CrispRVariants 1.15.0
Helen Lindsay
| Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020) |
| URL: https://git.bioconductor.org/packages/CrispRVariants |
| Branch: master |
| Last Commit: d7bf5eb |
| Last Changed Date: 2019-10-29 13:40:16 -0500 (Tue, 29 Oct 2019) |
| malbec2 | Linux (Ubuntu 18.04.3 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 | |
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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 CrispRVariants
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* checking for file ‘CrispRVariants/DESCRIPTION’ ... OK
* preparing ‘CrispRVariants’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘user_guide.Rmd’ using rmarkdown
Loading required package: ggplot2
Loading required package: Biostrings
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, which.max, which.min
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
gdata: read.xls support for 'XLS' (Excel 97-2004) files ENABLED.
gdata: read.xls support for 'XLSX' (Excel 2007+) files ENABLED.
Attaching package: 'gdata'
The following object is masked from 'package:IRanges':
trim
The following objects are masked from 'package:S4Vectors':
first, first<-
The following object is masked from 'package:stats4':
nobs
The following object is masked from 'package:BiocGenerics':
combine
The following object is masked from 'package:stats':
nobs
The following object is masked from 'package:utils':
object.size
The following object is masked from 'package:base':
startsWith
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Read 5 alignments, excluded 0
0 from 0 (NaN%) chimeras did not involve guide
0 from 0 (NaN%) remaining chimeric reads included
0 (NaN%) assigned to more than one target
Read 7 alignments, excluded 0
0 from 0 (NaN%) chimeras did not involve guide
0 from 0 (NaN%) remaining chimeric reads included
0 (NaN%) assigned to more than one target
Read 6 alignments, excluded 0
0 from 2 (0.00%) chimeras did not involve guide
2 from 2 (100.00%) remaining chimeric reads included
0 (0.00%) assigned to more than one target
Read 8 alignments, excluded 0
0 from 2 (0.00%) chimeras did not involve guide
2 from 2 (100.00%) remaining chimeric reads included
0 (0.00%) assigned to more than one target
Read 8 alignments, excluded 0
0 from 0 (NaN%) chimeras did not involve guide
0 from 0 (NaN%) remaining chimeric reads included
0 (NaN%) assigned to more than one target
4 of 5 nonchimeric reads span the target range
narrowing alignments
Initialising CrisprRun ptena 1
7 of 7 nonchimeric reads span the target range
narrowing alignments
Initialising CrisprRun ptena 2
4 of 4 nonchimeric reads span the target range
narrowing alignments
Initialising CrisprRun ptena 3
4 of 6 nonchimeric reads span the target range
narrowing alignments
Initialising CrisprRun ptena 4
8 of 8 nonchimeric reads span the target range
narrowing alignments
Initialising CrisprRun control
Initialising CrisprSet chr17:23648469-23648501 with 5 samples
Loading required package: AnnotationDbi
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: 'gridExtra'
The following object is masked from 'package:Biobase':
combine
The following object is masked from 'package:gdata':
combine
The following object is masked from 'package:BiocGenerics':
combine
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
Quitting from lines 428-435 (user_guide.Rmd)
Error: processing vignette 'user_guide.Rmd' failed with diagnostics:
Unknown colour name: transparent
--- failed re-building ‘user_guide.Rmd’
SUMMARY: processing the following file failed:
‘user_guide.Rmd’
Error: Vignette re-building failed.
Execution halted