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This page was generated on 2025-09-27 12:03 -0400 (Sat, 27 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4832
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4620
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4565
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: 2025-09-26 13:45 -0400 (Fri, 26 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 nebbiolo2

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: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:gCrisprTools.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings gCrisprTools_2.15.0.tar.gz
StartedAt: 2025-09-26 23:54:57 -0400 (Fri, 26 Sep 2025)
EndedAt: 2025-09-27 00:06:58 -0400 (Sat, 27 Sep 2025)
EllapsedTime: 721.7 seconds
RetCode: 0
Status:   OK  
CheckDir: gCrisprTools.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:gCrisprTools.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings gCrisprTools_2.15.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/gCrisprTools.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* 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 loading without being on the library search path ... 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            86.715  2.954  71.123
ct.makeReport         17.857  0.854  18.723
ct.seas               12.696  2.072  11.711
ct.guideCDF            9.157  0.426   9.583
ct.makeContrastReport  8.617  0.101   8.709
ct.compareContrasts    7.916  0.163   8.079
ct.upSet               7.307  0.483   7.833
ct.GCbias              6.395  0.424   6.826
ct.contrastBarchart    6.018  0.033   6.052
ct.makeQCReport        5.469  0.080   5.582
ct.stackGuides         4.667  0.544   5.213
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/gCrisprTools.Rcheck/00check.log’
for details.


Installation output

gCrisprTools.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL gCrisprTools
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-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 (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 -- Sat Sep 27 00:01:35 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 
  8.679   0.470   9.139 

Example timings

gCrisprTools.Rcheck/gCrisprTools-Ex.timings

nameusersystemelapsed
aln0.0020.0000.002
ann0.0580.0000.058
ct.CAT1.4260.2241.650
ct.DirectionalTests0.2420.0310.272
ct.GCbias6.3950.4246.826
ct.GREATdb86.715 2.95471.123
ct.PRC2.1180.0452.164
ct.ROC1.2800.0131.293
ct.RRAaPvals0.3070.0030.311
ct.RRAalpha0.2320.0050.237
ct.alignmentChart0.0040.0010.005
ct.alphaBeta0.0010.0000.000
ct.applyAlpha0.0000.0020.002
ct.buildSE0.3800.0030.383
ct.compareContrasts7.9160.1638.079
ct.contrastBarchart6.0180.0336.052
ct.expandAnnotation0.0580.0010.058
ct.filterReads0.2300.0080.238
ct.gRNARankByReplicate0.3860.0080.395
ct.generateResults0.4380.0100.448
ct.guideCDF9.1570.4269.583
ct.keyCheck0.0940.0010.095
ct.makeContrastReport8.6170.1018.709
ct.makeQCReport5.4690.0805.582
ct.makeReport17.857 0.85418.723
ct.makeRhoNull0.0010.0000.000
ct.normalizeBySlope1.2570.0451.302
ct.normalizeFQ0.8480.0420.889
ct.normalizeGuides3.0850.1463.231
ct.normalizeMedians0.7470.0310.778
ct.normalizeNTC0.8270.0170.843
ct.normalizeSpline0.9440.0510.994
ct.parseGeneSymbol0.0020.0000.002
ct.prepareAnnotation0.4950.0300.525
ct.preprocessFit1.6970.1781.880
ct.rankSimple3.9500.0694.041
ct.rawCountDensities0.1420.0060.148
ct.regularizeContrasts0.0890.0000.089
ct.resultCheck0.0550.0000.055
ct.scatter0.3440.0060.350
ct.seas12.696 2.07211.711
ct.seasPrep3.4720.5534.026
ct.signalSummary1.4690.0711.541
ct.simpleResult1.3080.1191.427
ct.softLog000
ct.stackGuides4.6670.5445.213
ct.targetSetEnrichment1.3690.1281.516
ct.topTargets0.3110.0080.320
ct.upSet7.3070.4837.833
ct.viewControls0.2240.0070.231
ct.viewGuides0.3060.0200.325
es0.0500.0040.054
essential.genes0.0020.0000.001
fit0.1810.0020.184
resultsDF0.0570.0000.058