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This page was generated on 2025-09-26 12:04 -0400 (Fri, 26 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4831
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4619
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4563
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4563
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 789/2334HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gCrisprTools 2.15.0  (landing page)
Russell Bainer
Snapshot Date: 2025-09-25 13:45 -0400 (Thu, 25 Sep 2025)
git_url: https://git.bioconductor.org/packages/gCrisprTools
git_branch: devel
git_last_commit: eaa1795
git_last_commit_date: 2025-04-15 11:04:56 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  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
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / 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: 2.15.0
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_2.15.0.tar.gz
StartedAt: 2025-09-25 21:16:33 -0400 (Thu, 25 Sep 2025)
EndedAt: 2025-09-25 21:24:26 -0400 (Thu, 25 Sep 2025)
EllapsedTime: 472.5 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_2.15.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/gCrisprTools.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gCrisprTools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gCrisprTools’ version ‘2.15.0’
* 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            81.956  2.334  85.285
ct.guideCDF           11.651 11.777  24.157
ct.makeReport         17.484  3.020  20.762
ct.makeContrastReport  9.224  2.016  11.603
ct.seas                9.991  0.999  10.902
ct.compareContrasts    9.574  0.818  10.528
ct.upSet               8.305  1.122   9.536
ct.contrastBarchart    6.783  0.067   6.924
ct.stackGuides         5.205  1.241   6.525
ct.GCbias              5.482  0.392   5.958
* 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-3.22-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/4.5-x86_64/Resources/library’
* installing *source* package ‘gCrisprTools’ ...
** this is package ‘gCrisprTools’ version ‘2.15.0’
** 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 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 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 -- Thu Sep 25 21:24:14 2025 
*********************************************** 
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 
  9.170   0.489   9.742 

Example timings

gCrisprTools.Rcheck/gCrisprTools-Ex.timings

nameusersystemelapsed
aln0.0020.0030.005
ann0.0760.0030.080
ct.CAT1.7130.1331.867
ct.DirectionalTests0.2740.2930.574
ct.GCbias5.4820.3925.958
ct.GREATdb81.956 2.33485.285
ct.PRC2.4770.2892.794
ct.ROC1.5770.0201.612
ct.RRAaPvals0.3140.0150.337
ct.RRAalpha0.2110.0090.222
ct.alignmentChart0.0050.0020.007
ct.alphaBeta0.0000.0000.001
ct.applyAlpha0.0010.0060.007
ct.buildSE0.4090.0140.428
ct.compareContrasts 9.574 0.81810.528
ct.contrastBarchart6.7830.0676.924
ct.expandAnnotation0.0740.0020.077
ct.filterReads0.2660.0120.281
ct.gRNARankByReplicate0.3920.0310.431
ct.generateResults0.4930.0170.513
ct.guideCDF11.65111.77724.157
ct.keyCheck0.1240.0080.133
ct.makeContrastReport 9.224 2.01611.603
ct.makeQCReport3.9920.4694.570
ct.makeReport17.484 3.02020.762
ct.makeRhoNull0.0000.0000.001
ct.normalizeBySlope1.2720.0611.347
ct.normalizeFQ0.7430.0630.813
ct.normalizeGuides2.9250.2283.200
ct.normalizeMedians0.6430.0520.708
ct.normalizeNTC0.7940.0700.875
ct.normalizeSpline0.9040.0670.983
ct.parseGeneSymbol0.0010.0010.003
ct.prepareAnnotation0.5470.0200.570
ct.preprocessFit1.8910.4702.390
ct.rankSimple4.2780.1454.473
ct.rawCountDensities0.1480.0100.162
ct.regularizeContrasts0.0990.0020.101
ct.resultCheck0.0520.0020.054
ct.scatter0.3380.0040.343
ct.seas 9.991 0.99910.902
ct.seasPrep2.3920.2592.681
ct.signalSummary1.5160.0441.576
ct.simpleResult1.3790.1821.574
ct.softLog0.0000.0000.001
ct.stackGuides5.2051.2416.525
ct.targetSetEnrichment1.3470.5751.940
ct.topTargets0.3040.0110.318
ct.upSet8.3051.1229.536
ct.viewControls0.2680.0150.288
ct.viewGuides0.2770.0110.291
es0.0520.0050.058
essential.genes0.0010.0020.004
fit0.1450.0090.155
resultsDF0.0630.0050.069