| Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-02-08 01:15:04 -0000 (Wed, 08 Feb 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4164 |
| 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: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 729/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| gCrisprTools 2.5.0 (landing page) Russell Bainer
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
| Package: gCrisprTools |
| Version: 2.5.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:gCrisprTools.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings gCrisprTools_2.5.0.tar.gz |
| StartedAt: 2023-02-07 02:05:16 -0000 (Tue, 07 Feb 2023) |
| EndedAt: 2023-02-07 02:20:10 -0000 (Tue, 07 Feb 2023) |
| EllapsedTime: 894.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: gCrisprTools.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:gCrisprTools.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings gCrisprTools_2.5.0.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/gCrisprTools.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* 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 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘gCrisprTools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gCrisprTools’ version ‘2.5.0’
* 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.guideCDF 41.730 0.021 43.179
ct.GREATdb 37.460 0.947 41.304
ct.makeReport 28.874 0.139 31.167
ct.compareContrasts 15.493 0.080 16.843
ct.makeContrastReport 12.998 0.124 14.545
ct.upSet 12.812 0.040 14.129
ct.seas 11.099 1.127 13.015
ct.contrastBarchart 9.867 0.000 10.076
ct.makeQCReport 7.229 0.085 7.662
ct.stackGuides 6.475 0.394 7.439
ct.GCbias 6.102 0.128 6.279
ct.rankSimple 6.094 0.000 6.701
* 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-3.17-bioc/meat/gCrisprTools.Rcheck/00check.log’
for details.
gCrisprTools.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL gCrisprTools ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/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 Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
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 Feb 7 02:13:06 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
8.962 0.229 10.031
gCrisprTools.Rcheck/gCrisprTools-Ex.timings
| name | user | system | elapsed | |
| aln | 0.003 | 0.000 | 0.003 | |
| ann | 0.062 | 0.004 | 0.067 | |
| ct.CAT | 2.891 | 0.104 | 3.051 | |
| ct.DirectionalTests | 0.271 | 0.075 | 0.348 | |
| ct.GCbias | 6.102 | 0.128 | 6.279 | |
| ct.GREATdb | 37.460 | 0.947 | 41.304 | |
| ct.PRC | 2.881 | 0.104 | 3.223 | |
| ct.ROC | 2.113 | 0.000 | 2.389 | |
| ct.RRAaPvals | 0.368 | 0.004 | 0.374 | |
| ct.RRAalpha | 0.245 | 0.000 | 0.246 | |
| ct.alignmentChart | 0.003 | 0.003 | 0.006 | |
| ct.alphaBeta | 0.000 | 0.000 | 0.001 | |
| ct.applyAlpha | 0.000 | 0.003 | 0.003 | |
| ct.buildSE | 0.425 | 0.001 | 0.441 | |
| ct.compareContrasts | 15.493 | 0.080 | 16.843 | |
| ct.contrastBarchart | 9.867 | 0.000 | 10.076 | |
| ct.expandAnnotation | 0.074 | 0.000 | 0.074 | |
| ct.filterReads | 0.387 | 0.004 | 0.419 | |
| ct.gRNARankByReplicate | 0.479 | 0.000 | 0.482 | |
| ct.generateResults | 0.588 | 0.000 | 0.592 | |
| ct.guideCDF | 41.730 | 0.021 | 43.179 | |
| ct.keyCheck | 0.101 | 0.000 | 0.104 | |
| ct.makeContrastReport | 12.998 | 0.124 | 14.545 | |
| ct.makeQCReport | 7.229 | 0.085 | 7.662 | |
| ct.makeReport | 28.874 | 0.139 | 31.167 | |
| ct.makeRhoNull | 0.000 | 0.000 | 0.001 | |
| ct.normalizeBySlope | 1.426 | 0.020 | 1.446 | |
| ct.normalizeFQ | 0.902 | 0.016 | 1.031 | |
| ct.normalizeGuides | 3.550 | 0.055 | 4.011 | |
| ct.normalizeMedians | 0.772 | 0.004 | 0.889 | |
| ct.normalizeNTC | 0.888 | 0.008 | 0.907 | |
| ct.normalizeSpline | 1.125 | 0.020 | 1.188 | |
| ct.parseGeneSymbol | 0.002 | 0.000 | 0.018 | |
| ct.prepareAnnotation | 0.692 | 0.008 | 1.038 | |
| ct.preprocessFit | 2.622 | 0.004 | 2.853 | |
| ct.rankSimple | 6.094 | 0.000 | 6.701 | |
| ct.rawCountDensities | 0.181 | 0.004 | 0.187 | |
| ct.regularizeContrasts | 0.125 | 0.000 | 0.125 | |
| ct.resultCheck | 0.064 | 0.000 | 0.064 | |
| ct.scatter | 0.698 | 0.003 | 0.795 | |
| ct.seas | 11.099 | 1.127 | 13.015 | |
| ct.seasPrep | 3.225 | 0.195 | 3.845 | |
| ct.signalSummary | 2.260 | 0.024 | 2.584 | |
| ct.simpleResult | 2.075 | 0.036 | 2.346 | |
| ct.softLog | 0.001 | 0.000 | 0.001 | |
| ct.stackGuides | 6.475 | 0.394 | 7.439 | |
| ct.targetSetEnrichment | 2.064 | 0.000 | 2.119 | |
| ct.topTargets | 0.334 | 0.004 | 0.337 | |
| ct.upSet | 12.812 | 0.040 | 14.129 | |
| ct.viewControls | 0.291 | 0.004 | 0.479 | |
| ct.viewGuides | 0.348 | 0.000 | 0.348 | |
| es | 0.053 | 0.000 | 0.053 | |
| essential.genes | 0.001 | 0.000 | 0.001 | |
| fit | 0.167 | 0.000 | 0.167 | |
| resultsDF | 0.062 | 0.003 | 0.065 | |