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BioC 3.3: CHECK report for CRISPRseek on moscato2

This page was generated on 2016-10-13 12:52:07 -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: rm -rf CRISPRseek.buildbin-libdir CRISPRseek.Rcheck && mkdir CRISPRseek.buildbin-libdir CRISPRseek.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CRISPRseek.buildbin-libdir CRISPRseek_1.12.0.tar.gz >CRISPRseek.Rcheck\00install.out 2>&1 && cp CRISPRseek.Rcheck\00install.out CRISPRseek-install.out && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=CRISPRseek.buildbin-libdir --install="check:CRISPRseek-install.out" --force-multiarch --no-vignettes --timings CRISPRseek_1.12.0.tar.gz
StartedAt: 2016-10-13 02:40:09 -0700 (Thu, 13 Oct 2016)
EndedAt: 2016-10-13 03:07:41 -0700 (Thu, 13 Oct 2016)
EllapsedTime: 1652.2 seconds
RetCode: 0
Status:  OK  
CheckDir: CRISPRseek.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf CRISPRseek.buildbin-libdir CRISPRseek.Rcheck && mkdir CRISPRseek.buildbin-libdir CRISPRseek.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CRISPRseek.buildbin-libdir CRISPRseek_1.12.0.tar.gz >CRISPRseek.Rcheck\00install.out 2>&1 && cp CRISPRseek.Rcheck\00install.out CRISPRseek-install.out  && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=CRISPRseek.buildbin-libdir --install="check:CRISPRseek-install.out" --force-multiarch --no-vignettes --timings CRISPRseek_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.3-bioc/meat/CRISPRseek.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                                 user system elapsed
CRISPRseek-package             434.80   5.96  563.08
offTargetAnalysis               28.66   0.20   31.54
searchHits                       8.96   0.11    9.21
offTargetAnalysisOfPeakRegions   6.85   0.10   21.71
annotateOffTargets               6.49   0.12   17.73
filterOffTarget                  5.94   0.06   13.56
compare2Sequences                2.61   0.02    6.44
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                                 user system elapsed
CRISPRseek-package             442.09   5.51  615.07
offTargetAnalysis               39.17   0.33   39.69
searchHits                       9.86   0.17   10.03
offTargetAnalysisOfPeakRegions   9.26   0.06   10.03
filterOffTarget                  7.60   0.12    7.72
annotateOffTargets               6.94   0.15    7.10
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  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
  'E:/biocbld/bbs-3.3-bioc/meat/CRISPRseek.Rcheck/00check.log'
for details.

CRISPRseek.Rcheck/00install.out:


install for i386

* 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

install for x64

* installing *source* package 'CRISPRseek' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CRISPRseek' as CRISPRseek_1.12.0.zip
* DONE (CRISPRseek)

CRISPRseek.Rcheck/examples_i386/CRISPRseek-Ex.timings:

nameusersystemelapsed
CRISPRseek-package434.80 5.96563.08
annotateOffTargets 6.49 0.1217.73
buildFeatureVectorForScoring0.110.000.11
calculategRNAEfficiency0.010.000.02
compare2Sequences2.610.026.44
filterOffTarget 5.94 0.0613.56
filtergRNA0.640.000.64
findgRNAs0.030.000.08
foldgRNAs000
getOfftargetScore0.110.000.11
isPatternUnique0.010.000.02
offTargetAnalysis28.66 0.2031.54
offTargetAnalysisOfPeakRegions 6.85 0.1021.71
searchHits8.960.119.21
translatePattern000
uniqueREs0.450.010.55
writeHits0.030.000.03

CRISPRseek.Rcheck/examples_x64/CRISPRseek-Ex.timings:

nameusersystemelapsed
CRISPRseek-package442.09 5.51615.07
annotateOffTargets6.940.157.10
buildFeatureVectorForScoring0.160.000.16
calculategRNAEfficiency0.040.000.05
compare2Sequences4.310.024.32
filterOffTarget7.600.127.72
filtergRNA0.810.020.83
findgRNAs0.040.000.05
foldgRNAs000
getOfftargetScore0.240.000.23
isPatternUnique0.030.000.03
offTargetAnalysis39.17 0.3339.69
offTargetAnalysisOfPeakRegions 9.26 0.0610.03
searchHits 9.86 0.1710.03
translatePattern000
uniqueREs0.570.020.57
writeHits0.030.000.03