Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-09-17 11:41 -0400 (Tue, 17 Sep 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4445 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4450 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4483 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4430 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4428 |
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 765/2258 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
gCrisprTools 2.11.0 (landing page) Russell Bainer
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
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: 2.11.0 |
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_2.11.0.tar.gz |
StartedAt: 2024-09-16 21:23:18 -0400 (Mon, 16 Sep 2024) |
EndedAt: 2024-09-16 21:25:28 -0400 (Mon, 16 Sep 2024) |
EllapsedTime: 129.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: gCrisprTools.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### 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_2.11.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/gCrisprTools.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.6.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘gCrisprTools/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘gCrisprTools’ version ‘2.11.0’ * 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 9.749 0.480 9.772 ct.guideCDF 5.566 2.080 7.653 ct.makeReport 6.020 0.938 6.973 * 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-3.20-bioc/meat/gCrisprTools.Rcheck/00check.log’ for details.
gCrisprTools.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL gCrisprTools ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘gCrisprTools’ ... ** 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 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-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 16 21:25:24 2024 *********************************************** 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 2.829 0.112 2.943
gCrisprTools.Rcheck/gCrisprTools-Ex.timings
name | user | system | elapsed | |
aln | 0.001 | 0.000 | 0.002 | |
ann | 0.024 | 0.001 | 0.025 | |
ct.CAT | 0.686 | 0.022 | 0.708 | |
ct.DirectionalTests | 0.112 | 0.066 | 0.178 | |
ct.GCbias | 2.440 | 0.107 | 2.550 | |
ct.GREATdb | 9.749 | 0.480 | 9.772 | |
ct.PRC | 1.099 | 0.063 | 0.969 | |
ct.ROC | 0.453 | 0.005 | 0.462 | |
ct.RRAaPvals | 0.135 | 0.011 | 0.146 | |
ct.RRAalpha | 0.111 | 0.006 | 0.117 | |
ct.alignmentChart | 0.002 | 0.001 | 0.003 | |
ct.alphaBeta | 0 | 0 | 0 | |
ct.applyAlpha | 0.001 | 0.001 | 0.002 | |
ct.buildSE | 0.178 | 0.008 | 0.187 | |
ct.compareContrasts | 3.547 | 0.296 | 3.843 | |
ct.contrastBarchart | 2.033 | 0.021 | 2.054 | |
ct.expandAnnotation | 0.027 | 0.001 | 0.029 | |
ct.filterReads | 0.091 | 0.011 | 0.102 | |
ct.gRNARankByReplicate | 0.137 | 0.012 | 0.151 | |
ct.generateResults | 0.185 | 0.013 | 0.199 | |
ct.guideCDF | 5.566 | 2.080 | 7.653 | |
ct.keyCheck | 0.040 | 0.005 | 0.044 | |
ct.makeContrastReport | 2.821 | 0.450 | 3.303 | |
ct.makeQCReport | 1.409 | 0.175 | 1.602 | |
ct.makeReport | 6.020 | 0.938 | 6.973 | |
ct.makeRhoNull | 0 | 0 | 0 | |
ct.normalizeBySlope | 0.559 | 0.035 | 0.597 | |
ct.normalizeFQ | 0.310 | 0.031 | 0.342 | |
ct.normalizeGuides | 1.180 | 0.100 | 1.283 | |
ct.normalizeMedians | 0.257 | 0.024 | 0.281 | |
ct.normalizeNTC | 0.318 | 0.029 | 0.347 | |
ct.normalizeSpline | 0.376 | 0.036 | 0.412 | |
ct.parseGeneSymbol | 0.001 | 0.000 | 0.000 | |
ct.prepareAnnotation | 0.246 | 0.065 | 0.311 | |
ct.preprocessFit | 0.508 | 0.016 | 0.524 | |
ct.rankSimple | 1.246 | 0.008 | 1.254 | |
ct.rawCountDensities | 0.055 | 0.005 | 0.059 | |
ct.regularizeContrasts | 0.038 | 0.001 | 0.039 | |
ct.resultCheck | 0.026 | 0.001 | 0.027 | |
ct.scatter | 0.119 | 0.002 | 0.120 | |
ct.seas | 4.507 | 0.370 | 3.740 | |
ct.seasPrep | 0.901 | 0.098 | 0.815 | |
ct.signalSummary | 0.502 | 0.011 | 0.513 | |
ct.simpleResult | 0.453 | 0.028 | 0.482 | |
ct.softLog | 0 | 0 | 0 | |
ct.stackGuides | 1.723 | 0.325 | 2.048 | |
ct.targetSetEnrichment | 0.438 | 0.008 | 0.446 | |
ct.topTargets | 0.146 | 0.010 | 0.157 | |
ct.upSet | 2.824 | 0.492 | 3.316 | |
ct.viewControls | 0.079 | 0.024 | 0.103 | |
ct.viewGuides | 0.120 | 0.007 | 0.128 | |
es | 0.023 | 0.003 | 0.027 | |
essential.genes | 0.000 | 0.001 | 0.001 | |
fit | 0.077 | 0.004 | 0.081 | |
resultsDF | 0.026 | 0.002 | 0.026 | |