Package: GUIDEseq

Version: 1.16.0

Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:GUIDEseq.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings GUIDEseq_1.16.0.tar.gz

StartedAt: 2020-04-15 03:24:29 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 03:29:39 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 310.1 seconds

RetCode: 0

Status:  OK

CheckDir: GUIDEseq.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:GUIDEseq.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings GUIDEseq_1.16.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/GUIDEseq.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (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 ‘1.16.0’
* 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 11.0Mb
  sub-directories of 1Mb or more:
    extdata  10.6Mb
* 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'
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
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
GUIDEseqAnalysis   10.016  0.216  10.318
annotateOffTargets  8.464  0.200   8.800
* 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
  ‘/home/biocbuild/bbs-3.10-bioc/meat/GUIDEseq.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL GUIDEseq
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘GUIDEseq’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (GUIDEseq)

name	user	system	elapsed
GUIDEseq-package	0.000	0.000	0.002
GUIDEseqAnalysis	10.016	0.216	10.318
annotateOffTargets	8.464	0.200	8.800
combineOfftargets	0.040	0.000	0.048
createBarcodeFasta	0.020	0.004	0.024
getPeaks	0.000	0.000	0.001
getUniqueCleavageEvents	0.000	0.000	0.001
getUsedBarcodes	0.048	0.000	0.047
mergePlusMinusPeaks	0.000	0.000	0.001
offTargetAnalysisOfPeakRegions	0.000	0.000	0.002
peaks.gr	0.036	0.004	0.042
uniqueCleavageEvents	0.06	0.00	0.06