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CHECK report for gCrisprTools on merida1

This page was generated on 2021-05-06 12:35:02 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the gCrisprTools package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 669/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gCrisprTools 1.18.0  (landing page)
Russell Bainer
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/gCrisprTools
Branch: RELEASE_3_12
Last Commit: e6168b2
Last Changed Date: 2020-10-27 11:17:28 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository

Summary

Package: gCrisprTools
Version: 1.18.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:gCrisprTools.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings gCrisprTools_1.18.0.tar.gz
StartedAt: 2021-05-06 01:56:32 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 02:03:15 -0400 (Thu, 06 May 2021)
EllapsedTime: 403.7 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: gCrisprTools.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:gCrisprTools.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings gCrisprTools_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/gCrisprTools.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gCrisprTools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gCrisprTools’ version ‘1.18.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘gCrisprTools’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  9.6Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    doc    1.4Mb
* 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
* 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 ... WARNING
'::' or ':::' imports not declared from:
  ‘methods’ ‘multiGSEA’
Missing object imported by a ':::' call: ‘multiGSEA:::GeneSetDb.list’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
ct.GCbias: no visible global function definition for ‘is’
ct.GREATdb: no visible global function definition for
  ‘getMSigGeneSetDb’
ct.buildSE: no visible global function definition for ‘is’
ct.inputCheck: no visible global function definition for ‘is’
ct.multiGSEA: no visible global function definition for ‘is’
ct.multiGSEA: no visible binding for global variable ‘sig’
ct.multiGSEA: no visible global function definition for
  ‘hyperGeometricTest’
ct.multiGSEA: no visible binding for global variable ‘genesetDB’
ct.multiGSEA: no visible binding for global variable ‘up’
ct.multiGSEA: no visible binding for global variable ‘universe’
ct.normalizeBySlope: no visible global function definition for ‘is’
Undefined global functions or variables:
  genesetDB getMSigGeneSetDb hyperGeometricTest is sig universe up
Consider adding
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                              user system elapsed
ct.makeReport               26.069  2.233  28.438
ct.PantherPathwayEnrichment 25.457  1.000  27.421
ct.guideCDF                 14.861  6.588  21.474
ct.makeContrastReport       12.076  0.938  13.081
ct.makeQCReport              7.748  0.255   8.035
ct.stackGuides               7.090  0.433   7.537
ct.signalSummary             5.905  0.407   6.328
ct.GCbias                    5.776  0.417   6.309
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘unit.tests.R’
 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: 1 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.12-bioc/meat/gCrisprTools.Rcheck/00check.log’
for details.



Installation output

gCrisprTools.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL gCrisprTools
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘gCrisprTools’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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
* DONE (gCrisprTools)

Tests output

gCrisprTools.Rcheck/tests/unit.tests.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> #require("BiocGenerics", quietly = TRUE)
> BiocGenerics:::testPackage("gCrisprTools")


RUNIT TEST PROTOCOL -- Thu May  6 02:03:05 2021 
*********************************************** 
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
gCrisprTools RUnit Tests - 0 test functions, 0 errors, 0 failures
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 10.645   0.442  15.544 

Example timings

gCrisprTools.Rcheck/gCrisprTools-Ex.timings

nameusersystemelapsed
aln0.0030.0020.005
ann0.0880.0040.091
ct.CAT0.2020.0100.211
ct.DirectionalTests0.5380.3300.870
ct.GCbias5.7760.4176.309
ct.PRC1.0540.0251.085
ct.PantherPathwayEnrichment25.457 1.00027.421
ct.ROC0.2010.0070.208
ct.RRAaPvals0.4880.0140.502
ct.RRAalpha0.2760.0040.280
ct.alignmentChart0.0050.0010.006
ct.alphaBeta0.0160.0010.017
ct.buildSE0.5480.0110.560
ct.ecdf0.0010.0010.002
ct.filterReads0.3410.0200.361
ct.gRNARankByReplicate0.4500.0300.481
ct.generateResults0.5950.0520.648
ct.guideCDF14.861 6.58821.474
ct.inputCheck0.1450.0060.151
ct.makeContrastReport12.076 0.93813.081
ct.makeQCReport7.7480.2558.035
ct.makeReport26.069 2.23328.438
ct.multiGSEA0.2060.0030.210
ct.normalizeBySlope1.3470.0441.393
ct.normalizeFQ0.9140.1301.149
ct.normalizeFactoredQuantiles0.8330.0570.892
ct.normalizeGuides3.2150.2413.468
ct.normalizeMedians0.7160.0490.769
ct.normalizeNTC0.9120.0750.990
ct.normalizeSpline0.9460.0450.993
ct.prepareAnnotation0.6590.0420.704
ct.preprocessFit3.1350.0293.170
ct.rawCountDensities0.1760.0060.181
ct.resultCheck0.1410.0030.143
ct.signalSummary5.9050.4076.328
ct.stackGuides7.0900.4337.537
ct.targetSetEnrichment0.1510.0030.154
ct.topTargets0.5290.0090.539
ct.viewControls0.4310.0880.519
ct.viewGuides0.4490.0110.460
es0.0740.0020.076
essential.genes0.0020.0020.005
fit0.2120.0070.220
resultsDF0.1440.0040.155