| Back to Mac ARM64 build report for BioC 3.18 |
|
This page was generated on 2024-04-18 11:32:10 -0400 (Thu, 18 Apr 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson1 | macOS 13.6.1 Ventura | arm64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4388 |
| 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 772/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| gCrisprTools 2.8.0 (landing page) Russell Bainer
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | OK | OK | OK | OK |  | |||||||
|
To the developers/maintainers of the gCrisprTools package: - 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: 2.8.0 |
| 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_2.8.0.tar.gz |
| StartedAt: 2024-04-17 14:16:38 -0400 (Wed, 17 Apr 2024) |
| EndedAt: 2024-04-17 14:23:22 -0400 (Wed, 17 Apr 2024) |
| EllapsedTime: 403.8 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_2.8.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/gCrisprTools.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-apple-darwin20 (64-bit)
* 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 13.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gCrisprTools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gCrisprTools’ version ‘2.8.0’
* 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 R 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 ... 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 31.018 1.655 32.766
ct.guideCDF 19.002 6.877 25.990
ct.makeReport 18.244 2.583 20.978
ct.compareContrasts 9.701 1.061 10.784
ct.upSet 9.042 1.184 10.252
ct.makeContrastReport 8.735 1.261 10.146
ct.seas 8.883 0.814 9.567
ct.GCbias 7.680 0.314 8.012
ct.stackGuides 5.415 1.201 6.628
ct.contrastBarchart 6.145 0.061 6.213
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘unit.tests.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/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/4.3-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 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (64-bit)
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 -- Wed Apr 17 14:23:11 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
9.269 0.380 9.655
gCrisprTools.Rcheck/gCrisprTools-Ex.timings
| name | user | system | elapsed | |
| aln | 0.004 | 0.002 | 0.005 | |
| ann | 0.091 | 0.004 | 0.096 | |
| ct.CAT | 1.449 | 0.069 | 1.518 | |
| ct.DirectionalTests | 0.405 | 0.203 | 0.610 | |
| ct.GCbias | 7.680 | 0.314 | 8.012 | |
| ct.GREATdb | 31.018 | 1.655 | 32.766 | |
| ct.PRC | 2.839 | 0.214 | 3.056 | |
| ct.ROC | 1.365 | 0.013 | 1.377 | |
| ct.RRAaPvals | 0.464 | 0.025 | 0.488 | |
| ct.RRAalpha | 0.383 | 0.011 | 0.395 | |
| ct.alignmentChart | 0.006 | 0.001 | 0.008 | |
| ct.alphaBeta | 0 | 0 | 0 | |
| ct.applyAlpha | 0.002 | 0.005 | 0.006 | |
| ct.buildSE | 0.603 | 0.019 | 0.622 | |
| ct.compareContrasts | 9.701 | 1.061 | 10.784 | |
| ct.contrastBarchart | 6.145 | 0.061 | 6.213 | |
| ct.expandAnnotation | 0.100 | 0.003 | 0.103 | |
| ct.filterReads | 0.296 | 0.022 | 0.319 | |
| ct.gRNARankByReplicate | 0.460 | 0.049 | 0.509 | |
| ct.generateResults | 0.609 | 0.027 | 0.635 | |
| ct.guideCDF | 19.002 | 6.877 | 25.990 | |
| ct.keyCheck | 0.131 | 0.010 | 0.141 | |
| ct.makeContrastReport | 8.735 | 1.261 | 10.146 | |
| ct.makeQCReport | 4.325 | 0.582 | 4.956 | |
| ct.makeReport | 18.244 | 2.583 | 20.978 | |
| ct.makeRhoNull | 0.001 | 0.000 | 0.001 | |
| ct.normalizeBySlope | 1.815 | 0.109 | 1.925 | |
| ct.normalizeFQ | 1.002 | 0.079 | 1.081 | |
| ct.normalizeGuides | 3.803 | 0.343 | 4.159 | |
| ct.normalizeMedians | 0.839 | 0.067 | 0.907 | |
| ct.normalizeNTC | 1.035 | 0.089 | 1.132 | |
| ct.normalizeSpline | 1.229 | 0.080 | 1.311 | |
| ct.parseGeneSymbol | 0.001 | 0.001 | 0.002 | |
| ct.prepareAnnotation | 0.726 | 0.050 | 0.783 | |
| ct.preprocessFit | 1.626 | 0.206 | 1.854 | |
| ct.rankSimple | 3.737 | 0.037 | 3.797 | |
| ct.rawCountDensities | 0.187 | 0.016 | 0.202 | |
| ct.regularizeContrasts | 0.134 | 0.003 | 0.137 | |
| ct.resultCheck | 0.095 | 0.002 | 0.098 | |
| ct.scatter | 0.405 | 0.007 | 0.412 | |
| ct.seas | 8.883 | 0.814 | 9.567 | |
| ct.seasPrep | 2.111 | 0.236 | 2.348 | |
| ct.signalSummary | 1.517 | 0.040 | 1.557 | |
| ct.simpleResult | 1.350 | 0.088 | 1.437 | |
| ct.softLog | 0 | 0 | 0 | |
| ct.stackGuides | 5.415 | 1.201 | 6.628 | |
| ct.targetSetEnrichment | 1.303 | 0.158 | 1.464 | |
| ct.topTargets | 0.495 | 0.029 | 0.527 | |
| ct.upSet | 9.042 | 1.184 | 10.252 | |
| ct.viewControls | 0.291 | 0.024 | 0.318 | |
| ct.viewGuides | 0.446 | 0.016 | 0.463 | |
| es | 0.085 | 0.007 | 0.092 | |
| essential.genes | 0.001 | 0.002 | 0.003 | |
| fit | 0.274 | 0.011 | 0.287 | |
| resultsDF | 0.093 | 0.003 | 0.097 | |