Package: GUIDEseq

Version: 1.12.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GUIDEseq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GUIDEseq_1.12.1.tar.gz

StartedAt: 2019-04-16 00:29:01 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 00:34:27 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 326.2 seconds

RetCode: 0

Status:  OK

CheckDir: GUIDEseq.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GUIDEseq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GUIDEseq_1.12.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/GUIDEseq.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GUIDEseq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GUIDEseq’ version ‘1.12.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘GUIDEseq’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 10.9Mb
  sub-directories of 1Mb or more:
    extdata  10.5Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
annotateOffTargets: no visible binding for global variable
  'offTarget_Start'
annotateOffTargets: no visible global function definition for 'exons'
annotateOffTargets: no visible global function definition for
  'seqlevelsStyle<-'
annotateOffTargets: no visible global function definition for 'genes'
annotateOffTargets: no visible global function definition for 'toTable'
getPeaks: no visible binding for global variable 'adjusted.p.value'
getPeaks: no visible binding for global variable 'SNratio'
getUniqueCleavageEvents: no visible binding for global variable
  'qwidth.first'
getUniqueCleavageEvents: no visible binding for global variable
  'qwidth.last'
getUniqueCleavageEvents: no visible binding for global variable
  'strand.last'
getUniqueCleavageEvents: no visible binding for global variable
  'strand.first'
getUniqueCleavageEvents: no visible binding for global variable
  'readName'
offTargetAnalysisOfPeakRegions: no visible binding for global variable
  'gRNAPlusPAM'
offTargetAnalysisOfPeakRegions: no visible binding for global variable
  'offTarget'
Undefined global functions or variables:
  SNratio adjusted.p.value exons gRNAPlusPAM genes offTarget
  offTarget_Start qwidth.first qwidth.last readName seqlevelsStyle<-
  strand.first strand.last toTable
* checking Rd files ... NOTE
prepare_Rd: annotateOffTargets.Rd:33-35: Dropping empty section \details
prepare_Rd: annotateOffTargets.Rd:43-45: Dropping empty section \references
prepare_Rd: createBarcodeFasta.Rd:42-43: Dropping empty section \value
prepare_Rd: createBarcodeFasta.Rd:44-46: Dropping empty section \references
prepare_Rd: getUsedBarcodes.Rd:39-41: Dropping empty section \references
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
GUIDEseqAnalysis   12.054  0.781  12.956
annotateOffTargets 10.642  0.485  11.238
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/GUIDEseq.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL GUIDEseq
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘GUIDEseq’ ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (GUIDEseq)

name	user	system	elapsed
GUIDEseq-package	0.003	0.001	0.003
GUIDEseqAnalysis	12.054	0.781	12.956
annotateOffTargets	10.642	0.485	11.238
combineOfftargets	0.050	0.003	0.054
createBarcodeFasta	0.038	0.001	0.039
getPeaks	0.001	0.001	0.001
getUniqueCleavageEvents	0.001	0.000	0.001
getUsedBarcodes	0.063	0.002	0.065
mergePlusMinusPeaks	0.001	0.000	0.001
offTargetAnalysisOfPeakRegions	0.003	0.000	0.003
peaks.gr	0.040	0.005	0.044
uniqueCleavageEvents	0.067	0.003	0.070