Lihua Julie Zhu
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/CRISPRseek |
| Branch: RELEASE_3_12 |
| Last Commit: 3b0270d |
| Last Changed Date: 2021-01-11 15:59:45 -0400 (Mon, 11 Jan 2021) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:34:38 -0400 (Thu, 06 May 2021).
|
To the developers/maintainers of the CRISPRseek package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 395/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CRISPRseek 1.30.1 (landing page) Lihua Julie Zhu
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: CRISPRseek |
| Version: 1.30.1 |
| 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_1.30.1.tar.gz |
| StartedAt: 2021-05-06 00:43:04 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 00:53:12 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 608.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CRISPRseek.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:CRISPRseek.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CRISPRseek_1.30.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/CRISPRseek.Rcheck’
* using R version 4.0.5 (2021-03-31)
* 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 ‘1.30.1’
* 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 ‘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 179.137 4.427 185.123
offTargetAnalysis 71.687 0.687 72.551
offTargetAnalysisWithoutBSgenome 62.597 0.373 63.088
compare2Sequences 11.387 0.119 11.551
filterOffTarget 5.187 0.127 5.321
* 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
‘/Users/biocbuild/bbs-3.12-bioc/meat/CRISPRseek.Rcheck/00check.log’
for details.
CRISPRseek.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL CRISPRseek ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/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)
CRISPRseek.Rcheck/tests/runTests.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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
0.259 0.060 0.296
CRISPRseek.Rcheck/CRISPRseek-Ex.timings
| name | user | system | elapsed | |
| CRISPRseek-package | 179.137 | 4.427 | 185.123 | |
| annotateOffTargets | 4.662 | 0.082 | 4.750 | |
| buildFeatureVectorForScoring | 0.090 | 0.002 | 0.093 | |
| calculategRNAEfficiency | 0.026 | 0.005 | 0.032 | |
| compare2Sequences | 11.387 | 0.119 | 11.551 | |
| filterOffTarget | 5.187 | 0.127 | 5.321 | |
| filtergRNA | 0.878 | 0.003 | 0.881 | |
| findgRNAs | 0.624 | 0.022 | 0.647 | |
| getOfftargetScore | 0.123 | 0.002 | 0.125 | |
| isPatternUnique | 0.021 | 0.001 | 0.022 | |
| offTargetAnalysis | 71.687 | 0.687 | 72.551 | |
| offTargetAnalysisWithoutBSgenome | 62.597 | 0.373 | 63.088 | |
| predictRelativeFreqIndels | 0.000 | 0.000 | 0.001 | |
| searchHits | 0.004 | 0.001 | 0.005 | |
| searchHits2 | 3.664 | 0.042 | 3.711 | |
| translatePattern | 0.001 | 0.000 | 0.001 | |
| uniqueREs | 0.475 | 0.030 | 0.506 | |
| writeHits | 0.001 | 0.001 | 0.002 | |
| writeHits2 | 0.177 | 0.008 | 0.184 | |