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This page was generated on 2021-12-01 17:17:25 -0500 (Wed, 01 Dec 2021).

CHECK results for gCrisprTools on nebbiolo2

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? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 704/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gCrisprTools 2.0.0  (landing page)
Russell Bainer
Snapshot Date: 2021-11-30 04:15:05 -0500 (Tue, 30 Nov 2021)
git_url: https://git.bioconductor.org/packages/gCrisprTools
git_branch: RELEASE_3_14
git_last_commit: 4783d8f
git_last_commit_date: 2021-10-26 12:29:53 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: gCrisprTools
Version: 2.0.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:gCrisprTools.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings gCrisprTools_2.0.0.tar.gz
StartedAt: 2021-11-30 09:13:53 -0500 (Tue, 30 Nov 2021)
EndedAt: 2021-11-30 09:19:04 -0500 (Tue, 30 Nov 2021)
EllapsedTime: 310.7 seconds
RetCode: 0
Status:   OK  
CheckDir: gCrisprTools.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:gCrisprTools.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings gCrisprTools_2.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/gCrisprTools.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gCrisprTools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gCrisprTools’ version ‘2.0.0’
* 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 ... NOTE
  installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
ct.seas: no visible global function definition for ‘ct.compileSparrow’
Undefined global functions or variables:
  ct.compileSparrow
* 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            30.344  2.453  32.436
ct.makeReport         17.802  0.261  18.073
ct.guideCDF            9.560  0.308   9.868
ct.compareContrasts    8.518  0.588   9.106
ct.makeContrastReport  8.717  0.154   8.878
ct.seas                6.988  1.771   6.882
ct.upSet               8.221  0.224   8.445
ct.GCbias              6.481  0.168   6.651
ct.contrastBarchart    6.060  0.004   6.065
ct.makeQCReport        5.262  0.106   5.375
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.14-bioc/meat/gCrisprTools.Rcheck/00check.log’
for details.



Installation output

gCrisprTools.Rcheck/00install.out

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##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL gCrisprTools
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-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)

Tests output

gCrisprTools.Rcheck/tests/unit.tests.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-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 Nov 30 09:19:01 2021 
*********************************************** 
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 
  9.700   0.480  10.166 

Example timings

gCrisprTools.Rcheck/gCrisprTools-Ex.timings

nameusersystemelapsed
aln0.0030.0000.004
ann0.0500.0080.058
ct.CAT1.3920.0881.480
ct.DirectionalTests0.2440.0600.304
ct.GCbias6.4810.1686.651
ct.GREATdb30.344 2.45332.436
ct.PRC2.1080.1842.292
ct.ROC1.3880.0001.389
ct.RRAaPvals0.3020.0040.307
ct.RRAalpha0.2370.0000.237
ct.alignmentChart0.0050.0000.005
ct.alphaBeta0.0120.0000.013
ct.applyAlpha0.0000.0020.002
ct.buildSE0.4290.0060.434
ct.compareContrasts8.5180.5889.106
ct.contrastBarchart6.0600.0046.065
ct.expandAnnotation0.060.000.06
ct.filterReads0.2540.0040.258
ct.gRNARankByReplicate0.4130.0080.420
ct.generateResults0.4230.0120.435
ct.guideCDF9.5600.3089.868
ct.keyCheck0.0860.0080.094
ct.makeContrastReport8.7170.1548.878
ct.makeQCReport5.2620.1065.375
ct.makeReport17.802 0.26118.073
ct.makeRhoNull0.0010.0000.001
ct.normalizeBySlope1.2860.0201.306
ct.normalizeFQ0.8220.0320.854
ct.normalizeGuides3.1670.0803.247
ct.normalizeMedians0.6990.0080.707
ct.normalizeNTC0.8520.0160.868
ct.normalizeSpline0.9690.0120.981
ct.parseGeneSymbol0.0010.0000.001
ct.prepareAnnotation0.5410.0200.561
ct.preprocessFit1.4440.0161.460
ct.rankSimple3.5710.0123.583
ct.rawCountDensities0.1060.0000.106
ct.regularizeContrasts0.2170.0000.217
ct.resultCheck0.0440.0000.045
ct.scatter0.2920.0000.292
ct.seas6.9881.7716.882
ct.seasPrep1.8750.0761.952
ct.signalSummary1.3940.0131.406
ct.simpleResult1.2380.0241.261
ct.softLog0.0010.0000.000
ct.stackGuides4.3880.4394.828
ct.targetSetEnrichment1.1280.0041.132
ct.topTargets0.2900.0040.294
ct.upSet8.2210.2248.445
ct.viewControls0.2060.0010.206
ct.viewGuides0.2750.0160.291
es0.0480.0000.048
essential.genes0.0010.0000.001
fit0.1530.0040.156
resultsDF0.0520.0000.051