derfinder 1.14.0
Leonardo Collado-Torres
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/derfinder |
| Branch: RELEASE_3_7 |
| Last Commit: 7be868d |
| Last Changed Date: 2018-04-30 10:35:34 -0400 (Mon, 30 Apr 2018) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | [ ERROR ] | skipped | skipped | |
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### chmod a+r derfinder -R && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data derfinder
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* checking for file 'derfinder/DESCRIPTION' ... OK
* preparing 'derfinder':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
Warning in citation("BiocStyle") :
no date field in DESCRIPTION file of package 'BiocStyle'
Warning in citation("BiocStyle") :
could not determine year for 'BiocStyle' from package DESCRIPTION file
Warning in citation("biovizBase") :
no date field in DESCRIPTION file of package 'biovizBase'
Warning in citation("biovizBase") :
could not determine year for 'biovizBase' from package DESCRIPTION file
Warning in citation("TxDb.Hsapiens.UCSC.hg19.knownGene") :
no date field in DESCRIPTION file of package 'TxDb.Hsapiens.UCSC.hg19.knownGene'
Warning in citation("BiocParallel") :
no date field in DESCRIPTION file of package 'BiocParallel'
Warning in citation("BiocParallel") :
could not determine year for 'BiocParallel' from package DESCRIPTION file
Warning in citation("GenomicFiles") :
no date field in DESCRIPTION file of package 'GenomicFiles'
Warning in citation("GenomicFiles") :
could not determine year for 'GenomicFiles' from package DESCRIPTION file
Warning in citation("Rsamtools") :
no date field in DESCRIPTION file of package 'Rsamtools'
Warning in citation("Rsamtools") :
could not determine year for 'Rsamtools' from package DESCRIPTION file
Writing 32 Bibtex entries ... OK
Results written to file 'quickstartRef.bib'
No methods found in package 'IRanges' for request: 'subset' when loading 'derfinder'
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, lengths, 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
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomeInfoDb
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
'convert "derfinder-quickstart_files/figure-html/vennRegions-1.png" -trim "derfinder-quickstart_files/figure-html/vennRegions-1.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
'convert "derfinder-quickstart_files/figure-html/firstfive-1.png" -trim "derfinder-quickstart_files/figure-html/firstfive-1.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
'convert "derfinder-quickstart_files/figure-html/firstfive-2.png" -trim "derfinder-quickstart_files/figure-html/firstfive-2.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
'convert "derfinder-quickstart_files/figure-html/firstfive-3.png" -trim "derfinder-quickstart_files/figure-html/firstfive-3.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
'convert "derfinder-quickstart_files/figure-html/firstfive-4.png" -trim "derfinder-quickstart_files/figure-html/firstfive-4.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
'convert "derfinder-quickstart_files/figure-html/firstfive-5.png" -trim "derfinder-quickstart_files/figure-html/firstfive-5.png"' execution failed with error code 4
Warning in `[[.bibentry`(bib, "derfinderHelper") :
subscript out of bounds
Quitting from lines 329-365 (derfinder-quickstart.Rmd)
Error: processing vignette 'derfinder-quickstart.Rmd' failed with diagnostics:
reached elapsed time limit
Execution halted