Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-10-19 13:23:25 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
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

CHECK results for OSAT on merida1


To the developers/maintainers of the OSAT package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/OSAT.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1390/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OSAT 1.44.0  (landing page)
Li Yan
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/OSAT
git_branch: RELEASE_3_15
git_last_commit: 135ebde
git_last_commit_date: 2022-04-26 11:11:25 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: OSAT
Version: 1.44.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:OSAT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings OSAT_1.44.0.tar.gz
StartedAt: 2022-10-19 05:47:37 -0400 (Wed, 19 Oct 2022)
EndedAt: 2022-10-19 05:48:31 -0400 (Wed, 19 Oct 2022)
EllapsedTime: 54.3 seconds
RetCode: 0
Status:   OK  
CheckDir: OSAT.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:OSAT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings OSAT_1.44.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/OSAT.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OSAT/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OSAT’ version ‘1.44.0’
* 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 ‘OSAT’ 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
assign.sample.to.container: no visible global function definition for
  ‘head’
barplot.gExperimentSetup: no visible global function definition for
  ‘layout’
barplot.gExperimentSetup: no visible global function definition for
  ‘barplot’
barplot.gExperimentSetup: no visible global function definition for
  ‘gray’
barplot.gExperimentSetup: no visible global function definition for
  ‘points’
barplot.gExperimentSetup: no visible global function definition for
  ‘mtext’
multi.barplot: no visible global function definition for ‘layout’
multi.barplot: no visible global function definition for ‘barplot’
multi.barplot: no visible global function definition for ‘gray’
multi.barplot: no visible global function definition for ‘mtext’
show,gAssembly: no visible global function definition for ‘head’
show,gAssembly: no visible global function definition for ‘tail’
show,gContainer: no visible global function definition for ‘head’
show,gContainer: no visible global function definition for ‘tail’
show,gExperimentSetup: no visible global function definition for ‘head’
show,gExperimentSetup: no visible global function definition for ‘tail’
show,gPlate: no visible global function definition for ‘head’
show,gPlate: no visible global function definition for ‘tail’
show,gSample: no visible global function definition for ‘head’
show,gSample: no visible global function definition for ‘tail’
Undefined global functions or variables:
  barplot gray head layout mtext points tail
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "barplot", "layout", "mtext", "points")
  importFrom("utils", "head", "tail")
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 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-3.15-bioc/meat/OSAT.Rcheck/00check.log’
for details.



Installation output

OSAT.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘OSAT’ ...
** 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 (OSAT)

Tests output


Example timings

OSAT.Rcheck/OSAT-Ex.timings

nameusersystemelapsed
BeadChip-class0.0170.0010.018
BeadPlate-class0.0120.0010.013
MSAroboticPlate-class0.4640.0200.487
QC2.1400.0472.209
create.optimized.setup1.8320.0311.876
example.setup0.0710.0090.081
gContainer-class0.0250.0010.027
gExperimentSetup-class0.0840.0020.088
gSample-class0.0190.0000.020
gSlide-class0.0540.0000.054
get.experiment.setup1.8310.0101.861
multi.barplot0.0290.0030.032
multi.chisq.test0.0190.0020.020
optimal.block2.4150.0092.470
optimal.shuffle1.8760.0141.911