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This page was generated on 2025-01-25 15:37 -0500 (Sat, 25 Jan 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" 4658
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" 4455
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4408
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 769/2286HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gCrisprTools 2.13.0  (landing page)
Russell Bainer
Snapshot Date: 2025-01-24 13:40 -0500 (Fri, 24 Jan 2025)
git_url: https://git.bioconductor.org/packages/gCrisprTools
git_branch: devel
git_last_commit: 1bb7f87
git_last_commit_date: 2024-10-29 10:13:45 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  


CHECK results for gCrisprTools on nebbiolo1

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: 2.13.0
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:gCrisprTools.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings gCrisprTools_2.13.0.tar.gz
StartedAt: 2025-01-24 22:26:15 -0500 (Fri, 24 Jan 2025)
EndedAt: 2025-01-24 22:35:39 -0500 (Fri, 24 Jan 2025)
EllapsedTime: 563.9 seconds
RetCode: 0
Status:   OK  
CheckDir: gCrisprTools.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:gCrisprTools.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings gCrisprTools_2.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/gCrisprTools.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘gCrisprTools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gCrisprTools’ version ‘2.13.0’
* 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 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 ... 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            26.161  1.791  27.637
ct.makeReport         17.751  0.222  17.991
ct.seas                9.063  1.265   9.022
ct.guideCDF            8.612  0.322   8.934
ct.makeContrastReport  8.567  0.153   8.707
ct.compareContrasts    8.031  0.378   8.409
ct.upSet               7.254  0.637   7.892
ct.GCbias              6.056  0.244   6.301
ct.contrastBarchart    5.986  0.043   6.029
ct.makeQCReport        5.530  0.085   5.620
ct.stackGuides         4.732  0.796   5.529
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/gCrisprTools.Rcheck/00check.log’
for details.


Installation output

gCrisprTools.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL gCrisprTools
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘gCrisprTools’ ...
** this is package ‘gCrisprTools’ version ‘2.13.0’
** 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 Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 Jan 24 22:31:39 2025 
*********************************************** 
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 
  7.453   0.404   7.843 

Example timings

gCrisprTools.Rcheck/gCrisprTools-Ex.timings

nameusersystemelapsed
aln0.0030.0000.003
ann0.0520.0030.056
ct.CAT1.4220.1421.564
ct.DirectionalTests0.2600.2610.521
ct.GCbias6.0560.2446.301
ct.GREATdb26.161 1.79127.637
ct.PRC2.0630.0932.156
ct.ROC1.3280.0031.331
ct.RRAaPvals0.3080.0000.308
ct.RRAalpha0.2380.0000.238
ct.alignmentChart0.0040.0010.005
ct.alphaBeta0.0010.0000.001
ct.applyAlpha0.0010.0040.005
ct.buildSE0.3900.0040.394
ct.compareContrasts8.0310.3788.409
ct.contrastBarchart5.9860.0436.029
ct.expandAnnotation0.0580.0000.058
ct.filterReads0.2440.0020.246
ct.gRNARankByReplicate0.4130.0070.420
ct.generateResults0.4530.0230.476
ct.guideCDF8.6120.3228.934
ct.keyCheck0.0950.0030.099
ct.makeContrastReport8.5670.1538.707
ct.makeQCReport5.5300.0855.620
ct.makeReport17.751 0.22217.991
ct.makeRhoNull0.0000.0000.001
ct.normalizeBySlope1.2400.0091.250
ct.normalizeFQ0.8150.0140.829
ct.normalizeGuides3.0530.0293.082
ct.normalizeMedians0.7020.0080.710
ct.normalizeNTC0.8230.0100.833
ct.normalizeSpline0.9550.0230.978
ct.parseGeneSymbol0.0010.0010.001
ct.prepareAnnotation0.4850.0060.490
ct.preprocessFit1.4980.0121.510
ct.rankSimple3.5050.0253.530
ct.rawCountDensities0.1320.0050.136
ct.regularizeContrasts0.0840.0020.086
ct.resultCheck0.0530.0010.054
ct.scatter0.3270.0010.328
ct.seas9.0631.2659.022
ct.seasPrep2.0100.3202.331
ct.signalSummary1.4710.0511.523
ct.simpleResult1.2460.1831.429
ct.softLog000
ct.stackGuides4.7320.7965.529
ct.targetSetEnrichment1.1960.1751.370
ct.topTargets0.3230.0150.339
ct.upSet7.2540.6377.892
ct.viewControls0.2140.0170.231
ct.viewGuides0.3520.0460.397
es0.0510.0030.054
essential.genes0.0000.0020.002
fit0.1820.0070.190
resultsDF0.0570.0050.062