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

This page was generated on 2025-08-30 12:08 -0400 (Sat, 30 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4615
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4562
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4541
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 784/2320HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gCrisprTools 2.15.0  (landing page)
Russell Bainer
Snapshot Date: 2025-08-29 13:45 -0400 (Fri, 29 Aug 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 taishan

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: 2.15.0
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_2.15.0.tar.gz
StartedAt: 2025-08-29 07:23:13 -0000 (Fri, 29 Aug 2025)
EndedAt: 2025-08-29 07:31:15 -0000 (Fri, 29 Aug 2025)
EllapsedTime: 481.6 seconds
RetCode: 0
Status:   OK  
CheckDir: gCrisprTools.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_2.15.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/gCrisprTools.Rcheck’
* using R version 4.5.0 (2025-04-11)
* 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)
* 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 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            75.603  1.197  76.706
ct.guideCDF           28.921  0.164  29.156
ct.makeReport         21.946  0.364  22.376
ct.compareContrasts   12.983  0.486  13.507
ct.seas               11.789  1.307  12.464
ct.upSet              11.905  0.627  12.565
ct.makeContrastReport 10.520  0.172  10.761
ct.contrastBarchart    9.584  0.024   9.636
ct.makeQCReport        6.345  0.088   6.468
ct.stackGuides         5.495  0.770   6.282
ct.rankSimple          5.844  0.198   6.058
ct.GCbias              5.786  0.148   5.945
* 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-3.22-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-4.5.0/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 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
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 -- Fri Aug 29 07:31:10 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 
  9.899   0.349  10.252 

Example timings

gCrisprTools.Rcheck/gCrisprTools-Ex.timings

nameusersystemelapsed
aln0.0030.0000.002
ann0.0550.0040.059
ct.CAT2.0610.1602.226
ct.DirectionalTests0.2390.0440.283
ct.GCbias5.7860.1485.945
ct.GREATdb75.603 1.19776.706
ct.PRC4.4180.0324.462
ct.ROC2.0560.0002.062
ct.RRAaPvals0.3600.0000.361
ct.RRAalpha0.2360.0000.237
ct.alignmentChart0.0060.0000.006
ct.alphaBeta000
ct.applyAlpha0.0000.0020.002
ct.buildSE0.4130.0020.415
ct.compareContrasts12.983 0.48613.507
ct.contrastBarchart9.5840.0249.636
ct.expandAnnotation0.0660.0000.065
ct.filterReads0.3330.0040.337
ct.gRNARankByReplicate0.4050.0120.418
ct.generateResults0.6120.0040.617
ct.guideCDF28.921 0.16429.156
ct.keyCheck0.1270.0040.131
ct.makeContrastReport10.520 0.17210.761
ct.makeQCReport6.3450.0886.468
ct.makeReport21.946 0.36422.376
ct.makeRhoNull0.0010.0000.001
ct.normalizeBySlope1.3700.0201.393
ct.normalizeFQ0.8810.1201.003
ct.normalizeGuides3.3860.1753.571
ct.normalizeMedians0.7510.0320.788
ct.normalizeNTC0.8580.0400.900
ct.normalizeSpline1.0150.0581.075
ct.parseGeneSymbol0.0020.0000.002
ct.prepareAnnotation0.6500.0280.679
ct.preprocessFit2.7910.1912.989
ct.rankSimple5.8440.1986.058
ct.rawCountDensities0.1830.0040.188
ct.regularizeContrasts0.1140.0000.114
ct.resultCheck0.060.000.06
ct.scatter0.4960.0000.497
ct.seas11.789 1.30712.464
ct.seasPrep3.3480.4823.843
ct.signalSummary2.2380.1872.432
ct.simpleResult1.9740.1842.164
ct.softLog0.0010.0000.000
ct.stackGuides5.4950.7706.282
ct.targetSetEnrichment2.0110.1232.140
ct.topTargets0.3070.0120.320
ct.upSet11.905 0.62712.565
ct.viewControls0.2930.0240.319
ct.viewGuides0.4260.0350.463
es0.0500.0000.049
essential.genes0.0020.0000.001
fit0.160.000.16
resultsDF0.0630.0080.071