Lihua Julie Zhu
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/CRISPRseek |
| Branch: RELEASE_3_11 |
| Last Commit: fa88ffa |
| Last Changed Date: 2020-04-27 14:37:33 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:58:19 -0400 (Sat, 17 Oct 2020).
| 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 391/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| CRISPRseek 1.28.0 Lihua Julie Zhu
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | [ OK ] | OK | |
| Package: CRISPRseek |
| Version: 1.28.0 |
| 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_1.28.0.tar.gz |
| StartedAt: 2020-10-17 00:07:29 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 00:19:04 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 694.9 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_1.28.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/CRISPRseek.Rcheck’
* using R version 4.0.3 (2020-10-10)
* 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 ‘1.28.0’
* 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 ‘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’
getSeqFromBed: no visible global function definition for ‘seqlengths’
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 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:250-252: Dropping empty section \details
prepare_Rd: compare2Sequences.Rd:292-294: 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: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:409-411: Dropping empty section \details
prepare_Rd: offTargetAnalysis.Rd:434-436: Dropping empty section \note
prepare_Rd: offTargetAnalysisWithoutBSgenome.Rd:417-419: Dropping empty section \details
prepare_Rd: offTargetAnalysisWithoutBSgenome.Rd:442-444: 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 203.529 5.135 211.778
offTargetAnalysis 89.564 0.922 90.553
offTargetAnalysisWithoutBSgenome 72.800 0.362 73.313
compare2Sequences 12.460 0.174 12.657
filterOffTarget 5.813 0.147 5.965
annotateOffTargets 5.228 0.089 5.333
* 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
‘/Users/biocbuild/bbs-3.11-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 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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
0.307 0.072 0.355
CRISPRseek.Rcheck/CRISPRseek-Ex.timings
| name | user | system | elapsed | |
| CRISPRseek-package | 203.529 | 5.135 | 211.778 | |
| annotateOffTargets | 5.228 | 0.089 | 5.333 | |
| buildFeatureVectorForScoring | 0.131 | 0.003 | 0.134 | |
| calculategRNAEfficiency | 0.028 | 0.004 | 0.034 | |
| compare2Sequences | 12.460 | 0.174 | 12.657 | |
| filterOffTarget | 5.813 | 0.147 | 5.965 | |
| filtergRNA | 1.100 | 0.003 | 1.105 | |
| findgRNAs | 0.773 | 0.028 | 0.805 | |
| getOfftargetScore | 0.167 | 0.003 | 0.169 | |
| isPatternUnique | 0.024 | 0.001 | 0.025 | |
| offTargetAnalysis | 89.564 | 0.922 | 90.553 | |
| offTargetAnalysisWithoutBSgenome | 72.800 | 0.362 | 73.313 | |
| searchHits | 0.005 | 0.002 | 0.007 | |
| searchHits2 | 3.993 | 0.051 | 4.049 | |
| translatePattern | 0.000 | 0.000 | 0.001 | |
| uniqueREs | 0.653 | 0.009 | 0.663 | |
| writeHits | 0.001 | 0.001 | 0.002 | |
| writeHits2 | 0.281 | 0.010 | 0.290 | |