Back to Multiple platform build/check report for BioC 3.10 |
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This page was generated on 2020-04-15 12:08:14 -0400 (Wed, 15 Apr 2020).
Package 380/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
CRISPRseek 1.26.0 Lihua Julie Zhu
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ OK ] | |||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||
merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
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 |
############################################################################## ############################################################################## ### ### 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 ### ############################################################################## ############################################################################## * 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.
CRISPRseek.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL CRISPRseek ### ############################################################################## ############################################################################## * 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)
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
CRISPRseek.Rcheck/CRISPRseek-Ex.timings
name | user | system | elapsed | |
CRISPRseek-package | 184.916 | 7.312 | 199.477 | |
annotateOffTargets | 4.552 | 0.096 | 4.665 | |
buildFeatureVectorForScoring | 0.072 | 0.000 | 0.071 | |
calculategRNAEfficiency | 0.020 | 0.068 | 0.090 | |
compare2Sequences | 5.940 | 0.644 | 6.696 | |
filterOffTarget | 4.624 | 0.232 | 4.879 | |
filtergRNA | 1.032 | 0.044 | 1.081 | |
findgRNAs | 0.200 | 0.116 | 0.351 | |
getOfftargetScore | 0.124 | 0.020 | 0.145 | |
isPatternUnique | 0.016 | 0.008 | 0.022 | |
offTargetAnalysis | 35.228 | 0.936 | 36.247 | |
searchHits | 0.004 | 0.000 | 0.002 | |
searchHits2 | 3.648 | 0.308 | 3.961 | |
translatePattern | 0 | 0 | 0 | |
uniqueREs | 0.560 | 0.024 | 0.594 | |
writeHits | 0.000 | 0.000 | 0.001 | |
writeHits2 | 0.216 | 0.012 | 0.232 | |