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This page was generated on 2023-10-20 09:38:02 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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 761/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gCrisprTools 2.6.0  (landing page)
Russell Bainer
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/gCrisprTools
git_branch: RELEASE_3_17
git_last_commit: 0a41bea
git_last_commit_date: 2023-04-25 10:49:24 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for gCrisprTools on kjohnson2


To the developers/maintainers of the gCrisprTools package:
- 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: 2.6.0
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_2.6.0.tar.gz
StartedAt: 2023-10-17 20:44:41 -0400 (Tue, 17 Oct 2023)
EndedAt: 2023-10-17 20:54:23 -0400 (Tue, 17 Oct 2023)
EllapsedTime: 582.0 seconds
RetCode: 0
Status:   OK  
CheckDir: gCrisprTools.Rcheck
Warnings: 0

Command output

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###
### 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_2.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/gCrisprTools.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* 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 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gCrisprTools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gCrisprTools’ version ‘2.6.0’
* 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.makeReport         29.215  1.406  44.216
ct.GREATdb            27.859  1.257  43.878
ct.guideCDF           11.864  3.639  23.159
ct.makeContrastReport 12.821  1.232  24.959
ct.compareContrasts    9.426  0.605  15.128
ct.upSet               8.619  0.668  14.817
ct.seas                8.457  0.684  13.454
ct.makeQCReport        7.873  0.351  12.637
ct.contrastBarchart    7.159  0.103  11.121
ct.stackGuides         5.897  0.680   9.932
ct.GCbias              5.375  0.308   8.747
ct.rankSimple          4.319  0.055   6.187
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/gCrisprTools.Rcheck/00check.log’
for details.



Installation output

gCrisprTools.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL gCrisprTools
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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 Oct 17 20:54:05 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 
  8.115   0.439  13.392 

Example timings

gCrisprTools.Rcheck/gCrisprTools-Ex.timings

nameusersystemelapsed
aln0.0030.0020.008
ann0.0690.0040.109
ct.CAT2.1370.1193.482
ct.DirectionalTests0.3130.2200.815
ct.GCbias5.3750.3088.747
ct.GREATdb27.859 1.25743.878
ct.PRC2.6280.2213.714
ct.ROC1.5990.0402.080
ct.RRAaPvals0.3480.0240.474
ct.RRAalpha0.2590.0100.347
ct.alignmentChart0.0060.0010.010
ct.alphaBeta0.0010.0000.002
ct.applyAlpha0.0020.0040.007
ct.buildSE0.4410.0160.587
ct.compareContrasts 9.426 0.60515.128
ct.contrastBarchart 7.159 0.10311.121
ct.expandAnnotation0.0730.0020.117
ct.filterReads0.2840.0170.458
ct.gRNARankByReplicate0.3950.0360.663
ct.generateResults0.5060.0240.808
ct.guideCDF11.864 3.63923.159
ct.keyCheck0.1270.0080.206
ct.makeContrastReport12.821 1.23224.959
ct.makeQCReport 7.873 0.35112.637
ct.makeReport29.215 1.40644.216
ct.makeRhoNull0.0000.0000.001
ct.normalizeBySlope1.4830.0832.365
ct.normalizeFQ0.8470.0591.379
ct.normalizeGuides3.2600.2244.576
ct.normalizeMedians0.7160.0541.052
ct.normalizeNTC0.8780.0661.374
ct.normalizeSpline1.0120.0751.575
ct.parseGeneSymbol0.0020.0000.006
ct.prepareAnnotation0.6280.0290.963
ct.preprocessFit1.9460.1033.067
ct.rankSimple4.3190.0556.187
ct.rawCountDensities0.1580.0090.253
ct.regularizeContrasts0.1070.0030.170
ct.resultCheck0.0640.0020.103
ct.scatter0.4380.0090.681
ct.seas 8.457 0.68413.454
ct.seasPrep2.4660.2304.105
ct.signalSummary1.6000.0492.431
ct.simpleResult1.5570.0962.501
ct.softLog000
ct.stackGuides5.8970.6809.932
ct.targetSetEnrichment1.5080.1532.427
ct.topTargets0.3610.0150.582
ct.upSet 8.619 0.66814.817
ct.viewControls0.2590.0170.435
ct.viewGuides0.4070.0340.681
es0.0600.0050.101
essential.genes0.0010.0020.008
fit0.1860.0100.294
resultsDF0.0680.0030.110