Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:38 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the GUIDEseq package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GUIDEseq.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. |
Package 829/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GUIDEseq 1.22.0 (landing page) Lihua Julie Zhu
| nebbiolo1 | Linux (Ubuntu 20.04.2 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: GUIDEseq |
Version: 1.22.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GUIDEseq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GUIDEseq_1.22.0.tar.gz |
StartedAt: 2021-10-14 19:51:06 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 19:59:00 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 474.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: GUIDEseq.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GUIDEseq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GUIDEseq_1.22.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/GUIDEseq.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 ‘GUIDEseq/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘GUIDEseq’ version ‘1.22.0’ * 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 ‘GUIDEseq’ can be installed ... OK * checking installed package size ... NOTE installed size is 11.0Mb sub-directories of 1Mb or more: extdata 10.5Mb * 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 binding for global variable 'offTarget_Start' annotateOffTargets: no visible global function definition for 'exons' annotateOffTargets: no visible global function definition for 'seqlevelsStyle<-' annotateOffTargets: no visible global function definition for 'genes' getPeaks: no visible binding for global variable 'adjusted.p.value' getPeaks: no visible binding for global variable 'SNratio' getUniqueCleavageEvents: no visible binding for global variable 'qwidth.first' getUniqueCleavageEvents: no visible binding for global variable 'qwidth.last' getUniqueCleavageEvents: no visible binding for global variable 'strand.last' getUniqueCleavageEvents: no visible binding for global variable 'strand.first' getUniqueCleavageEvents: no visible binding for global variable 'readName' getUniqueCleavageEvents: no visible binding for global variable 'UMI' offTargetAnalysisOfPeakRegions: no visible binding for global variable 'thePeak' offTargetAnalysisOfPeakRegions: no visible binding for global variable 'gRNAPlusPAM' offTargetAnalysisOfPeakRegions: no visible binding for global variable 'offTarget' Undefined global functions or variables: SNratio UMI adjusted.p.value exons gRNAPlusPAM genes offTarget offTarget_Start qwidth.first qwidth.last readName seqlevelsStyle<- strand.first strand.last thePeak * checking Rd files ... NOTE prepare_Rd: annotateOffTargets.Rd:33-35: Dropping empty section \details prepare_Rd: annotateOffTargets.Rd:43-45: Dropping empty section \references prepare_Rd: createBarcodeFasta.Rd:42-43: Dropping empty section \value prepare_Rd: createBarcodeFasta.Rd:44-46: Dropping empty section \references prepare_Rd: getUsedBarcodes.Rd:39-41: Dropping empty section \references * 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... 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 GUIDEseqAnalysis 14.651 0.709 15.507 annotateOffTargets 12.451 0.524 13.244 * 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/GUIDEseq.Rcheck/00check.log’ for details.
GUIDEseq.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL GUIDEseq ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’ * installing *source* package ‘GUIDEseq’ ... ** using staged installation ** R ** data ** 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 (GUIDEseq)
GUIDEseq.Rcheck/GUIDEseq-Ex.timings
name | user | system | elapsed | |
GUIDEseq-package | 0.002 | 0.001 | 0.003 | |
GUIDEseqAnalysis | 14.651 | 0.709 | 15.507 | |
annotateOffTargets | 12.451 | 0.524 | 13.244 | |
combineOfftargets | 0.045 | 0.004 | 0.052 | |
createBarcodeFasta | 0.043 | 0.002 | 0.048 | |
getPeaks | 0.001 | 0.001 | 0.001 | |
getUniqueCleavageEvents | 0.001 | 0.001 | 0.001 | |
getUsedBarcodes | 0.076 | 0.002 | 0.082 | |
mergePlusMinusPeaks | 0.000 | 0.000 | 0.001 | |
offTargetAnalysisOfPeakRegions | 0.002 | 0.000 | 0.002 | |
peaks.gr | 0.064 | 0.013 | 0.083 | |
uniqueCleavageEvents | 0.097 | 0.004 | 0.105 | |