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This page was generated on 2024-06-11 15:42 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4679
palomino4Windows Server 2022 Datacenterx644.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 4414
merida1macOS 12.7.4 Montereyx86_644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4441
kjohnson1macOS 13.6.6 Venturaarm644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4394
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 1138/2239HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
matchBox 1.47.0  (landing page)
Luigi Marchionni , Anuj Gupta
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/matchBox
git_branch: devel
git_last_commit: de7a7ca
git_last_commit_date: 2024-04-30 10:29:28 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for matchBox on merida1

To the developers/maintainers of the matchBox package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/matchBox.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: matchBox
Version: 1.47.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:matchBox.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings matchBox_1.47.0.tar.gz
StartedAt: 2024-06-10 05:44:39 -0400 (Mon, 10 Jun 2024)
EndedAt: 2024-06-10 05:45:22 -0400 (Mon, 10 Jun 2024)
EllapsedTime: 43.0 seconds
RetCode: 0
Status:   OK  
CheckDir: matchBox.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:matchBox.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings matchBox_1.47.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/matchBox.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* using platform: x86_64-apple-darwin20
* 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 12.7.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘matchBox/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘matchBox’ version ‘1.47.0’
* 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 ‘matchBox’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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 dependencies in R code ... NOTE
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘is.odd’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
calcHypPI : <anonymous>: no visible global function definition for
  ‘qhyper’
computeCat: no visible global function definition for ‘combn’
medianM: no visible global function definition for ‘median’
plotCat: no visible global function definition for ‘layout’
plotCat: no visible global function definition for ‘rainbow’
plotCat: no visible global function definition for ‘par’
plotCat: no visible global function definition for ‘colors’
plotCat: no visible global function definition for ‘polygon’
plotCat: no visible global function definition for ‘points’
plotCat: no visible global function definition for ‘mtext’
plotCat: no visible global function definition for ‘plot.new’
Undefined global functions or variables:
  colors combn layout median mtext par plot.new points polygon qhyper
  rainbow
Consider adding
  importFrom("grDevices", "colors", "rainbow")
  importFrom("graphics", "layout", "mtext", "par", "plot.new", "points",
             "polygon")
  importFrom("stats", "median", "qhyper")
  importFrom("utils", "combn")
to your NAMESPACE file.
* checking Rd files ... NOTE
checkRd: (-1) matchBox-package.Rd:26-27: Lost braces
    26 |     {Enables to identify the common set of features across
       |     ^
checkRd: (-1) matchBox-package.Rd:29-30: Lost braces
    29 |     {Enables to merge multiple data.frames based on
       |     ^
checkRd: (-1) matchBox-package.Rd:32-33: Lost braces
    32 |     {Computes the overlap proportion between any pair of ranked
       |     ^
checkRd: (-1) matchBox-package.Rd:35-36: Lost braces
    35 |     {Creates plots of the proportion of overlap along
       |     ^
checkRd: (-1) matchBoxExpression.Rd:29: Lost braces
    29 |     {\code{GENENAME}: Gene name column;}
       |     ^
checkRd: (-1) matchBoxExpression.Rd:31: Lost braces
    31 |     {\code{ENTREZID}: ENTREZ Gene identifier column;}
       |     ^
checkRd: (-1) matchBoxExpression.Rd:33: Lost braces
    33 |     {\code{logFC}: Log2 fold-change column;}
       |     ^
checkRd: (-1) matchBoxExpression.Rd:35: Lost braces
    35 |     {\code{AveExpr}: Average expression (A-value) column;}
       |     ^
checkRd: (-1) matchBoxExpression.Rd:37: Lost braces
    37 |     {\code{t}: moderated t-statistics column;}
       |     ^
checkRd: (-1) matchBoxExpression.Rd:39: Lost braces
    39 |     {\code{P.Value}: P-value column;}
       |     ^
checkRd: (-1) matchBoxExpression.Rd:41: Lost braces
    41 |     {\code{adj.P.Val}: adjusted P-value column;}
       |     ^
checkRd: (-1) matchBoxExpression.Rd:43: Lost braces
    43 |     {\code{B}: B-statitics (log-odds) column;}
       |     ^
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* 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
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/matchBox.Rcheck/00check.log’
for details.


Installation output

matchBox.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘matchBox’ ...
** 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 (matchBox)

Tests output


Example timings

matchBox.Rcheck/matchBox-Ex.timings

nameusersystemelapsed
calcHypPI0.1560.0220.211
computeCat0.3650.0550.490
filterRedundant0.0350.0040.048
mergeData0.0740.0060.095
plotCat0.2960.0250.372