Back to Multiple platform build/check report for BioC 3.22:   simplified   long
ABCDEF[G]HIJKLMNOPQRSTUVWXYZ

This page was generated on 2025-09-23 12:04 -0400 (Tue, 23 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4816
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4605
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4549
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4560
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: 2025-09-22 13:45 -0400 (Mon, 22 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: 2025-09-22 21:09:46 -0400 (Mon, 22 Sep 2025)
EndedAt: 2025-09-22 21:17:43 -0400 (Mon, 22 Sep 2025)
EllapsedTime: 477.2 seconds
RetCode: 0
Status:   OK  
CheckDir: gCrisprTools.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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            80.805  2.146  83.905
ct.guideCDF           11.887 11.127  23.869
ct.makeReport         17.582  3.419  21.306
ct.seas               10.247  0.926  11.129
ct.makeContrastReport  8.853  2.080  11.253
ct.compareContrasts    9.476  0.801  10.402
ct.upSet               8.207  1.040   9.331
ct.contrastBarchart    6.948  0.065   7.234
ct.stackGuides         5.190  1.279   6.550
ct.GCbias              5.855  0.495   6.587
* 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 -- Mon Sep 22 21:17:32 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 
  9.115   0.495   9.689 

Example timings

gCrisprTools.Rcheck/gCrisprTools-Ex.timings

nameusersystemelapsed
aln0.0020.0030.007
ann0.0670.0050.072
ct.CAT1.7620.1301.914
ct.DirectionalTests0.2780.5500.932
ct.GCbias5.8550.4956.587
ct.GREATdb80.805 2.14683.905
ct.PRC2.4560.2572.740
ct.ROC1.4440.0191.471
ct.RRAaPvals0.2990.0150.318
ct.RRAalpha0.2160.0100.228
ct.alignmentChart0.0050.0010.006
ct.alphaBeta000
ct.applyAlpha0.0020.0070.009
ct.buildSE0.3980.0160.419
ct.compareContrasts 9.476 0.80110.402
ct.contrastBarchart6.9480.0657.234
ct.expandAnnotation0.0570.0010.059
ct.filterReads0.2330.0110.245
ct.gRNARankByReplicate0.3740.0330.412
ct.generateResults0.4500.0140.466
ct.guideCDF11.88711.12723.869
ct.keyCheck0.1300.0130.145
ct.makeContrastReport 8.853 2.08011.253
ct.makeQCReport3.8480.4524.454
ct.makeReport17.582 3.41921.306
ct.makeRhoNull0.0000.0000.001
ct.normalizeBySlope1.2820.0831.382
ct.normalizeFQ0.7990.0610.879
ct.normalizeGuides2.7940.2283.059
ct.normalizeMedians0.6420.0610.708
ct.normalizeNTC0.7720.0540.833
ct.normalizeSpline0.8970.0610.970
ct.parseGeneSymbol0.0020.0010.002
ct.prepareAnnotation0.5430.0270.575
ct.preprocessFit1.8220.5332.391
ct.rankSimple4.1730.1404.352
ct.rawCountDensities0.1560.0110.169
ct.regularizeContrasts0.1010.0030.105
ct.resultCheck0.0610.0020.065
ct.scatter0.4010.0060.413
ct.seas10.247 0.92611.129
ct.seasPrep2.3460.2442.619
ct.signalSummary1.5280.0411.586
ct.simpleResult1.4060.1661.588
ct.softLog0.0000.0000.001
ct.stackGuides5.1901.2796.550
ct.targetSetEnrichment1.3790.5641.972
ct.topTargets0.3010.0150.321
ct.upSet8.2071.0409.331
ct.viewControls0.2510.0240.282
ct.viewGuides0.2720.0120.285
es0.0530.0060.060
essential.genes0.0010.0020.003
fit0.1380.0090.147
resultsDF0.0670.0030.070