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BioC 3.2: CHECK report for CRISPRseek on moscato1

This page was generated on 2016-04-23 10:19:53 -0700 (Sat, 23 Apr 2016).

Package 236/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CRISPRseek 1.10.3
Lihua Julie Zhu
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/CRISPRseek
Last Changed Rev: 115109 / Revision: 116712
Last Changed Date: 2016-03-22 09:24:22 -0700 (Tue, 22 Mar 2016)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: CRISPRseek
Version: 1.10.3
Command: rm -rf CRISPRseek.buildbin-libdir CRISPRseek.Rcheck && mkdir CRISPRseek.buildbin-libdir CRISPRseek.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CRISPRseek.buildbin-libdir CRISPRseek_1.10.3.tar.gz >CRISPRseek.Rcheck\00install.out 2>&1 && cp CRISPRseek.Rcheck\00install.out CRISPRseek-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=CRISPRseek.buildbin-libdir --install="check:CRISPRseek-install.out" --force-multiarch --no-vignettes --timings CRISPRseek_1.10.3.tar.gz
StartedAt: 2016-04-23 01:14:34 -0700 (Sat, 23 Apr 2016)
EndedAt: 2016-04-23 01:43:15 -0700 (Sat, 23 Apr 2016)
EllapsedTime: 1721.2 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: CRISPRseek.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf CRISPRseek.buildbin-libdir CRISPRseek.Rcheck && mkdir CRISPRseek.buildbin-libdir CRISPRseek.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CRISPRseek.buildbin-libdir CRISPRseek_1.10.3.tar.gz >CRISPRseek.Rcheck\00install.out 2>&1 && cp CRISPRseek.Rcheck\00install.out CRISPRseek-install.out  && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=CRISPRseek.buildbin-libdir --install="check:CRISPRseek-install.out" --force-multiarch --no-vignettes --timings CRISPRseek_1.10.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/CRISPRseek.Rcheck'
* using R version 3.2.4 (2016-03-10)
* 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 '1.10.3'
* 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 ... WARNING
'::' or ':::' import not declared from: 'GeneRfold'
'library' or 'require' call not declared from: 'GeneRfold'
'library' or 'require' call to 'GeneRfold' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Unexported object imported by a ':::' call: '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'
getSeqFromBed: no visible global function definition for 'seqlengths'
uniqueREs: no visible global function definition for 'seqlengths'
* 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:35-37: Dropping empty section \details
prepare_Rd: buildFeatureVectorForScoring.Rd:64-66: Dropping empty section \note
prepare_Rd: buildFeatureVectorForScoring.Rd:58-60: Dropping empty section \references
prepare_Rd: calculategRNAEfficiency.Rd:44-46: Dropping empty section \note
prepare_Rd: compare2Sequences.Rd:150-152: Dropping empty section \details
prepare_Rd: compare2Sequences.Rd:192-194: 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:96-98: 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:227-229: Dropping empty section \details
prepare_Rd: offTargetAnalysis.Rd:249-251: 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' ... [12m] OK
Examples with CPU or elapsed time > 5s
                                 user system elapsed
CRISPRseek-package             565.52   5.46  626.16
offTargetAnalysis               50.62   0.39   51.93
searchHits                      12.39   0.17   13.32
offTargetAnalysisOfPeakRegions  10.08   0.12   11.18
annotateOffTargets               8.33   0.14    8.47
filterOffTarget                  7.83   0.12    8.73
** running examples for arch 'x64' ... [12m] OK
Examples with CPU or elapsed time > 5s
                                 user system elapsed
CRISPRseek-package             572.87   5.76  584.69
offTargetAnalysis               49.32   0.29   50.19
offTargetAnalysisOfPeakRegions   9.55   0.13   11.50
searchHits                       9.09   0.11   10.48
filterOffTarget                  8.99   0.07    9.45
annotateOffTargets               8.32   0.17    8.49
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R' [0s]
 [1s] OK
** running tests for arch 'x64' ...
  Running 'runTests.R' [3s]
 [3s] 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: 1 WARNING, 2 NOTEs
See
  'D:/biocbld/bbs-3.2-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_1.10.3.zip
* DONE (CRISPRseek)

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

nameusersystemelapsed
CRISPRseek-package565.52 5.46626.16
annotateOffTargets8.330.148.47
buildFeatureVectorForScoring0.060.000.06
calculategRNAEfficiency0.030.000.03
compare2Sequences4.150.024.23
filterOffTarget7.830.128.73
filtergRNA0.840.000.84
findgRNAs0.050.000.05
foldgRNAs000
getOfftargetScore0.090.020.11
isPatternUnique0.030.000.03
offTargetAnalysis50.62 0.3951.93
offTargetAnalysisOfPeakRegions10.08 0.1211.18
searchHits12.39 0.1713.32
translatePattern000
uniqueREs0.670.020.69
writeHits0.030.000.03

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

nameusersystemelapsed
CRISPRseek-package572.87 5.76584.69
annotateOffTargets8.320.178.49
buildFeatureVectorForScoring0.090.000.09
calculategRNAEfficiency0.050.000.05
compare2Sequences4.840.014.88
filterOffTarget8.990.079.45
filtergRNA1.170.002.01
findgRNAs0.070.000.06
foldgRNAs000
getOfftargetScore0.090.000.10
isPatternUnique0.020.000.01
offTargetAnalysis49.32 0.2950.19
offTargetAnalysisOfPeakRegions 9.55 0.1311.50
searchHits 9.09 0.1110.48
translatePattern000
uniqueREs0.640.030.68
writeHits0.050.000.04