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BioC 3.1: CHECK report for CRISPRseek on moscato2

This page was generated on 2015-10-09 09:30:50 -0700 (Fri, 09 Oct 2015).

Package 226/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CRISPRseek 1.8.1
Lihua Julie Zhu
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/CRISPRseek
Last Changed Rev: 104469 / Revision: 109384
Last Changed Date: 2015-06-02 06:08:39 -0700 (Tue, 02 Jun 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  WARNINGS UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: CRISPRseek
Version: 1.8.1
Command: rm -rf CRISPRseek.buildbin-libdir CRISPRseek.Rcheck && mkdir CRISPRseek.buildbin-libdir CRISPRseek.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CRISPRseek.buildbin-libdir CRISPRseek_1.8.1.tar.gz >CRISPRseek.Rcheck\00install.out 2>&1 && cp CRISPRseek.Rcheck\00install.out CRISPRseek-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=CRISPRseek.buildbin-libdir --install="check:CRISPRseek-install.out" --force-multiarch --no-vignettes --timings CRISPRseek_1.8.1.tar.gz
StartedAt: 2015-10-09 00:51:24 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 01:15:42 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 1457.5 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: CRISPRseek.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf CRISPRseek.buildbin-libdir CRISPRseek.Rcheck && mkdir CRISPRseek.buildbin-libdir CRISPRseek.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CRISPRseek.buildbin-libdir CRISPRseek_1.8.1.tar.gz >CRISPRseek.Rcheck\00install.out 2>&1 && cp CRISPRseek.Rcheck\00install.out CRISPRseek-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=CRISPRseek.buildbin-libdir --install="check:CRISPRseek-install.out" --force-multiarch --no-vignettes --timings CRISPRseek_1.8.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/CRISPRseek.Rcheck'
* using R version 3.2.2 (2015-08-14)
* 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 '1.8.1'
* 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 ... WARNING
Found the following significant warnings:
  Warning: replacing previous import by 'seqinr::translate' when loading 'CRISPRseek'
See 'E:/biocbld/bbs-3.1-bioc/meat/CRISPRseek.Rcheck/00install.out' for details.
* 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... OK
* checking dependencies in R code ... WARNING
'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.
* 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 'Rle'
annotateOffTargets: no visible global function definition for 'IRanges'
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
  'overlapsAny'
annotateOffTargets: no visible global function definition for 'genes'
annotateOffTargets: no visible global function definition for
  'findOverlaps'
annotateOffTargets: no visible global function definition for
  'queryHits'
annotateOffTargets: no visible global function definition for
  'subjectHits'
annotateOffTargets: no visible global function definition for 'toTable'
filterOffTarget: no visible global function definition for 'seqlengths'
foldgRNAs: no visible global function definition for 'fold'
foldgRNAs : <anonymous>: no visible global function definition for
  'fold'
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:40-42: Dropping empty section \note
prepare_Rd: compare2Sequences.Rd:131-133: Dropping empty section \details
prepare_Rd: compare2Sequences.Rd:173-175: 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:92-94: 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:210-212: Dropping empty section \details
prepare_Rd: offTargetAnalysis.Rd:232-234: Dropping empty section \note
prepare_Rd: searchHits.Rd:53-55: Dropping empty section \details
prepare_Rd: searchHits.Rd:75-77: Dropping empty section \note
prepare_Rd: searchHits.Rd:69-71: 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' ... [11m] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
CRISPRseek-package 506.50   5.60  550.90
offTargetAnalysis   42.30   0.17   42.48
annotateOffTargets  14.52   0.15   14.68
filterOffTarget     14.44   0.15   14.61
searchHits          11.19   0.08   11.28
** running examples for arch 'x64' ... [591s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
CRISPRseek-package 500.33   5.35  505.86
offTargetAnalysis   38.64   0.19   38.88
annotateOffTargets  11.96   0.12   12.09
filterOffTarget     11.12   0.08   11.20
searchHits           9.03   0.15    9.19
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R' [0s]
 [0s] OK
** running tests for arch 'x64' ...
  Running 'runTests.R' [0s]
 [1s] 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 WARNINGs, 2 NOTEs
See
  'E:/biocbld/bbs-3.1-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
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
Warning: replacing previous import by 'seqinr::translate' when loading 'CRISPRseek'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
Warning: replacing previous import by 'seqinr::translate' when loading 'CRISPRseek'

install for x64

* installing *source* package 'CRISPRseek' ...
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
Warning: replacing previous import by 'seqinr::translate' when loading 'CRISPRseek'
* MD5 sums
packaged installation of 'CRISPRseek' as CRISPRseek_1.8.1.zip
* DONE (CRISPRseek)

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

nameusersystemelapsed
CRISPRseek-package506.5 5.6550.9
annotateOffTargets14.52 0.1514.68
buildFeatureVectorForScoring0.120.000.12
calculategRNAEfficiency0.040.000.04
compare2Sequences3.710.023.72
filterOffTarget14.44 0.1514.61
filtergRNA0.720.020.73
findgRNAs0.050.000.05
foldgRNAs000
getOfftargetScore0.060.000.06
isPatternUnique0.020.000.01
offTargetAnalysis42.30 0.1742.48
searchHits11.19 0.0811.28
translatePattern000
uniqueREs0.560.030.60
writeHits0.030.000.03

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

nameusersystemelapsed
CRISPRseek-package500.33 5.35505.86
annotateOffTargets11.96 0.1212.09
buildFeatureVectorForScoring0.060.000.06
calculategRNAEfficiency0.030.000.03
compare2Sequences3.200.003.23
filterOffTarget11.12 0.0811.20
filtergRNA0.830.000.82
findgRNAs0.040.000.05
foldgRNAs000
getOfftargetScore0.060.000.06
isPatternUnique0.020.000.01
offTargetAnalysis38.64 0.1938.88
searchHits9.030.159.19
translatePattern000
uniqueREs0.570.020.60
writeHits0.040.000.03