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

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### Running command:
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###   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
###
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* 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.

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