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BioC 3.3: CHECK report for CRISPRseek on zin2

This page was generated on 2016-10-13 12:44:20 -0700 (Thu, 13 Oct 2016).

Package 257/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CRISPRseek 1.12.0
Lihua Julie Zhu
Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/CRISPRseek
Last Changed Rev: 117079 / Revision: 122332
Last Changed Date: 2016-05-03 14:20:18 -0700 (Tue, 03 May 2016)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: CRISPRseek
Version: 1.12.0
Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings CRISPRseek_1.12.0.tar.gz
StartedAt: 2016-10-13 00:59:45 -0700 (Thu, 13 Oct 2016)
EndedAt: 2016-10-13 01:06:49 -0700 (Thu, 13 Oct 2016)
EllapsedTime: 424.3 seconds
RetCode: 0
Status:  OK 
CheckDir: CRISPRseek.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings CRISPRseek_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/CRISPRseek.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.12.0’
* 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 ... NOTE
':::' call which should be '::': ‘S4Vectors:::orderIntegerPairs’
  See the note in ?`:::` about the use of this operator.
* 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 ‘genes’
annotateOffTargets: no visible global function definition for ‘toTable’
filterOffTarget: no visible global function definition for ‘seqlengths’
foldgRNAs: no visible global function definition for ‘fold’
getSeqFromBed: no visible global function definition for ‘seqlengths’
uniqueREs: no visible global function definition for ‘seqlengths’
Undefined global functions or variables:
  GRanges exons fold genes seqlengths seqlevels seqlevels<- toTable
* checking Rd files ... NOTE
prepare_Rd: annotateOffTargets.Rd:47-49: Dropping empty section \details
prepare_Rd: annotateOffTargets.Rd:59-61: Dropping empty section \note
prepare_Rd: buildFeatureVectorForScoring.Rd:41-43: Dropping empty section \details
prepare_Rd: buildFeatureVectorForScoring.Rd:70-72: Dropping empty section \note
prepare_Rd: buildFeatureVectorForScoring.Rd:64-66: Dropping empty section \references
prepare_Rd: calculategRNAEfficiency.Rd:49-51: Dropping empty section \note
prepare_Rd: compare2Sequences.Rd:206-208: Dropping empty section \details
prepare_Rd: compare2Sequences.Rd:248-250: Dropping empty section \note
prepare_Rd: filterOffTarget.Rd:98-100: Dropping empty section \details
prepare_Rd: filterOffTarget.Rd:112-114: 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:101-103: Dropping empty section \references
prepare_Rd: foldgRNAs.Rd:28-30: Dropping empty section \details
prepare_Rd: foldgRNAs.Rd:44-46: Dropping empty section \note
prepare_Rd: foldgRNAs.Rd:38-40: 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:273-275: Dropping empty section \details
prepare_Rd: offTargetAnalysis.Rd:296-298: Dropping empty section \note
prepare_Rd: offTargetAnalysisOfPeakRegions.Rd:82-84: Dropping empty section \details
prepare_Rd: offTargetAnalysisOfPeakRegions.Rd:102-104: Dropping empty section \note
prepare_Rd: searchHits.Rd:55-57: Dropping empty section \details
prepare_Rd: searchHits.Rd:77-79: Dropping empty section \note
prepare_Rd: searchHits.Rd:71-73: 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:50-52: Dropping empty section \details
prepare_Rd: writeHits.Rd:62-64: 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                                  user system elapsed
CRISPRseek-package             220.931 10.457 238.445
offTargetAnalysis               21.633  0.637  22.731
offTargetAnalysisOfPeakRegions   6.819  0.113   6.954
* 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
  ‘/home/biocbuild/bbs-3.3-bioc/meat/CRISPRseek.Rcheck/00check.log’
for details.


CRISPRseek.Rcheck/00install.out:

* installing *source* package ‘CRISPRseek’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (CRISPRseek)

CRISPRseek.Rcheck/CRISPRseek-Ex.timings:

nameusersystemelapsed
CRISPRseek-package220.931 10.457238.445
annotateOffTargets4.1700.1084.304
buildFeatureVectorForScoring0.1090.0000.110
calculategRNAEfficiency0.0250.0500.113
compare2Sequences2.4510.1302.595
filterOffTarget4.6190.1404.807
filtergRNA0.6630.0040.671
findgRNAs0.0330.0000.036
foldgRNAs0.0010.0000.001
getOfftargetScore0.1220.0000.122
isPatternUnique0.0150.0000.015
offTargetAnalysis21.633 0.63722.731
offTargetAnalysisOfPeakRegions6.8190.1136.954
searchHits3.9920.2924.356
translatePattern0.0000.0000.001
uniqueREs0.3930.0040.407
writeHits0.0290.0000.037