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This page was generated on 2021-10-15 15:05:38 -0400 (Fri, 15 Oct 2021).

CHECK results for CRISPRseek on nebbiolo1

To the developers/maintainers of the CRISPRseek package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CRISPRseek.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 409/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CRISPRseek 1.32.0  (landing page)
Lihua Julie Zhu
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/CRISPRseek
git_branch: RELEASE_3_13
git_last_commit: b64de86
git_last_commit_date: 2021-05-19 12:01:57 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: CRISPRseek
Version: 1.32.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:CRISPRseek.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings CRISPRseek_1.32.0.tar.gz
StartedAt: 2021-10-14 09:25:23 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 09:33:14 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 470.9 seconds
RetCode: 0
Status:   OK  
CheckDir: CRISPRseek.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:CRISPRseek.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings CRISPRseek_1.32.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/CRISPRseek.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (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 ... OK
* 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  9.3Mb
  sub-directories of 1Mb or more:
    extdata   8.9Mb
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                    user system elapsed
CRISPRseek-package               152.548 10.963 163.560
offTargetAnalysis                 57.341  2.011  59.384
offTargetAnalysisWithoutBSgenome  37.241  0.148  37.391
compare2Sequences                  6.578  0.062   6.629
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.13-bioc/meat/CRISPRseek.Rcheck/00check.log’
for details.



Installation output

CRISPRseek.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL CRISPRseek
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/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)

Tests output

CRISPRseek.Rcheck/tests/runTests.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 
  0.192   0.022   0.200 

Example timings

CRISPRseek.Rcheck/CRISPRseek-Ex.timings

nameusersystemelapsed
CRISPRseek-package152.548 10.963163.560
annotateOffTargets3.8480.1293.977
buildFeatureVectorForScoring0.0720.0000.071
calculategRNAEfficiency0.0120.0030.016
compare2Sequences6.5780.0626.629
filterOffTarget3.5310.0373.565
filtergRNA0.6180.0000.617
findgRNAs0.4820.0320.511
getOfftargetScore0.0850.0000.085
isPatternUnique0.0160.0000.016
offTargetAnalysis57.341 2.01159.384
offTargetAnalysisWithoutBSgenome37.241 0.14837.391
predictRelativeFreqIndels0.0000.0000.001
searchHits0.0000.0010.002
searchHits23.1700.3173.487
translatePattern0.0000.0010.000
uniqueREs0.4020.0310.432
writeHits0.0000.0000.001
writeHits20.1520.0040.156