Package: CSAR

Version: 1.39.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data CSAR

StartedAt: 2020-01-15 20:18:04 -0500 (Wed, 15 Jan 2020)

EndedAt: 2020-01-15 20:18:57 -0500 (Wed, 15 Jan 2020)

EllapsedTime: 53.1 seconds

RetCode: 1

Status:  ERROR

PackageFile: None

PackageFileSize: NA

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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 CSAR
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* checking for file ‘CSAR/DESCRIPTION’ ... OK
* preparing ‘CSAR’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘CSAR.Rnw’ using Sweave
Loading required package: S4Vectors
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, which.max,
    which.min


Attaching package: ‘S4Vectors’

The following object is masked from ‘package:base’:

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
mappedReads2Nhits has just finished   CHR1v01212004 ...
mappedReads2Nhits has just finished   CHR1v01212004 ...
CHR1v01212004  done...
CHR1v01212004 done...
CHR1v01212004 done...
Starting CHR1v01212004 ...
mappedReads2Nhits has just finished   CHR1v01212004 ...
mappedReads2Nhits has just finished   CHR1v01212004 ...
CHR1v01212004  done...
CHR1v01212004 done...
Win file for permutation 1 can be found at test-1.permutatedWin
mappedReads2Nhits has just finished   CHR1v01212004 ...
mappedReads2Nhits has just finished   CHR1v01212004 ...
CHR1v01212004  done...
CHR1v01212004 done...
Win file for permutation 2 can be found at test-2.permutatedWin
Read 128 items
Read 122 items
Warning in getThreshold(winscores = values(win)$score, permutatedScores = nulldist,  :
  The number of permutated scores is low.
Error: processing vignette 'CSAR.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'CSAR.tex' failed.
LaTeX errors:
! Package inputenc Error: Invalid UTF-8 byte sequence.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Package inputenc Error: Invalid UTF-8 byte sequence.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
--- failed re-building ‘CSAR.Rnw’

SUMMARY: processing the following file failed:
  ‘CSAR.Rnw’

Error: Vignette re-building failed.
Execution halted