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CHECK report for CRISPRseek on malbec1

This page was generated on 2020-04-15 12:08:14 -0400 (Wed, 15 Apr 2020).

Package 380/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CRISPRseek 1.26.0
Lihua Julie Zhu
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/CRISPRseek
Branch: RELEASE_3_10
Last Commit: 4ebbce2
Last Changed Date: 2019-10-29 13:08:51 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: CRISPRseek
Version: 1.26.0
Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:CRISPRseek.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings CRISPRseek_1.26.0.tar.gz
StartedAt: 2020-04-15 01:59:09 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 02:07:10 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 480.9 seconds
RetCode: 0
Status:  OK 
CheckDir: CRISPRseek.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:CRISPRseek.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings CRISPRseek_1.26.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/CRISPRseek.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 ‘CRISPRseek/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CRISPRseek’ version ‘1.26.0’
* 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 ... OK
* 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 ‘as’
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’
buildFeatureVectorForScoring: no visible global function definition for
  ‘as’
buildFeatureVectorForScoring2: no visible global function definition
  for ‘as’
filterOffTarget: no visible global function definition for ‘seqlengths’
getSeqFromBed: no visible global function definition for ‘seqlengths’
uniqueREs: no visible global function definition for ‘seqlengths’
writeHits: no visible global function definition for ‘as’
writeHits2: no visible global function definition for ‘as’
Undefined global functions or variables:
  GRanges GRangesList as exons genes seqlengths seqlevels seqlevels<-
Consider adding
  importFrom("methods", "as")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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:226-228: Dropping empty section \details
prepare_Rd: compare2Sequences.Rd:268-270: Dropping empty section \note
prepare_Rd: filterOffTarget.Rd:106-108: Dropping empty section \details
prepare_Rd: filterOffTarget.Rd:120-122: 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:117-119: 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:301-303: Dropping empty section \details
prepare_Rd: offTargetAnalysis.Rd:324-326: Dropping empty section \note
prepare_Rd: searchHits.Rd:58-60: Dropping empty section \details
prepare_Rd: searchHits.Rd:80-82: Dropping empty section \note
prepare_Rd: searchHits.Rd:74-76: Dropping empty section \references
prepare_Rd: searchHits2.Rd:66-68: Dropping empty section \details
prepare_Rd: searchHits2.Rd:88-90: Dropping empty section \note
prepare_Rd: searchHits2.Rd:82-84: 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:73-75: Dropping empty section \details
prepare_Rd: writeHits.Rd:85-87: Dropping empty section \note
prepare_Rd: writeHits2.Rd:76-78: Dropping empty section \details
prepare_Rd: writeHits2.Rd:88-90: 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 or elapsed time > 5s
                      user system elapsed
CRISPRseek-package 184.916  7.312 199.477
offTargetAnalysis   35.228  0.936  36.247
compare2Sequences    5.940  0.644   6.696
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.10-bioc/meat/CRISPRseek.Rcheck/00check.log’
for details.



Installation output

CRISPRseek.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL CRISPRseek
###
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* installing to library ‘/home/biocbuild/bbs-3.10-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 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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 
  0.224   0.028   0.249 

Example timings

CRISPRseek.Rcheck/CRISPRseek-Ex.timings

nameusersystemelapsed
CRISPRseek-package184.916 7.312199.477
annotateOffTargets4.5520.0964.665
buildFeatureVectorForScoring0.0720.0000.071
calculategRNAEfficiency0.0200.0680.090
compare2Sequences5.9400.6446.696
filterOffTarget4.6240.2324.879
filtergRNA1.0320.0441.081
findgRNAs0.2000.1160.351
getOfftargetScore0.1240.0200.145
isPatternUnique0.0160.0080.022
offTargetAnalysis35.228 0.93636.247
searchHits0.0040.0000.002
searchHits23.6480.3083.961
translatePattern000
uniqueREs0.5600.0240.594
writeHits0.0000.0000.001
writeHits20.2160.0120.232