Back to the "Multiple platform build/check report" A  B  C  D  E  F [G] H  I  J  K  L  M  N  O  P  Q  R  S  T  U  V  W  X  Y  Z 

BioC 3.5: CHECK report for GUIDEseq on tokay2

This page was generated on 2017-08-16 13:25:03 -0400 (Wed, 16 Aug 2017).

Package 607/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GUIDEseq 1.6.1
Lihua Julie Zhu
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/GUIDEseq
Last Changed Rev: 129917 / Revision: 131943
Last Changed Date: 2017-05-26 10:41:28 -0400 (Fri, 26 May 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: GUIDEseq
Version: 1.6.1
Command: rm -rf GUIDEseq.buildbin-libdir GUIDEseq.Rcheck && mkdir GUIDEseq.buildbin-libdir GUIDEseq.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GUIDEseq.buildbin-libdir GUIDEseq_1.6.1.tar.gz >GUIDEseq.Rcheck\00install.out 2>&1 && cp GUIDEseq.Rcheck\00install.out GUIDEseq-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=GUIDEseq.buildbin-libdir --install="check:GUIDEseq-install.out" --force-multiarch --no-vignettes --timings GUIDEseq_1.6.1.tar.gz
StartedAt: 2017-08-16 00:23:38 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 00:39:44 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 965.7 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-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GUIDEseq.buildbin-libdir GUIDEseq_1.6.1.tar.gz >GUIDEseq.Rcheck\00install.out 2>&1 && cp GUIDEseq.Rcheck\00install.out GUIDEseq-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=GUIDEseq.buildbin-libdir --install="check:GUIDEseq-install.out" --force-multiarch --no-vignettes --timings GUIDEseq_1.6.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/GUIDEseq.Rcheck'
* using R version 3.4.1 (2017-06-30)
* 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 '1.6.1'
* 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 'GUIDEseq' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 11.0Mb
  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   10.14   0.37  232.78
annotateOffTargets  8.83   0.46   40.90
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
GUIDEseqAnalysis   12.59    0.5  263.67
annotateOffTargets  7.84    0.6   35.15
* 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-3.5-bioc/meat/GUIDEseq.Rcheck/00check.log'
for details.


GUIDEseq.Rcheck/00install.out:


install for i386

* installing *source* package 'GUIDEseq' ...
** R
** data
** 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 'GUIDEseq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GUIDEseq' as GUIDEseq_1.6.1.zip
* DONE (GUIDEseq)

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

nameusersystemelapsed
GUIDEseq-package000
GUIDEseqAnalysis 10.14 0.37232.78
annotateOffTargets 8.83 0.4640.90
combineOfftargets0.080.000.08
createBarcodeFasta0.030.000.03
getPeaks000
getUniqueCleavageEvents000
getUsedBarcodes0.080.000.07
mergePlusMinusPeaks000
offTargetAnalysisOfPeakRegions000
peaks.gr0.070.000.08
uniqueCleavageEvents0.190.000.18

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

nameusersystemelapsed
GUIDEseq-package0.020.000.02
GUIDEseqAnalysis 12.59 0.50263.67
annotateOffTargets 7.84 0.6035.15
combineOfftargets0.010.010.03
createBarcodeFasta0.030.000.03
getPeaks000
getUniqueCleavageEvents000
getUsedBarcodes0.050.000.05
mergePlusMinusPeaks000
offTargetAnalysisOfPeakRegions000
peaks.gr0.090.000.10
uniqueCleavageEvents0.170.010.18