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This page was generated on 2021-10-15 15:05:41 -0400 (Fri, 15 Oct 2021).

CHECK results for gCrisprTools on nebbiolo1

To the developers/maintainers of the gCrisprTools package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/gCrisprTools.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 695/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gCrisprTools 1.20.0  (landing page)
Russell Bainer
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/gCrisprTools
git_branch: RELEASE_3_13
git_last_commit: ea57239
git_last_commit_date: 2021-05-19 12:22:51 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: gCrisprTools
Version: 1.20.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:gCrisprTools.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings gCrisprTools_1.20.0.tar.gz
StartedAt: 2021-10-14 09:54:51 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 09:59:43 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 292.3 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: gCrisprTools.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:gCrisprTools.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings gCrisprTools_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/gCrisprTools.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (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 ‘1.20.0’
* 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    1.3Mb
* 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.PantherPathwayEnrichment 22.400  1.155  24.705
ct.makeReport               18.992  0.198  19.193
ct.guideCDF                 11.384  0.116  11.500
ct.makeContrastReport        8.299  0.200   8.512
ct.GCbias                    6.416  0.156   6.640
ct.signalSummary             6.155  0.080   6.235
ct.makeQCReport              5.178  0.146   5.329
ct.stackGuides               4.995  0.035   5.031
* 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
  ‘/home/biocbuild/bbs-3.13-bioc/meat/gCrisprTools.Rcheck/00check.log’
for details.



Installation output

gCrisprTools.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL gCrisprTools
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/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 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 Oct 14 09:59:39 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 
  7.301   0.360   7.642 

Example timings

gCrisprTools.Rcheck/gCrisprTools-Ex.timings

nameusersystemelapsed
aln0.0020.0010.003
ann0.7490.0140.762
ct.CAT0.1400.0040.143
ct.DirectionalTests0.2370.3480.586
ct.GCbias6.4160.1566.640
ct.PRC0.9000.0280.929
ct.PantherPathwayEnrichment22.400 1.15524.705
ct.ROC0.1470.0110.159
ct.RRAaPvals0.4910.0040.494
ct.RRAalpha0.2500.0240.275
ct.alignmentChart0.0050.0000.005
ct.alphaBeta0.0130.0000.014
ct.buildSE0.4440.0040.448
ct.ecdf0.0010.0000.001
ct.filterReads1.3900.0121.403
ct.gRNARankByReplicate0.440.000.44
ct.generateResults0.4450.0030.448
ct.guideCDF11.384 0.11611.500
ct.inputCheck0.0830.0080.091
ct.makeContrastReport8.2990.2008.512
ct.makeQCReport5.1780.1465.329
ct.makeReport18.992 0.19819.193
ct.multiGSEA0.1510.0120.163
ct.normalizeBySlope1.3020.0351.338
ct.normalizeFQ0.8690.0200.889
ct.normalizeFactoredQuantiles0.8250.0120.837
ct.normalizeGuides3.2990.0433.343
ct.normalizeMedians0.7180.0150.734
ct.normalizeNTC0.8590.0310.891
ct.normalizeSpline1.0380.0081.046
ct.prepareAnnotation0.4750.0070.483
ct.preprocessFit1.4530.0001.453
ct.rawCountDensities0.1470.0000.146
ct.resultCheck0.0970.0000.097
ct.signalSummary6.1550.0806.235
ct.stackGuides4.9950.0355.031
ct.targetSetEnrichment0.0980.0080.106
ct.topTargets0.3350.0080.342
ct.viewControls0.2160.0160.231
ct.viewGuides0.2750.0120.287
es0.0460.0000.047
essential.genes0.0020.0000.002
fit0.1500.0080.158
resultsDF0.0970.0040.100