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This page was generated on 2021-10-14 12:05:35 -0400 (Thu, 14 Oct 2021).

CHECK results for GUIDEseq on riesling1

To the developers/maintainers of the GUIDEseq package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GUIDEseq.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 828/2056HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GUIDEseq 1.23.0  (landing page)
Lihua Julie Zhu
Snapshot Date: 2021-10-13 14:50:09 -0400 (Wed, 13 Oct 2021)
git_url: https://git.bioconductor.org/packages/GUIDEseq
git_branch: master
git_last_commit: ae56235
git_last_commit_date: 2021-05-19 12:16:19 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: GUIDEseq
Version: 1.23.0
Command: D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GUIDEseq.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings GUIDEseq_1.23.0.tar.gz
StartedAt: 2021-10-14 01:24:38 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 01:31:26 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 407.9 seconds
RetCode: 0
Status:   OK  
CheckDir: GUIDEseq.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GUIDEseq.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings GUIDEseq_1.23.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.14-bioc/meat/GUIDEseq.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '1.23.0'
* 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 11.0Mb
  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'
getPeaks: no visible binding for global variable 'adjusted.p.value'
getPeaks: no visible binding for global variable 'SNratio'
getPeaks.old: no visible global function definition for 'clusterExport'
getPeaks.old: no visible global function definition for 'parLapply'
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'
getUniqueCleavageEvents: no visible binding for global variable 'UMI'
importBEDAlignments: no visible global function definition for
  'parLapply'
offTargetAnalysisOfPeakRegions: no visible binding for global variable
  'thePeak'
offTargetAnalysisOfPeakRegions: no visible global function definition
  for 'parLapply'
offTargetAnalysisOfPeakRegions: no visible binding for global variable
  'gRNAPlusPAM'
offTargetAnalysisOfPeakRegions: no visible binding for global variable
  'offTarget'
Undefined global functions or variables:
  SNratio UMI adjusted.p.value clusterExport exons gRNAPlusPAM genes
  offTarget offTarget_Start parLapply qwidth.first qwidth.last readName
  seqlevelsStyle<- strand.first strand.last thePeak
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
GUIDEseqAnalysis   8.31   0.20    8.52
annotateOffTargets 6.05   0.31    6.40
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
GUIDEseqAnalysis 6.64   0.44     7.1
* 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
  'D:/biocbuild/bbs-3.14-bioc/meat/GUIDEseq.Rcheck/00check.log'
for details.



Installation output

GUIDEseq.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/GUIDEseq_1.23.0.tar.gz && rm -rf GUIDEseq.buildbin-libdir && mkdir GUIDEseq.buildbin-libdir && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GUIDEseq.buildbin-libdir GUIDEseq_1.23.0.tar.gz && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL GUIDEseq_1.23.0.zip && rm GUIDEseq_1.23.0.tar.gz GUIDEseq_1.23.0.zip
###
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##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0 4528k    0 13525    0     0   114k      0  0:00:39 --:--:--  0:00:39  114k
100 4528k  100 4528k    0     0  4288k      0  0:00:01  0:00:01 --:--:-- 4288k

install for i386

* installing *source* package 'GUIDEseq' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'GUIDEseq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GUIDEseq' as GUIDEseq_1.23.0.zip
* DONE (GUIDEseq)
* installing to library 'D:/biocbuild/bbs-3.14-bioc/R/library'
package 'GUIDEseq' successfully unpacked and MD5 sums checked

Tests output


Example timings

GUIDEseq.Rcheck/examples_i386/GUIDEseq-Ex.timings

nameusersystemelapsed
GUIDEseq-package000
GUIDEseqAnalysis8.310.208.52
annotateOffTargets6.050.316.40
combineOfftargets0.020.000.01
createBarcodeFasta0.010.000.02
getPeaks000
getUniqueCleavageEvents000
getUsedBarcodes0.010.000.02
mergePlusMinusPeaks000
offTargetAnalysisOfPeakRegions000
peaks.gr0.030.000.03
uniqueCleavageEvents0.040.000.04

GUIDEseq.Rcheck/examples_x64/GUIDEseq-Ex.timings

nameusersystemelapsed
GUIDEseq-package000
GUIDEseqAnalysis6.640.447.10
annotateOffTargets4.110.374.48
combineOfftargets0.010.000.01
createBarcodeFasta0.020.000.02
getPeaks000
getUniqueCleavageEvents000
getUsedBarcodes0.020.000.01
mergePlusMinusPeaks000
offTargetAnalysisOfPeakRegions000
peaks.gr0.020.000.01
uniqueCleavageEvents0.010.020.04