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This page was generated on 2025-10-09 11:41 -0400 (Thu, 09 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4832
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4613
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4554
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4585
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 788/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gCrisprTools 2.14.0  (landing page)
Russell Bainer
Snapshot Date: 2025-10-06 13:40 -0400 (Mon, 06 Oct 2025)
git_url: https://git.bioconductor.org/packages/gCrisprTools
git_branch: RELEASE_3_21
git_last_commit: d9fd3ad
git_last_commit_date: 2025-04-15 11:04:56 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for gCrisprTools on kunpeng2

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: gCrisprTools
Version: 2.14.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:gCrisprTools.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings gCrisprTools_2.14.0.tar.gz
StartedAt: 2025-10-07 09:35:07 -0000 (Tue, 07 Oct 2025)
EndedAt: 2025-10-07 09:42:43 -0000 (Tue, 07 Oct 2025)
EllapsedTime: 456.4 seconds
RetCode: 0
Status:   OK  
CheckDir: gCrisprTools.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:gCrisprTools.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings gCrisprTools_2.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/gCrisprTools.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gCrisprTools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gCrisprTools’ version ‘2.14.0’
* 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.guideCDF           45.533  0.367  45.998
ct.makeReport         24.999  0.484  25.561
ct.compareContrasts   14.986  0.194  15.220
ct.makeContrastReport 12.865  0.454  13.398
ct.upSet              12.669  0.200  12.899
ct.seas                9.624  0.813  10.065
ct.contrastBarchart    9.945  0.120  10.090
ct.GREATdb             7.453  0.191   7.649
ct.makeQCReport        6.766  0.230   7.028
ct.stackGuides         6.575  0.239   6.830
ct.GCbias              5.922  0.224   6.158
ct.rankSimple          5.899  0.060   5.972
ct.seasPrep            4.367  0.682   5.061
* 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
  ‘/home/biocbuild/bbs-3.21-bioc/meat/gCrisprTools.Rcheck/00check.log’
for details.


Installation output

gCrisprTools.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL gCrisprTools
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’
* installing *source* package ‘gCrisprTools’ ...
** this is package ‘gCrisprTools’ version ‘2.14.0’
** 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 Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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 -- Tue Oct  7 09:42:38 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 
 10.285   0.603  10.898 

Example timings

gCrisprTools.Rcheck/gCrisprTools-Ex.timings

nameusersystemelapsed
aln0.0020.0000.003
ann0.0580.0000.058
ct.CAT2.2680.1162.390
ct.DirectionalTests0.2320.0430.277
ct.GCbias5.9220.2246.158
ct.GREATdb7.4530.1917.649
ct.PRC2.8890.0962.993
ct.ROC2.0910.0402.136
ct.RRAaPvals0.3880.0040.392
ct.RRAalpha0.2300.0040.234
ct.alignmentChart0.0060.0000.006
ct.alphaBeta0.0010.0000.000
ct.applyAlpha0.0020.0000.001
ct.buildSE0.3930.0320.426
ct.compareContrasts14.986 0.19415.220
ct.contrastBarchart 9.945 0.12010.090
ct.expandAnnotation0.0580.0070.066
ct.filterReads0.4140.0040.418
ct.gRNARankByReplicate0.4620.0320.497
ct.generateResults0.6050.0080.615
ct.guideCDF45.533 0.36745.998
ct.keyCheck0.120.000.12
ct.makeContrastReport12.865 0.45413.398
ct.makeQCReport6.7660.2307.028
ct.makeReport24.999 0.48425.561
ct.makeRhoNull0.0010.0000.001
ct.normalizeBySlope1.3870.0361.426
ct.normalizeFQ0.8990.0070.910
ct.normalizeGuides3.5260.0593.595
ct.normalizeMedians0.7500.0160.767
ct.normalizeNTC0.8810.0120.895
ct.normalizeSpline1.1010.0081.114
ct.parseGeneSymbol0.0020.0000.002
ct.prepareAnnotation0.6830.0160.700
ct.preprocessFit2.6330.0802.720
ct.rankSimple5.8990.0605.972
ct.rawCountDensities0.1830.0000.184
ct.regularizeContrasts0.1200.0060.126
ct.resultCheck0.0510.0040.055
ct.scatter0.5550.0320.589
ct.seas 9.624 0.81310.065
ct.seasPrep4.3670.6825.061
ct.signalSummary2.2630.1202.387
ct.simpleResult2.0930.0962.192
ct.softLog000
ct.stackGuides6.5750.2396.830
ct.targetSetEnrichment2.0190.0802.103
ct.topTargets0.3140.0000.315
ct.upSet12.669 0.20012.899
ct.viewControls0.3240.0160.340
ct.viewGuides0.3210.0160.338
es0.0480.0000.048
essential.genes0.0010.0000.001
fit0.1560.0000.156
resultsDF0.0620.0000.062