both strands
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Loading required package: Biobase
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Loading required package: Biobase
Welcome to Bioconductor

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Loading required package: GenomicFeatures
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  66 genes were dropped because they have exons located on both strands
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    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
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Loading required package: Biobase
Welcome to Bioconductor

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label: nfya-regionplot (with options) 
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Warning message:
In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
  GRanges object contains 3 out-of-bound ranges located on sequences
  chrM, chrUn_GL456392, and chrX_GL456233_random. Note that ranges
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  sequences). You can use trim() to trim these ranges. See
  ?`trim,GenomicRanges-method` for more information.


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Loading required package: Biobase
Welcome to Bioconductor

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output file: h3k9ac.knit.md

Warning message:
In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
  GRanges object contains 4 out-of-bound ranges located on sequences
  chr4_JH584293_random, chr4_JH584294_random, chr4_JH584295_random, and
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  circularity flags of the underlying sequences). You can use trim() to
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processing file: cbp.Rmd

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snapshotDate(): 2021-01-15
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Loading required package: GenomeInfoDb
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Attaching package: 'BiocGenerics'

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    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
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    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
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    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
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Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
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output file: cbp.knit.md

Warning message:
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processing file: h3k27me3.Rmd

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see ?chipseqDBData and browseVignettes('chipseqDBData') for documentation
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see ?chipseqDBData and browseVignettes('chipseqDBData') for documentation
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see ?chipseqDBData and browseVignettes('chipseqDBData') for documentation
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Loading required package: GenomeInfoDb
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

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    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

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    Filter, Find, Map, Position, Reduce, anyDuplicated, 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: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

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    windows

Loading required package: GenomicRanges
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Attaching package: 'Biostrings'

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    strsplit


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[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
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[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/3a384699162b_2110
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/3a384699162b_2110
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/3a384699162b_2110
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[E::bgzf_read] Read block operation failed with error -1 after 24 of 32 bytes
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[E::bgzf_read] Read block operation failed with error -1 after 24 of 32 bytes
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[E::bgzf_read] Read block operation failed with error -1 after 24 of 32 bytes
Loading required package: dbplyr
adding rname 'http://hgdownload.cse.ucsc.edu/goldenPath/mm10/bigZips/chromOut.tar.gz'

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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

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[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
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[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
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[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/3a384699162b_2110
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/3a384699162b_2110
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/3a384699162b_2110
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
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[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/3a384699162b_2110
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/3a384699162b_2110
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/3a384699162b_2110
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/3a384699162b_2110
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/3a384699162b_2110
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/3a384699162b_2110
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/3a384699162b_2110
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the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/3a384699162b_2110
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/3a384699162b_2110
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/3a384699162b_2110
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/3a384699162b_2110
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/3a384699162b_2110
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/3a384699162b_2110
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/3a384699162b_2110
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[E::bgzf_read] Read block operation failed with error -1 after 24 of 32 bytes
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/3a384699162b_2110
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/3a384699162b_2110
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/3a384699162b_2110
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/3a384699162b_2110
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/3a384699162b_2110
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/3a384699162b_2110
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/3a384699162b_2110
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/3a384699162b_2110
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/3a384699162b_2110
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/3a384699162b_2110
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/3a384699162b_2110
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/3a384699162b_2110
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/3a384699162b_2110
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/3a384699162b_2110
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/3a384699162b_2110
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::hts_idx_load2] The index file is older than the data file: C:\
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label: h3k27me3-bghistplot (with options) 
List of 1
 $ fig.cap: chr "Histogram of average abundances across all 10 kbp genomic bins. The filter threshold is shown as the red line."


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label: h3k27me3-compoplot (with options) 
List of 3
 $ fig.width: num 12
 $ fig.asp  : num 0.5
 $ fig.cap  : chr "Mean-difference plots for the bin counts, comparing sample 1 to all other samples. The red line represents the "| __truncated__


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Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/3a384699162b_2110
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/3a384699162b_2110
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/3a384699162b_2110
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/3a384699162b_2110
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/3a384699162b_2110
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/3a384699162b_2110
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/3a384699162b_2110
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[E::bgzf_read] Read block operation failed with error -1 after 24 of 32 bytes
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/3a384699162b_2110
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/3a384699162b_2110
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/3a384699162b_2110
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/3a384699162b_2110
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
Loading required package: limma

Attaching package: 'limma'

The following object is masked from 'package:BiocGenerics':

    plotMA


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label: h3k27me3-bcvplot (with options) 
List of 1
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label: h3k27me3-qlplot (with options) 
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label: h3k27me3-mdsplot (with options) 
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[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/3a384699162b_2110
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/3a384699162b_2110
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/3a384699162b_2110
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/3a384699162b_2110
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/3a384699162b_2110
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/3a384699162b_2110
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/3a384699162b_2110
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/3a384699162b_2110
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/3a384699162b_2110
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/3a384699162b_2110
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/3a384699162b_2110
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::hts_idx_load2] The index file is older than 
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the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/3a384699162b_2110
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/3a384699162b_2110
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/3a384699162b_2110
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/3a384699162b_2110
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/3a384699162b_2110
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/3a384699162b_2110
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/3a384699162b_2110
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[E::bgzf_read] Read block operation failed with error -1 after 24 of 32 bytes
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/3a384699162b_2110
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/3a384699162b_2110
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/3a384699162b_2110
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/422c15f13024_2109
[W::hts_idx_load2] The index file is older than the data file: C:\Users\biocbuild\AppData\Local\ExperimentHub\ExperimentHub\Cache/3a384699162b_2110
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi


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label: unnamed-chunk-20
  66 genes were dropped because they have exons located on both strands
  of the same reference sequence or on more than one reference sequence,
  so cannot be represented by a single genomic range.
  Use 'single.strand.genes.only=FALSE' to get all the genes in a
  GRangesList object, or use suppressMessages() to suppress this message.

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label: unnamed-chunk-21 (with options) 
List of 2
 $ results: chr "hide"
 $ echo   : logi FALSE

Quitting from lines 328-331 (h3k27me3.Rmd) 
Error in eval(expr, envir, enclos) : 
  Cdx2 should be significantly upregulated in WT
Calls: local ... handle -> withCallingHandlers -> withVisible -> eval -> eval

Execution halted
Error in Rscript_render(f, render_args, render_meta, add1, add2) : 
  Failed to compile h3k27me3.Rmd
Calls: <Anonymous> -> render_new_session -> Rscript_render
Execution halted
make: *** [Makefile:4: compiled] Error 1
Error in tools::buildVignettes(dir = ".", tangle = TRUE) : 
  running 'make' failed
Execution halted