| Back to Build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-05-31 05:44:34 -0000 (Wed, 31 May 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | 4.3.0 (2023-04-21) -- "Already Tomorrow" | 4219 |
| 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 | ||||
|
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. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 750/2197 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| gCrisprTools 2.7.0 (landing page) Russell Bainer
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
| Package: gCrisprTools |
| Version: 2.7.0 |
| Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:gCrisprTools.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings gCrisprTools_2.7.0.tar.gz |
| StartedAt: 2023-05-30 07:49:50 -0000 (Tue, 30 May 2023) |
| EndedAt: 2023-05-30 08:04:41 -0000 (Tue, 30 May 2023) |
| EllapsedTime: 891.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: gCrisprTools.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:gCrisprTools.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings gCrisprTools_2.7.0.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/gCrisprTools.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘gCrisprTools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gCrisprTools’ version ‘2.7.0’
* 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 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 ... 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 41.653 1.692 42.991
ct.guideCDF 41.432 0.964 42.397
ct.makeReport 28.726 0.413 29.149
ct.compareContrasts 14.355 0.244 14.600
ct.makeContrastReport 13.062 0.146 13.149
ct.upSet 12.686 0.368 13.057
ct.seas 11.389 1.454 12.129
ct.contrastBarchart 10.054 0.012 10.066
ct.makeQCReport 7.402 0.128 7.527
ct.stackGuides 6.353 0.596 6.950
ct.GCbias 6.147 0.276 6.423
ct.rankSimple 5.902 0.016 5.918
* 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 ...
‘Contrast_Comparisons.Rmd’ using ‘UTF-8’... OK
‘Crispr_example_workflow.Rmd’ using ‘UTF-8’... OK
‘gCrisprTools_Vignette.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/home/biocbuild/bbs-3.18-bioc/meat/gCrisprTools.Rcheck/00check.log’
for details.
gCrisprTools.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL gCrisprTools ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.0/site-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 4.3.0 (2023-04-21) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (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 -- Tue May 30 07:57:44 2023
***********************************************
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
9.823 0.616 10.422
gCrisprTools.Rcheck/gCrisprTools-Ex.timings
| name | user | system | elapsed | |
| aln | 0.004 | 0.000 | 0.003 | |
| ann | 0.066 | 0.004 | 0.070 | |
| ct.CAT | 2.836 | 0.240 | 3.076 | |
| ct.DirectionalTests | 0.278 | 0.100 | 0.378 | |
| ct.GCbias | 6.147 | 0.276 | 6.423 | |
| ct.GREATdb | 41.653 | 1.692 | 42.991 | |
| ct.PRC | 2.824 | 0.208 | 3.033 | |
| ct.ROC | 2.143 | 0.016 | 2.159 | |
| ct.RRAaPvals | 0.376 | 0.000 | 0.376 | |
| ct.RRAalpha | 0.246 | 0.000 | 0.246 | |
| ct.alignmentChart | 0.006 | 0.000 | 0.006 | |
| ct.alphaBeta | 0 | 0 | 0 | |
| ct.applyAlpha | 0.003 | 0.000 | 0.002 | |
| ct.buildSE | 0.421 | 0.004 | 0.425 | |
| ct.compareContrasts | 14.355 | 0.244 | 14.600 | |
| ct.contrastBarchart | 10.054 | 0.012 | 10.066 | |
| ct.expandAnnotation | 0.074 | 0.000 | 0.074 | |
| ct.filterReads | 0.400 | 0.004 | 0.403 | |
| ct.gRNARankByReplicate | 0.438 | 0.008 | 0.445 | |
| ct.generateResults | 0.611 | 0.000 | 0.610 | |
| ct.guideCDF | 41.432 | 0.964 | 42.397 | |
| ct.keyCheck | 0.102 | 0.000 | 0.101 | |
| ct.makeContrastReport | 13.062 | 0.146 | 13.149 | |
| ct.makeQCReport | 7.402 | 0.128 | 7.527 | |
| ct.makeReport | 28.726 | 0.413 | 29.149 | |
| ct.makeRhoNull | 0.000 | 0.000 | 0.001 | |
| ct.normalizeBySlope | 1.386 | 0.032 | 1.418 | |
| ct.normalizeFQ | 0.897 | 0.008 | 0.905 | |
| ct.normalizeGuides | 3.477 | 0.056 | 3.533 | |
| ct.normalizeMedians | 0.752 | 0.012 | 0.764 | |
| ct.normalizeNTC | 0.871 | 0.020 | 0.891 | |
| ct.normalizeSpline | 1.071 | 0.012 | 1.084 | |
| ct.parseGeneSymbol | 0.002 | 0.000 | 0.002 | |
| ct.prepareAnnotation | 0.684 | 0.012 | 0.697 | |
| ct.preprocessFit | 2.566 | 0.004 | 2.570 | |
| ct.rankSimple | 5.902 | 0.016 | 5.918 | |
| ct.rawCountDensities | 0.167 | 0.008 | 0.175 | |
| ct.regularizeContrasts | 0.122 | 0.000 | 0.122 | |
| ct.resultCheck | 0.064 | 0.000 | 0.064 | |
| ct.scatter | 0.519 | 0.000 | 0.519 | |
| ct.seas | 11.389 | 1.454 | 12.129 | |
| ct.seasPrep | 3.259 | 0.392 | 3.651 | |
| ct.signalSummary | 2.255 | 0.088 | 2.343 | |
| ct.simpleResult | 2.067 | 0.140 | 2.207 | |
| ct.softLog | 0.001 | 0.000 | 0.000 | |
| ct.stackGuides | 6.353 | 0.596 | 6.950 | |
| ct.targetSetEnrichment | 2.028 | 0.104 | 2.132 | |
| ct.topTargets | 0.342 | 0.004 | 0.347 | |
| ct.upSet | 12.686 | 0.368 | 13.057 | |
| ct.viewControls | 0.276 | 0.020 | 0.297 | |
| ct.viewGuides | 0.352 | 0.012 | 0.364 | |
| es | 0.055 | 0.000 | 0.055 | |
| essential.genes | 0.001 | 0.000 | 0.002 | |
| fit | 0.169 | 0.000 | 0.169 | |
| resultsDF | 0.063 | 0.004 | 0.067 | |