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This page was generated on 2024-06-11 14:39 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4757
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4491
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4522
kjohnson3macOS 13.6.5 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4468
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: 2024-06-09 14:00 -0400 (Sun, 09 Jun 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
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


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: 2.10.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:gCrisprTools.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings gCrisprTools_2.10.0.tar.gz
StartedAt: 2024-06-09 23:11:27 -0400 (Sun, 09 Jun 2024)
EndedAt: 2024-06-09 23:20:39 -0400 (Sun, 09 Jun 2024)
EllapsedTime: 552.2 seconds
RetCode: 0
Status:   OK  
CheckDir: gCrisprTools.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:gCrisprTools.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings gCrisprTools_2.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/gCrisprTools.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* 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 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            26.614  1.491  27.784
ct.makeReport         17.746  1.322  19.079
ct.seas               10.143  1.362  10.177
ct.compareContrasts    8.897  0.272   9.168
ct.makeContrastReport  8.352  0.204   8.516
ct.upSet               7.186  0.623   7.810
ct.guideCDF            7.489  0.052   7.541
ct.GCbias              6.458  0.200   6.658
ct.makeQCReport        5.269  0.143   5.412
ct.contrastBarchart    5.331  0.023   5.355
ct.stackGuides         4.563  0.691   5.255
* 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-3.19-bioc/meat/gCrisprTools.Rcheck/00check.log’
for details.


Installation output

gCrisprTools.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL gCrisprTools
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/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)

Tests output

gCrisprTools.Rcheck/tests/unit.tests.Rout


R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 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 -- Sun Jun  9 23:16:49 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 
  7.240   0.431   7.661 

Example timings

gCrisprTools.Rcheck/gCrisprTools-Ex.timings

nameusersystemelapsed
aln0.0030.0000.003
ann0.0540.0080.062
ct.CAT1.8920.1522.044
ct.DirectionalTests0.2560.2640.520
ct.GCbias6.4580.2006.658
ct.GREATdb26.614 1.49127.784
ct.PRC2.0060.1402.146
ct.ROC1.2260.0041.229
ct.RRAaPvals0.2990.0000.298
ct.RRAalpha0.2330.0000.233
ct.alignmentChart0.0050.0000.005
ct.alphaBeta000
ct.applyAlpha0.0000.0040.005
ct.buildSE0.3830.0080.391
ct.compareContrasts8.8970.2729.168
ct.contrastBarchart5.3310.0235.355
ct.expandAnnotation0.0560.0030.060
ct.filterReads0.2280.0080.237
ct.gRNARankByReplicate0.4060.0120.417
ct.generateResults0.4880.0040.492
ct.guideCDF7.4890.0527.541
ct.keyCheck0.0850.0040.089
ct.makeContrastReport8.3520.2048.516
ct.makeQCReport5.2690.1435.412
ct.makeReport17.746 1.32219.079
ct.makeRhoNull0.0000.0010.001
ct.normalizeBySlope1.2940.0431.337
ct.normalizeFQ0.8440.0480.893
ct.normalizeGuides3.3500.1083.458
ct.normalizeMedians0.7510.0200.771
ct.normalizeNTC0.8780.0120.890
ct.normalizeSpline0.9880.0431.032
ct.parseGeneSymbol0.0030.0000.002
ct.prepareAnnotation0.4870.0400.526
ct.preprocessFit1.5610.1161.677
ct.rankSimple3.4070.0643.472
ct.rawCountDensities0.1270.0080.135
ct.regularizeContrasts0.0880.0000.089
ct.resultCheck0.0550.0000.055
ct.scatter0.3490.0000.348
ct.seas10.143 1.36210.177
ct.seasPrep2.0000.2912.292
ct.signalSummary1.4440.1401.584
ct.simpleResult1.2350.1881.424
ct.softLog0.0010.0010.000
ct.stackGuides4.5630.6915.255
ct.targetSetEnrichment1.2020.1161.318
ct.topTargets0.2980.0080.306
ct.upSet7.1860.6237.810
ct.viewControls0.1970.0080.205
ct.viewGuides0.2850.0080.293
es0.0470.0040.051
essential.genes0.0010.0010.002
fit0.1690.0020.172
resultsDF0.0510.0040.055