| Back to Multiple platform build/check report for BioC 3.24: simplified long |
|
This page was generated on 2026-05-19 12:54 -0400 (Tue, 19 May 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 RC (2026-04-17 r89917) -- "Because it was There" | 4898 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.6.0 Patched (2026-05-01 r89994) -- "Because it was There" | 4617 |
| 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 809/2377 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| gCrisprTools 2.19.0 (landing page) Russell Bainer
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | OK | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | ||||||||||
| See other builds for gCrisprTools in R Universe. | ||||||||||||||
|
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. |
| Package: gCrisprTools |
| Version: 2.19.0 |
| 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_2.19.0.tar.gz |
| StartedAt: 2026-05-18 21:39:22 -0400 (Mon, 18 May 2026) |
| EndedAt: 2026-05-18 21:42:00 -0400 (Mon, 18 May 2026) |
| EllapsedTime: 157.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: gCrisprTools.Rcheck |
| Warnings: 0 |
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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_2.19.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.24-bioc/meat/gCrisprTools.Rcheck’
* using R version 4.6.0 Patched (2026-05-01 r89994)
* using platform: aarch64-apple-darwin23
* R was compiled by
Apple clang version 17.0.0 (clang-1700.3.19.1)
GNU Fortran (GCC) 14.2.0
* running under: macOS Tahoe 26.3.1
* using session charset: UTF-8
* current time: 2026-05-19 01:39:22 UTC
* using option ‘--no-vignettes’
* checking for file ‘gCrisprTools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gCrisprTools’ version ‘2.19.0’
* 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 ... OK
* 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 ... OK
* 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 28.356 0.346 28.688
ct.makeReport 6.280 0.153 6.447
ct.guideCDF 5.714 0.328 6.052
* 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: OK
gCrisprTools.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL gCrisprTools ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/library’ * installing *source* package ‘gCrisprTools’ ... ** this is package ‘gCrisprTools’ version ‘2.19.0’ ** 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)
gCrisprTools.Rcheck/tests/unit.tests.Rout
R version 4.6.0 Patched (2026-05-01 r89994) -- "Because it was There"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin23
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 May 18 21:41:55 2026
***********************************************
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
3.122 0.108 3.246
gCrisprTools.Rcheck/gCrisprTools-Ex.timings
| name | user | system | elapsed | |
| aln | 0.001 | 0.001 | 0.001 | |
| ann | 0.024 | 0.001 | 0.025 | |
| ct.CAT | 0.774 | 0.014 | 0.789 | |
| ct.DirectionalTests | 0.110 | 0.076 | 0.186 | |
| ct.GCbias | 2.160 | 0.090 | 2.253 | |
| ct.GREATdb | 28.356 | 0.346 | 28.688 | |
| ct.PRC | 0.923 | 0.028 | 0.951 | |
| ct.ROC | 0.490 | 0.003 | 0.494 | |
| ct.RRAaPvals | 0.124 | 0.006 | 0.129 | |
| ct.RRAalpha | 0.098 | 0.002 | 0.100 | |
| ct.alignmentChart | 0.002 | 0.000 | 0.003 | |
| ct.alphaBeta | 0 | 0 | 0 | |
| ct.applyAlpha | 0.001 | 0.001 | 0.002 | |
| ct.buildSE | 0.161 | 0.002 | 0.166 | |
| ct.compareContrasts | 3.077 | 0.089 | 3.188 | |
| ct.contrastBarchart | 2.090 | 0.004 | 2.095 | |
| ct.expandAnnotation | 0.029 | 0.001 | 0.030 | |
| ct.filterReads | 0.093 | 0.005 | 0.099 | |
| ct.gRNARankByReplicate | 0.139 | 0.008 | 0.147 | |
| ct.generateResults | 0.174 | 0.006 | 0.178 | |
| ct.guideCDF | 5.714 | 0.328 | 6.052 | |
| ct.keyCheck | 0.041 | 0.002 | 0.042 | |
| ct.makeContrastReport | 3.028 | 0.118 | 3.182 | |
| ct.makeQCReport | 1.379 | 0.115 | 1.507 | |
| ct.makeReport | 6.280 | 0.153 | 6.447 | |
| ct.makeRhoNull | 0 | 0 | 0 | |
| ct.normalizeBySlope | 0.561 | 0.018 | 0.580 | |
| ct.normalizeFQ | 0.307 | 0.012 | 0.319 | |
| ct.normalizeGenewise | 0.710 | 0.022 | 0.732 | |
| ct.normalizeGuides | 1.166 | 0.067 | 1.241 | |
| ct.normalizeMedians | 0.254 | 0.013 | 0.268 | |
| ct.normalizeNTC | 0.317 | 0.022 | 0.348 | |
| ct.normalizeSpline | 0.377 | 0.015 | 0.392 | |
| ct.parseGeneSymbol | 0.000 | 0.000 | 0.001 | |
| ct.prepareAnnotation | 0.219 | 0.003 | 0.224 | |
| ct.preprocessFit | 0.514 | 0.009 | 0.524 | |
| ct.rankSimple | 1.261 | 0.006 | 1.269 | |
| ct.rawCountDensities | 0.058 | 0.003 | 0.061 | |
| ct.regularizeContrasts | 0.039 | 0.001 | 0.039 | |
| ct.resultCheck | 0.025 | 0.000 | 0.026 | |
| ct.scatter | 0.116 | 0.001 | 0.118 | |
| ct.seas | 4.044 | 0.669 | 4.511 | |
| ct.seasPrep | 0.746 | 0.135 | 0.885 | |
| ct.signalSummary | 0.495 | 0.034 | 0.535 | |
| ct.simpleResult | 0.467 | 0.068 | 0.535 | |
| ct.softLog | 0 | 0 | 0 | |
| ct.stackGuides | 1.895 | 0.198 | 2.107 | |
| ct.targetSetEnrichment | 0.433 | 0.002 | 0.436 | |
| ct.topTargets | 0.131 | 0.003 | 0.135 | |
| ct.upSet | 2.767 | 0.305 | 3.081 | |
| ct.viewControls | 0.084 | 0.009 | 0.093 | |
| ct.viewGuides | 0.114 | 0.005 | 0.118 | |
| es | 0.022 | 0.001 | 0.023 | |
| essential.genes | 0.000 | 0.000 | 0.001 | |
| fit | 0.063 | 0.002 | 0.065 | |
| resultsDF | 0.022 | 0.001 | 0.023 | |
| se | 0.028 | 0.001 | 0.028 | |