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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CRISPRseek.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CRISPRseek_1.32.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/CRISPRseek.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CRISPRseek/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CRISPRseek’ version ‘1.32.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘CRISPRseek’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  9.6Mb
  sub-directories of 1Mb or more:
    extdata   9.1Mb
* 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 global function definition for ‘GRanges’
annotateOffTargets: no visible global function definition for ‘exons’
annotateOffTargets: no visible global function definition for
  ‘seqlevels<-’
annotateOffTargets: no visible global function definition for
  ‘seqlevels’
annotateOffTargets: no visible global function definition for
  ‘GRangesList’
annotateOffTargets: no visible global function definition for ‘genes’
designPEs: no visible binding for global variable
  ‘ReversegRNA.cut.5prime.targetEnd’
designPEs: no visible binding for global variable
  ‘ReversegRNA.RT.template.length’
designPEs: no visible binding for global variable
  ‘ForwardgRNA.cut.5prime.targetStart’
designPEs: no visible binding for global variable
  ‘ForwardgRNA.RT.template.length’
filterOffTarget: no visible global function definition for ‘seqlengths’
filterOffTargetWithoutBSgenome: no visible global function definition
  for ‘seqlengths’
getExtendedSequence: no visible global function definition for
  ‘seqlengths’
getSeqFromBed: no visible global function definition for ‘seqlengths’
predictRelativeFreqIndels : <anonymous>: no visible global function
  definition for ‘predIndelFreq’
uniqueREs: no visible global function definition for ‘seqlengths’
Undefined global functions or variables:
  ForwardgRNA.RT.template.length ForwardgRNA.cut.5prime.targetStart
  GRanges GRangesList ReversegRNA.RT.template.length
  ReversegRNA.cut.5prime.targetEnd exons genes predIndelFreq seqlengths
  seqlevels seqlevels<-
* checking Rd files ... NOTE
prepare_Rd: annotateOffTargets.Rd:50-52: Dropping empty section \details
prepare_Rd: annotateOffTargets.Rd:62-64: Dropping empty section \note
prepare_Rd: buildFeatureVectorForScoring.Rd:48-50: Dropping empty section \details
prepare_Rd: buildFeatureVectorForScoring.Rd:77-79: Dropping empty section \note
prepare_Rd: buildFeatureVectorForScoring.Rd:71-73: Dropping empty section \references
prepare_Rd: calculategRNAEfficiency.Rd:49-51: Dropping empty section \note
prepare_Rd: compare2Sequences.Rd:253-255: Dropping empty section \details
prepare_Rd: compare2Sequences.Rd:295-297: Dropping empty section \note
prepare_Rd: filterOffTarget.Rd:110-112: Dropping empty section \details
prepare_Rd: filterOffTarget.Rd:124-126: Dropping empty section \note
prepare_Rd: filtergRNA.Rd:48-50: Dropping empty section \details
prepare_Rd: filtergRNA.Rd:62-64: Dropping empty section \note
prepare_Rd: filtergRNA.Rd:56-58: Dropping empty section \references
prepare_Rd: findgRNAs.Rd:200-202: Dropping empty section \references
prepare_Rd: getOfftargetScore.Rd:73-75: Dropping empty section \note
prepare_Rd: isPatternUnique.Rd:22-24: Dropping empty section \details
prepare_Rd: isPatternUnique.Rd:34-36: Dropping empty section \note
prepare_Rd: isPatternUnique.Rd:28-30: Dropping empty section \references
prepare_Rd: isPatternUnique.Rd:40-41: Dropping empty section \seealso
prepare_Rd: offTargetAnalysis.Rd:441-443: Dropping empty section \details
prepare_Rd: offTargetAnalysis.Rd:486-488: Dropping empty section \note
prepare_Rd: offTargetAnalysisWithoutBSgenome.Rd:444-446: Dropping empty section \details
prepare_Rd: offTargetAnalysisWithoutBSgenome.Rd:489-491: Dropping empty section \note
prepare_Rd: searchHits.Rd:75-77: Dropping empty section \details
prepare_Rd: searchHits.Rd:97-99: Dropping empty section \note
prepare_Rd: searchHits.Rd:91-93: Dropping empty section \references
prepare_Rd: searchHits2.Rd:83-85: Dropping empty section \details
prepare_Rd: searchHits2.Rd:105-107: Dropping empty section \note
prepare_Rd: searchHits2.Rd:99-101: Dropping empty section \references
prepare_Rd: translatePattern.Rd:22-24: Dropping empty section \details
prepare_Rd: translatePattern.Rd:34-36: Dropping empty section \note
prepare_Rd: translatePattern.Rd:28-30: Dropping empty section \references
prepare_Rd: translatePattern.Rd:40-42: Dropping empty section \seealso
prepare_Rd: uniqueREs.Rd:40-42: Dropping empty section \details
prepare_Rd: uniqueREs.Rd:53-55: Dropping empty section \note
prepare_Rd: uniqueREs.Rd:47-49: Dropping empty section \references
prepare_Rd: uniqueREs.Rd:59-60: Dropping empty section \seealso
prepare_Rd: writeHits.Rd:90-92: Dropping empty section \details
prepare_Rd: writeHits.Rd:102-104: Dropping empty section \note
prepare_Rd: writeHits2.Rd:92-94: Dropping empty section \details
prepare_Rd: writeHits2.Rd:104-106: Dropping empty section \note
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                    user system elapsed
CRISPRseek-package               187.871  4.391 192.609
offTargetAnalysis                 78.662  0.958  79.789
offTargetAnalysisWithoutBSgenome  62.586  0.357  63.084
compare2Sequences                 10.781  0.100  10.934
annotateOffTargets                 5.742  0.166   5.914
filterOffTarget                    5.576  0.107   5.687
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* 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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/CRISPRseek.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL CRISPRseek
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘CRISPRseek’ ...
** using staged installation
** R
** 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 (CRISPRseek)

R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> #BiocGenerics:::testPackage("CRISPRseek")
> 
> proc.time()
   user  system elapsed 
  0.292   0.068   0.334