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This page was generated on 2024-03-27 11:39:27 -0400 (Wed, 27 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4698
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" 4436
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4461
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" 4376
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 773/2264HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gCrisprTools 2.9.0  (landing page)
Russell Bainer
Snapshot Date: 2024-03-26 14:00:18 -0400 (Tue, 26 Mar 2024)
git_url: https://git.bioconductor.org/packages/gCrisprTools
git_branch: devel
git_last_commit: 5d5f6da
git_last_commit_date: 2023-10-24 10:52:32 -0400 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for gCrisprTools on lconway


To the developers/maintainers of the gCrisprTools package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: gCrisprTools
Version: 2.9.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:gCrisprTools.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings gCrisprTools_2.9.0.tar.gz
StartedAt: 2024-03-26 20:43:53 -0400 (Tue, 26 Mar 2024)
EndedAt: 2024-03-26 20:50:49 -0400 (Tue, 26 Mar 2024)
EllapsedTime: 416.6 seconds
RetCode: 0
Status:   OK  
CheckDir: gCrisprTools.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:gCrisprTools.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings gCrisprTools_2.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/gCrisprTools.Rcheck’
* using R Under development (unstable) (2024-03-18 r86148)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gCrisprTools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gCrisprTools’ version ‘2.9.0’
* 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 ... OK
* 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 code 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 ... NOTE
Namespace in Imports field not imported from: ‘RobustRankAggreg’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 ... NOTE
Documented arguments not in \usage in Rd file 'ct.targetSetEnrichment.Rd':
  ‘pvalue.cutoff’ ‘organism’ ‘db.cut’ ‘species’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
ct.GREATdb            29.066  2.003  31.492
ct.makeReport         20.391  3.349  24.206
ct.guideCDF           12.958  9.869  23.313
ct.compareContrasts   10.649  0.960  11.790
ct.makeContrastReport  9.326  2.270  11.920
ct.seas                9.004  1.099  10.005
ct.upSet               8.126  0.904   9.141
ct.stackGuides         5.502  1.860   7.476
ct.contrastBarchart    7.173  0.137   7.430
ct.GCbias              5.556  0.439   6.089
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘unit.tests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/gCrisprTools.Rcheck/00check.log’
for details.


Installation output

gCrisprTools.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/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 Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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 -- Tue Mar 26 20:50:38 2024 
*********************************************** 
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 
  8.997   0.548   9.650 

Example timings

gCrisprTools.Rcheck/gCrisprTools-Ex.timings

nameusersystemelapsed
aln0.0030.0020.005
ann0.0700.0040.075
ct.CAT2.3330.1482.520
ct.DirectionalTests0.3300.2490.589
ct.GCbias5.5560.4396.089
ct.GREATdb29.066 2.00331.492
ct.PRC2.5360.5153.100
ct.ROC1.7250.0361.793
ct.RRAaPvals0.3570.0190.380
ct.RRAalpha0.2520.0140.272
ct.alignmentChart0.0060.0010.008
ct.alphaBeta000
ct.applyAlpha0.0020.0050.008
ct.buildSE0.4220.0260.451
ct.compareContrasts10.649 0.96011.790
ct.contrastBarchart7.1730.1377.430
ct.expandAnnotation0.0690.0030.073
ct.filterReads0.2630.0200.288
ct.gRNARankByReplicate0.3890.0440.441
ct.generateResults0.5300.0250.562
ct.guideCDF12.958 9.86923.313
ct.keyCheck0.1150.0140.131
ct.makeContrastReport 9.326 2.27011.920
ct.makeQCReport4.1070.5574.775
ct.makeReport20.391 3.34924.206
ct.makeRhoNull0.0010.0000.001
ct.normalizeBySlope1.3800.0951.500
ct.normalizeFQ0.8130.0720.906
ct.normalizeGuides3.0370.3583.499
ct.normalizeMedians0.6690.0770.760
ct.normalizeNTC0.8380.0710.924
ct.normalizeSpline0.9690.0841.085
ct.parseGeneSymbol0.0020.0010.003
ct.prepareAnnotation0.6580.4801.186
ct.preprocessFit2.1420.0652.231
ct.rankSimple4.5280.0634.653
ct.rawCountDensities0.1580.0160.175
ct.regularizeContrasts0.1030.0030.106
ct.resultCheck0.0590.0020.061
ct.scatter0.4140.0190.439
ct.seas 9.004 1.09910.005
ct.seasPrep2.5790.3022.922
ct.signalSummary1.6890.0581.773
ct.simpleResult1.4150.1141.548
ct.softLog0.0010.0000.000
ct.stackGuides5.5021.8607.476
ct.targetSetEnrichment1.4120.0611.495
ct.topTargets0.3430.0250.373
ct.upSet8.1260.9049.141
ct.viewControls0.2260.0220.253
ct.viewGuides0.3380.0180.359
es0.0600.0100.072
essential.genes0.0010.0020.003
fit0.2000.0160.221
resultsDF0.0640.0030.068