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This page was generated on 2023-10-20 09:38:14 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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Package 2187/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
VDJdive 1.2.0  (landing page)
Kelly Street
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/VDJdive
git_branch: RELEASE_3_17
git_last_commit: b657994
git_last_commit_date: 2023-04-25 11:39:52 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for VDJdive on kjohnson2


To the developers/maintainers of the VDJdive 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: VDJdive
Version: 1.2.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:VDJdive.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings VDJdive_1.2.0.tar.gz
StartedAt: 2023-10-19 09:37:05 -0400 (Thu, 19 Oct 2023)
EndedAt: 2023-10-19 09:44:26 -0400 (Thu, 19 Oct 2023)
EllapsedTime: 440.7 seconds
RetCode: 0
Status:   OK  
CheckDir: VDJdive.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:VDJdive.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings VDJdive_1.2.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/VDJdive.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 ‘VDJdive/DESCRIPTION’ ... OK
* this is package ‘VDJdive’ version ‘1.2.0’
* 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 ‘VDJdive’ can be installed ... NOTE
Found the following notes/warnings:
  Non-staged installation was used
See ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/VDJdive.Rcheck/00install.out’ for details.
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
abundanceVDJ,clonoStats: no visible binding for global variable ‘count’
abundanceVDJ,clonoStats: no visible binding for global variable ‘y’
barVDJ,Matrix: no visible binding for global variable ‘count’
boxVDJ,matrix: no visible binding for global variable ‘group’
boxVDJ,matrix: no visible binding for global variable ‘Diversity’
pieVDJ,Matrix: no visible binding for global variable ‘count’
scatterVDJ,matrix: no visible binding for global variable ‘clono’
scatterVDJ,matrix: no visible binding for global variable ‘normentropy’
scatterVDJ,matrix: no visible binding for global variable ‘sampleType’
Undefined global functions or variables:
  Diversity clono count group normentropy sampleType y
* 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 line endings in shell scripts ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
abundanceVDJ 4.801  1.154  11.887
runBreakaway 3.242  0.169   5.822
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.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
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/VDJdive.Rcheck/00check.log’
for details.



Installation output

VDJdive.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL VDJdive
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘VDJdive’ ...
** using non-staged installation via StagedInstall field
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (VDJdive)

Tests output

VDJdive.Rcheck/tests/testthat.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.

> library(testthat)
> library(VDJdive)
> 
> test_check("VDJdive")
An object of class "clonoStats"
clonotypes: 7 
cells: 24 
groups(2): sample1 sample2
has assignment: FALSEAn object of class "clonoStats"
clonotypes: 7 
cells: 24 
groups(2): sample1 sample2
has assignment: TRUE[ FAIL 0 | WARN 0 | SKIP 0 | PASS 125 ]
> 
> proc.time()
   user  system elapsed 
 39.725   1.917  75.935 

Example timings

VDJdive.Rcheck/VDJdive-Ex.timings

nameusersystemelapsed
abundanceVDJ 4.801 1.15411.887
addVDJtoSCE0.4240.0120.702
barVDJ1.0690.0201.815
boxVDJ1.0470.0191.709
calculateDiversity0.7800.0161.143
clonoStats-class0.6820.0141.186
clonoStats0.7000.0151.089
contigs0.7100.0171.195
pieVDJ1.1740.0202.085
readVDJcontigs0.0910.0060.162
runBreakaway3.2420.1695.822
runVDJPCA1.1380.0232.062
scatterVDJ0.8670.0441.406
splitClonotypes1.0320.0361.783
summarizeClonotypes0.9560.0231.716
writeVDJcontigs0.0870.0040.149