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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data progeny
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* 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.
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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)]) :
NAs introduced by coercion
Warning in data.matrix(drug_table[, 3:ncol(drug_table)]) :
NAs introduced by coercion
Warning in data.matrix(drug_table[, 3:ncol(drug_table)]) :
NAs introduced by coercion
Warning in data.matrix(drug_table[, 3:ncol(drug_table)]) :
NAs introduced by coercion
Warning in data.matrix(drug_table[, 3:ncol(drug_table)]) :
NAs introduced by coercion
Warning in data.matrix(drug_table[, 3:ncol(drug_table)]) :
NAs introduced by coercion
Warning in data.matrix(drug_table[, 3:ncol(drug_table)]) :
NAs introduced by coercion
Warning in data.matrix(drug_table[, 3:ncol(drug_table)]) :
NAs introduced by coercion
Warning in data.matrix(drug_table[, 3:ncol(drug_table)]) :
NAs introduced by coercion
Warning in data.matrix(drug_table[, 3:ncol(drug_table)]) :
NAs introduced by coercion
Warning in data.matrix(drug_table[, 3:ncol(drug_table)]) :
NAs introduced by coercion
Warning in data.matrix(drug_table[, 3:ncol(drug_table)]) :
NAs introduced by coercion
Warning in data.matrix(drug_table[, 3:ncol(drug_table)]) :
NAs introduced by coercion
Warning in data.matrix(drug_table[, 3:ncol(drug_table)]) :
NAs introduced by coercion
Warning in data.matrix(drug_table[, 3:ncol(drug_table)]) :
NAs introduced by coercion
Warning in data.matrix(drug_table[, 3:ncol(drug_table)]) :
NAs introduced by coercion
Warning in data.matrix(drug_table[, 3:ncol(drug_table)]) :
NAs introduced by coercion
Warning in data.matrix(drug_table[, 3:ncol(drug_table)]) :
NAs introduced by coercion
Warning in data.matrix(drug_table[, 3:ncol(drug_table)]) :
NAs introduced by coercion
Warning in data.matrix(drug_table[, 3:ncol(drug_table)]) :
NAs introduced by coercion
Warning in data.matrix(drug_table[, 3:ncol(drug_table)]) :
NAs introduced by coercion
Warning in data.matrix(drug_table[, 3:ncol(drug_table)]) :
NAs introduced by coercion
Warning in data.matrix(drug_table[, 3:ncol(drug_table)]) :
NAs introduced by coercion
Warning in data.matrix(drug_table[, 3:ncol(drug_table)]) :
NAs introduced by coercion
Warning in data.matrix(drug_table[, 3:ncol(drug_table)]) :
NAs introduced by coercion
Warning in data.matrix(drug_table[, 3:ncol(drug_table)]) :
NAs introduced by coercion
Warning in data.matrix(drug_table[, 3:ncol(drug_table)]) :
NAs introduced by coercion
Warning in data.matrix(drug_table[, 3:ncol(drug_table)]) :
NAs introduced by coercion
Warning in data.matrix(drug_table[, 3:ncol(drug_table)]) :
NAs introduced by coercion
Warning in data.matrix(drug_table[, 3:ncol(drug_table)]) :
NAs introduced by coercion
Warning in data.matrix(drug_table[, 3:ncol(drug_table)]) :
NAs introduced by coercion
Warning in data.matrix(drug_table[, 3:ncol(drug_table)]) :
NAs introduced by coercion
Warning in data.matrix(drug_table[, 3:ncol(drug_table)]) :
NAs introduced by coercion
Warning in data.matrix(drug_table[, 3:ncol(drug_table)]) :
NAs introduced by coercion
Warning in data.matrix(drug_table[, 3:ncol(drug_table)]) :
NAs introduced by coercion
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