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This page was generated on 2024-07-16 11:40 -0400 (Tue, 16 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4677
palomino6Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4416
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4444
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4393
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4373
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 574/2243HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
divergence 1.21.0  (landing page)
Wikum Dinalankara , Luigi Marchionni
Snapshot Date: 2024-07-15 14:00 -0400 (Mon, 15 Jul 2024)
git_url: https://git.bioconductor.org/packages/divergence
git_branch: devel
git_last_commit: a8fbbe9
git_last_commit_date: 2024-04-30 11:12:17 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino6Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  
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
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  


CHECK results for divergence on palomino6

To the developers/maintainers of the divergence package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/divergence.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: divergence
Version: 1.21.0
Command: C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:divergence.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings divergence_1.21.0.tar.gz
StartedAt: 2024-07-15 23:34:25 -0400 (Mon, 15 Jul 2024)
EndedAt: 2024-07-15 23:37:31 -0400 (Mon, 15 Jul 2024)
EllapsedTime: 186.0 seconds
RetCode: 0
Status:   OK  
CheckDir: divergence.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:divergence.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings divergence_1.21.0.tar.gz
###
##############################################################################
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* using log directory 'C:/Users/biocbuild/bbs-3.20-bioc/meat/divergence.Rcheck'
* using R version 4.4.1 (2024-06-14 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'divergence/DESCRIPTION' ... OK
* this is package 'divergence' version '1.21.0'
* 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 whether package 'divergence' 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 ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
check_SE: no visible binding for global variable 'data'
computeSingleFeaturesetBinaryVector: no visible global function
  definition for 'dist'
computeSingleFeaturesetSupport: no visible global function definition
  for 'dist'
computeSingleFeaturesetSupport: no visible global function definition
  for 'quantile'
computeSingleRange: no visible global function definition for
  'quantile'
getRangesBySections: no visible global function definition for
  'detectCores'
rowChiSq: no visible global function definition for 'chisq.test'
rowChiSq: no visible global function definition for 'xtabs'
Undefined global functions or variables:
  chisq.test data detectCores dist quantile xtabs
Consider adding
  importFrom("stats", "chisq.test", "dist", "quantile", "xtabs")
  importFrom("utils", "data")
to your NAMESPACE file.
* checking Rd files ... NOTE
checkRd: (-1) computeMultivariateDigitization.Rd:26: Lost braces; missing escapes or markup?
    26 | By default gamma = {0.01, 0.02, ... 0.09, 0.1, 0.2, ..., 0.9}.}
       |                    ^
checkRd: (-1) computeUnivariateDigitization.Rd:22: Lost braces; missing escapes or markup?
    22 | By default gamma = {0.01, 0.02, ... 0.09, 0.1, 0.2, ..., 0.9}.}
       |                    ^
* 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 LazyData ... 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
computeChiSquaredTest          16.43   0.43   15.30
computeUnivariateDigitization  10.73   0.80   11.53
findUnivariateGammaWithSupport 10.77   0.55   11.22
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... NOTE
Package vignette with \VignetteEngine{} not specifying an engine package:
  'divergence.Rmd'
Engines should be specified as \VignetteEngine{PKG::ENG}.
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.20-bioc/meat/divergence.Rcheck/00check.log'
for details.


Installation output

divergence.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL divergence
###
##############################################################################
##############################################################################


* installing to library 'C:/Users/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'divergence' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (divergence)

Tests output


Example timings

divergence.Rcheck/divergence-Ex.timings

nameusersystemelapsed
computeChiSquaredTest16.43 0.4315.30
computeMultivariateBinaryMatrix1.700.101.79
computeMultivariateDigitization3.350.263.61
computeMultivariateSupport0.220.050.27
computeQuantileMatrix0.030.000.03
computeUnivariateDigitization10.73 0.8011.53
computeUnivariateSupport1.020.001.02
computeUnivariateTernaryMatrix1.120.011.14
findMultivariateGammaWithSupport0.470.020.48
findUnivariateGammaWithSupport10.77 0.5511.22