Back to Multiple platform build/check report for BioC 3.19:   simplified   long
ABCDEF[G]HIJKLMNOPQRSTUVWXYZ

This page was generated on 2024-05-04 11:39:14 -0400 (Sat, 04 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4753
palomino3Windows Server 2022 Datacenterx644.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" 4486
lconwaymacOS 12.7.1 Montereyx86_644.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" 4519
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4479
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 783/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gCrisprTools 2.10.0  (landing page)
Russell Bainer
Snapshot Date: 2024-05-03 14:00:19 -0400 (Fri, 03 May 2024)
git_url: https://git.bioconductor.org/packages/gCrisprTools
git_branch: RELEASE_3_19
git_last_commit: 757cdf3
git_last_commit_date: 2024-04-30 10:53:27 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for gCrisprTools on lconway


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.

raw results


Summary

Package: gCrisprTools
Version: 2.10.0
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_2.10.0.tar.gz
StartedAt: 2024-05-03 22:02:26 -0400 (Fri, 03 May 2024)
EndedAt: 2024-05-03 22:09:24 -0400 (Fri, 03 May 2024)
EllapsedTime: 418.8 seconds
RetCode: 0
Status:   OK  
CheckDir: gCrisprTools.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_2.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/gCrisprTools.Rcheck’
* using R version 4.4.0 beta (2024-04-14 r86421)
* using platform: x86_64-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 Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gCrisprTools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gCrisprTools’ version ‘2.10.0’
* 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            29.920  1.979  32.311
ct.guideCDF           13.006 11.672  25.353
ct.makeReport         19.804  3.936  24.305
ct.makeContrastReport  9.497  2.299  12.152
ct.compareContrasts   10.210  1.005  11.400
ct.seas                8.676  0.944   9.543
ct.upSet               8.432  0.964   9.535
ct.contrastBarchart    6.905  0.160   7.156
ct.stackGuides         5.615  1.301   7.040
ct.GCbias              5.541  0.460   6.094
* 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-3.19-bioc/meat/gCrisprTools.Rcheck/00check.log’
for details.


Installation output

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-x86_64/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)

Tests output

gCrisprTools.Rcheck/tests/unit.tests.Rout


R version 4.4.0 beta (2024-04-14 r86421) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-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 -- Fri May  3 22:09:13 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 
  8.700   0.555   9.378 

Example timings

gCrisprTools.Rcheck/gCrisprTools-Ex.timings

nameusersystemelapsed
aln0.0030.0020.006
ann0.0670.0040.072
ct.CAT2.2080.1462.386
ct.DirectionalTests0.3020.2440.559
ct.GCbias5.5410.4606.094
ct.GREATdb29.920 1.97932.311
ct.PRC2.6200.3282.993
ct.ROC1.5820.0261.628
ct.RRAaPvals0.3830.0200.412
ct.RRAalpha0.2800.0130.296
ct.alignmentChart0.0060.0020.007
ct.alphaBeta0.0010.0010.001
ct.applyAlpha0.0020.0070.009
ct.buildSE0.4600.0230.493
ct.compareContrasts10.210 1.00511.400
ct.contrastBarchart6.9050.1607.156
ct.expandAnnotation0.0760.0020.079
ct.filterReads0.2830.0190.309
ct.gRNARankByReplicate0.3870.0400.435
ct.generateResults0.5540.0580.623
ct.guideCDF13.00611.67225.353
ct.keyCheck0.1220.0120.135
ct.makeContrastReport 9.497 2.29912.152
ct.makeQCReport4.0790.5054.757
ct.makeReport19.804 3.93624.305
ct.makeRhoNull0.0010.0000.001
ct.normalizeBySlope1.3390.0891.450
ct.normalizeFQ0.8010.0670.885
ct.normalizeGuides3.0930.2973.455
ct.normalizeMedians0.6540.0770.743
ct.normalizeNTC0.8080.0720.895
ct.normalizeSpline0.9540.0771.051
ct.parseGeneSymbol0.0020.0010.002
ct.prepareAnnotation0.5990.0400.653
ct.preprocessFit2.1680.5862.820
ct.rankSimple4.3470.1394.585
ct.rawCountDensities0.1420.0100.153
ct.regularizeContrasts0.1010.0040.106
ct.resultCheck0.0590.0030.063
ct.scatter0.3760.0300.412
ct.seas8.6760.9449.543
ct.seasPrep2.4020.2862.725
ct.signalSummary1.6670.0611.760
ct.simpleResult1.4450.1471.620
ct.softLog0.0000.0010.001
ct.stackGuides5.6151.3017.040
ct.targetSetEnrichment1.5180.7632.337
ct.topTargets0.3390.0170.361
ct.upSet8.4320.9649.535
ct.viewControls0.2580.0160.276
ct.viewGuides0.3320.0190.364
es0.0630.0070.072
essential.genes0.0020.0020.004
fit0.1910.0120.205
resultsDF0.0620.0040.066