Back to Multiple platform build/check report for BioC 3.6
ABCDEF[G]HIJKLMNOPQRSTUVWXYZ

CHECK report for GUIDEseq on tokay1

This page was generated on 2018-04-12 13:27:01 -0400 (Thu, 12 Apr 2018).

Package 631/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GUIDEseq 1.8.1
Lihua Julie Zhu
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/GUIDEseq
Branch: RELEASE_3_6
Last Commit: 292fe21
Last Changed Date: 2018-03-29 15:01:57 -0400 (Thu, 29 Mar 2018)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: GUIDEseq
Version: 1.8.1
Command: rm -rf GUIDEseq.buildbin-libdir GUIDEseq.Rcheck && mkdir GUIDEseq.buildbin-libdir GUIDEseq.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GUIDEseq.buildbin-libdir GUIDEseq_1.8.1.tar.gz >GUIDEseq.Rcheck\00install.out 2>&1 && cp GUIDEseq.Rcheck\00install.out GUIDEseq-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=GUIDEseq.buildbin-libdir --install="check:GUIDEseq-install.out" --force-multiarch --no-vignettes --timings GUIDEseq_1.8.1.tar.gz
StartedAt: 2018-04-12 00:36:55 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 00:44:14 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 439.4 seconds
RetCode: 0
Status:  OK  
CheckDir: GUIDEseq.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf GUIDEseq.buildbin-libdir GUIDEseq.Rcheck && mkdir GUIDEseq.buildbin-libdir GUIDEseq.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GUIDEseq.buildbin-libdir GUIDEseq_1.8.1.tar.gz >GUIDEseq.Rcheck\00install.out 2>&1 && cp GUIDEseq.Rcheck\00install.out GUIDEseq-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=GUIDEseq.buildbin-libdir --install="check:GUIDEseq-install.out" --force-multiarch --no-vignettes --timings GUIDEseq_1.8.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/GUIDEseq.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GUIDEseq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GUIDEseq' version '1.8.1'
* 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 whether package 'GUIDEseq' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 11.2Mb
  sub-directories of 1Mb or more:
    extdata  10.5Mb
* 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 ... 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 binding for global variable
  'offTarget_Start'
annotateOffTargets: no visible global function definition for 'exons'
annotateOffTargets: no visible global function definition for
  'seqlevelsStyle<-'
annotateOffTargets: no visible global function definition for 'genes'
annotateOffTargets: no visible global function definition for 'toTable'
getPeaks: no visible binding for global variable 'adjusted.p.value'
getPeaks: no visible binding for global variable 'SNratio'
getUniqueCleavageEvents: no visible binding for global variable
  'qwidth.first'
getUniqueCleavageEvents: no visible binding for global variable
  'qwidth.last'
getUniqueCleavageEvents: no visible binding for global variable
  'strand.last'
getUniqueCleavageEvents: no visible binding for global variable
  'strand.first'
getUniqueCleavageEvents: no visible binding for global variable
  'readName'
offTargetAnalysisOfPeakRegions: no visible binding for global variable
  'gRNAPlusPAM'
offTargetAnalysisOfPeakRegions: no visible binding for global variable
  'offTarget'
Undefined global functions or variables:
  SNratio adjusted.p.value exons gRNAPlusPAM genes offTarget
  offTarget_Start qwidth.first qwidth.last readName seqlevelsStyle<-
  strand.first strand.last toTable
* checking Rd files ... NOTE
prepare_Rd: annotateOffTargets.Rd:33-35: Dropping empty section \details
prepare_Rd: annotateOffTargets.Rd:43-45: Dropping empty section \references
prepare_Rd: createBarcodeFasta.Rd:42-43: Dropping empty section \value
prepare_Rd: createBarcodeFasta.Rd:44-46: Dropping empty section \references
prepare_Rd: getUsedBarcodes.Rd:39-41: Dropping empty section \references
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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
GUIDEseqAnalysis   10.8   0.45   11.87
annotateOffTargets  7.2   0.47    8.47
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
GUIDEseqAnalysis   14.02    0.5   14.53
annotateOffTargets  9.02    0.3    9.31
* 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
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/GUIDEseq.Rcheck/00check.log'
for details.



Installation output

GUIDEseq.Rcheck/00install.out


install for i386

* installing *source* package 'GUIDEseq' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'GUIDEseq'
    finding HTML links ... done
    GUIDEseq-package                        html  
    GUIDEseqAnalysis                        html  
    annotateOffTargets                      html  
    combineOfftargets                       html  
    createBarcodeFasta                      html  
    getPeaks                                html  
    getUniqueCleavageEvents                 html  
    getUsedBarcodes                         html  
    mergePlusMinusPeaks                     html  
    offTargetAnalysisOfPeakRegions          html  
    peaks.gr                                html  
    uniqueCleavageEvents                    html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'GUIDEseq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GUIDEseq' as GUIDEseq_1.8.1.zip
* DONE (GUIDEseq)
In R CMD INSTALL
In R CMD INSTALL

Tests output


Example timings

GUIDEseq.Rcheck/examples_i386/GUIDEseq-Ex.timings

nameusersystemelapsed
GUIDEseq-package000
GUIDEseqAnalysis10.80 0.4511.87
annotateOffTargets7.200.478.47
combineOfftargets0.040.000.03
createBarcodeFasta0.030.000.03
getPeaks000
getUniqueCleavageEvents000
getUsedBarcodes0.040.000.05
mergePlusMinusPeaks000
offTargetAnalysisOfPeakRegions000
peaks.gr0.070.000.06
uniqueCleavageEvents0.090.000.09

GUIDEseq.Rcheck/examples_x64/GUIDEseq-Ex.timings

nameusersystemelapsed
GUIDEseq-package000
GUIDEseqAnalysis14.02 0.5014.53
annotateOffTargets9.020.309.31
combineOfftargets0.040.000.04
createBarcodeFasta0.030.000.03
getPeaks0.020.000.02
getUniqueCleavageEvents000
getUsedBarcodes0.090.000.09
mergePlusMinusPeaks0.020.000.02
offTargetAnalysisOfPeakRegions000
peaks.gr0.070.010.09
uniqueCleavageEvents0.160.020.17