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BUILD report for progeny on celaya2

This page was generated on 2019-04-09 13:19:16 -0400 (Tue, 09 Apr 2019).

Package 1232/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
progeny 1.5.1
Michael Schubert
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/progeny
Branch: master
Last Commit: 1e8b954
Last Changed Date: 2019-01-25 08:03:33 -0400 (Fri, 25 Jan 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  ERROR  skipped 
tokay2 Windows Server 2012 R2 Standard / x64  OK  ERROR  skipped  skipped 
celaya2 OS X 10.11.6 El Capitan / x86_64  OK [ ERROR ] skipped  skipped 
merida2 OS X 10.11.6 El Capitan / x86_64  OK  ERROR  skipped  skipped 

Summary

Package: progeny
Version: 1.5.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data progeny
StartedAt: 2019-04-08 22:45:09 -0400 (Mon, 08 Apr 2019)
EndedAt: 2019-04-08 22:48:00 -0400 (Mon, 08 Apr 2019)
EllapsedTime: 170.1 seconds
RetCode: 1
Status:  ERROR 
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data progeny
###
##############################################################################
##############################################################################


* checking for file ‘progeny/DESCRIPTION’ ... OK
* preparing ‘progeny’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘progeny.Rmd’ using rmarkdown
Loading required package: SummarizedExperiment
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, 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: S4Vectors

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
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

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following objects are masked from 'package:base':

    aperm, apply, rowsum

Registered S3 methods overwritten by 'ggplot2':
  method         from 
  [.quosures     rlang
  c.quosures     rlang
  print.quosures rlang
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates

Attaching package: 'dplyr'

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

    select

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

    count

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

    combine

The following objects are masked from 'package:GenomicRanges':

    intersect, setdiff, union

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

    intersect

The following objects are masked from 'package:IRanges':

    collapse, desc, intersect, setdiff, slice, union

The following objects are masked from 'package:S4Vectors':

    first, intersect, rename, setdiff, setequal, union

The following objects are masked from 'package:BiocGenerics':

    combine, intersect, setdiff, union

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Loading required package: dbplyr

Attaching package: 'dbplyr'

The following objects are masked from 'package:dplyr':

    ident, sql

adding rname 'http://www.cancerrxgene.org/gdsc1000/GDSC1000_WebResources/Data/suppData/TableS4A.xlsx'
adding rname 'http://www.cancerrxgene.org/gdsc1000/GDSC1000_WebResources/Data/preprocessed/Cell_line_RMA_proc_basalExp.txt.zip'
New names:
* `` -> ...1
* `` -> ...2
* `BMS-708163` -> `BMS-708163...15`
* UNC0638 -> UNC0638...70
* UNC0638 -> UNC0638...71
* … and 15 more problems
Parsed with column specification:
cols(
  .default = col_double(),
  GENE_SYMBOLS = col_character(),
  GENE_title = col_character()
)
See spec(...) for full column specifications.
Warning in data.matrix(drug_table[, 3:ncol(drug_table)]) :
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Warning in data.matrix(drug_table[, 3:ncol(drug_table)]) :
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Warning in data.matrix(drug_table[, 3:ncol(drug_table)]) :
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Warning in data.matrix(drug_table[, 3:ncol(drug_table)]) :
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Warning in data.matrix(drug_table[, 3:ncol(drug_table)]) :
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Warning in data.matrix(drug_table[, 3:ncol(drug_table)]) :
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Warning in data.matrix(drug_table[, 3:ncol(drug_table)]) :
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Warning in data.matrix(drug_table[, 3:ncol(drug_table)]) :
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Warning in data.matrix(drug_table[, 3:ncol(drug_table)]) :
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Warning in data.matrix(drug_table[, 3:ncol(drug_table)]) :
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Warning in data.matrix(drug_table[, 3:ncol(drug_table)]) :
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Warning in data.matrix(drug_table[, 3:ncol(drug_table)]) :
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Warning in data.matrix(drug_table[, 3:ncol(drug_table)]) :
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Warning in data.matrix(drug_table[, 3:ncol(drug_table)]) :
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Warning in data.matrix(drug_table[, 3:ncol(drug_table)]) :
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Warning in data.matrix(drug_table[, 3:ncol(drug_table)]) :
  NAs introduced by coercion
Warning in data.matrix(drug_table[, 3:ncol(drug_table)]) :
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Warning in data.matrix(drug_table[, 3:ncol(drug_table)]) :
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Warning in data.matrix(drug_table[, 3:ncol(drug_table)]) :
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Warning in data.matrix(drug_table[, 3:ncol(drug_table)]) :
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Warning in data.matrix(drug_table[, 3:ncol(drug_table)]) :
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Warning in data.matrix(drug_table[, 3:ncol(drug_table)]) :
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Warning in data.matrix(drug_table[, 3:ncol(drug_table)]) :
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Warning: Unknown or uninitialised column: '..1'.
Quitting from lines 177-183 (progeny.Rmd) 
Error: processing vignette 'progeny.Rmd' failed with diagnostics:
0 (non-NA) cases
--- failed re-building ‘progeny.Rmd’

SUMMARY: processing the following file failed:
  ‘progeny.Rmd’

Error: Vignette re-building failed.
Execution halted