Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2024-11-09 21:30 -0500 (Sat, 09 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4505
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4506
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4538
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4486
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4493
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 731/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowCyBar 1.42.0  (landing page)
Joachim Schumann
Snapshot Date: 2024-11-08 13:40 -0500 (Fri, 08 Nov 2024)
git_url: https://git.bioconductor.org/packages/flowCyBar
git_branch: RELEASE_3_20
git_last_commit: 66b9307
git_last_commit_date: 2024-10-29 09:51:20 -0500 (Tue, 29 Oct 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows 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  YES
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  


CHECK results for flowCyBar on kjohnson3

To the developers/maintainers of the flowCyBar package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/flowCyBar.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: flowCyBar
Version: 1.42.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:flowCyBar.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings flowCyBar_1.42.0.tar.gz
StartedAt: 2024-11-09 02:27:23 -0500 (Sat, 09 Nov 2024)
EndedAt: 2024-11-09 02:31:22 -0500 (Sat, 09 Nov 2024)
EllapsedTime: 239.4 seconds
RetCode: 0
Status:   OK  
CheckDir: flowCyBar.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:flowCyBar.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings flowCyBar_1.42.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/flowCyBar.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-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 Ventura 13.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flowCyBar/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowCyBar’ version ‘1.42.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ‘flowCyBar’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
correlation,data.frame : <anonymous>: no visible global function
  definition for ‘as.dist’
correlation,data.frame : est: no visible global function definition for
  ‘cor.test’
correlation,data.frame : pval: no visible global function definition
  for ‘cor.test’
correlation,matrix : <anonymous>: no visible global function definition
  for ‘as.dist’
correlation,matrix : est: no visible global function definition for
  ‘cor.test’
correlation,matrix : pval: no visible global function definition for
  ‘cor.test’
cybar_plot,data.frame-data.frame: no visible global function definition
  for ‘layout’
cybar_plot,data.frame-data.frame: no visible global function definition
  for ‘par’
cybar_plot,data.frame-data.frame: no visible global function definition
  for ‘boxplot’
cybar_plot,data.frame-matrix: no visible global function definition for
  ‘layout’
cybar_plot,data.frame-matrix: no visible global function definition for
  ‘par’
cybar_plot,data.frame-matrix: no visible global function definition for
  ‘boxplot’
cybar_plot,matrix-data.frame: no visible global function definition for
  ‘layout’
cybar_plot,matrix-data.frame: no visible global function definition for
  ‘par’
cybar_plot,matrix-data.frame: no visible global function definition for
  ‘boxplot’
cybar_plot,matrix-matrix: no visible global function definition for
  ‘layout’
cybar_plot,matrix-matrix: no visible global function definition for
  ‘par’
cybar_plot,matrix-matrix: no visible global function definition for
  ‘boxplot’
cybar_plot,missing-data.frame: no visible global function definition
  for ‘boxplot’
cybar_plot,missing-matrix: no visible global function definition for
  ‘boxplot’
nmds,data.frame: no visible global function definition for ‘text’
nmds,data.frame: no visible global function definition for ‘points’
nmds,data.frame: no visible global function definition for ‘legend’
nmds,matrix: no visible global function definition for ‘text’
nmds,matrix: no visible global function definition for ‘points’
nmds,matrix: no visible global function definition for ‘legend’
normalize,data.frame : <anonymous>: no visible global function
  definition for ‘head’
normalize,matrix : <anonymous>: no visible global function definition
  for ‘head’
Undefined global functions or variables:
  as.dist boxplot cor.test head layout legend par points text
Consider adding
  importFrom("graphics", "boxplot", "layout", "legend", "par", "points",
             "text")
  importFrom("stats", "as.dist", "cor.test")
  importFrom("utils", "head")
to your NAMESPACE file.
* 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 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/flowCyBar.Rcheck/00check.log’
for details.


Installation output

flowCyBar.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘flowCyBar’ ...
files ‘build/vignette.rds’, ‘inst/doc/flowCyBar-manual.R’, ‘inst/doc/flowCyBar-manual.Rnw’, ‘inst/doc/flowCyBar-manual.bib’, ‘inst/doc/flowCyBar-manual.pdf’ are missing
files ‘DESCRIPTION’, ‘R/correlation.R’, ‘R/cybar_plot.R’, ‘R/nmds.R’, ‘R/normalize.R’, ‘man/correlation.Rd’, ‘man/cybar_plot.Rd’, ‘man/flowCyBar-package.Rd’, ‘man/nmds.Rd’, ‘man/normalize.Rd’, ‘vignettes/flowCyBar-manual.Rnw’ have the wrong MD5 checksums
** using staged installation
** R
** data
** 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 (flowCyBar)

Tests output


Example timings

flowCyBar.Rcheck/flowCyBar-Ex.timings

nameusersystemelapsed
correlation0.4680.0090.480
cybar_plot0.0560.0040.060
nmds0.1140.0110.125
normalize0.0070.0010.008