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This page was generated on 2024-05-21 11:36:56 -0400 (Tue, 21 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4751
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4485
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4515
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 769/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
funtooNorm 1.28.0  (landing page)
Kathleen Klein
Snapshot Date: 2024-05-20 14:00:15 -0400 (Mon, 20 May 2024)
git_url: https://git.bioconductor.org/packages/funtooNorm
git_branch: RELEASE_3_19
git_last_commit: 55ffa54
git_last_commit_date: 2024-04-30 10:55:52 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for funtooNorm on palomino3


To the developers/maintainers of the funtooNorm package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/funtooNorm.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: funtooNorm
Version: 1.28.0
Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:funtooNorm.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings funtooNorm_1.28.0.tar.gz
StartedAt: 2024-05-21 01:51:40 -0400 (Tue, 21 May 2024)
EndedAt: 2024-05-21 01:59:48 -0400 (Tue, 21 May 2024)
EllapsedTime: 488.2 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: funtooNorm.Rcheck
Warnings: 2

Command output

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###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:funtooNorm.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings funtooNorm_1.28.0.tar.gz
###
##############################################################################
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* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/funtooNorm.Rcheck'
* using R version 4.4.0 (2024-04-24 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 'funtooNorm/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'funtooNorm' version '1.28.0'
* 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 whether package 'funtooNorm' can be installed ... OK
* checking installed package size ... OK
* checking package 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 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 ... OK
* checking Rd files ... NOTE
checkRd: (-1) fromRGChannelSet.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Creates an object of class SampleSet from a RGChannelSet {minfi}}
       |                                                                 ^
* 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 ... WARNING
Documented arguments not in \usage in Rd file 'show-SampleSet-method.Rd':
  '...'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking R/sysdata.rda ... OK
* checking files in 'vignettes' ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
  'MyEndnoteLibrary.bib' 'funtooNorm.Rmd' 'funtooNorm.pdf'
  'validationcurvesPCRlow.jpg'
Files named as vignettes but with no recognized vignette engine:
   'vignettes/funtooNorm.Rmd'
(Is a VignetteBuilder field missing?)
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
getNormBeta           28.01   1.70   29.61
getSnpM               24.54   1.35   25.92
plotValidationGraph   24.25   1.06   25.31
funtooNorm            23.49   1.36   24.83
getNormM              23.05   1.75   24.79
fromRGChannelSet      14.83   0.80   19.62
getGRanges             6.48   0.59    7.08
getRawBeta             6.41   0.53    6.92
show-SampleSet-method  4.95   0.59    5.55
* checking package vignettes ... NOTE
Package has 'vignettes' subdirectory but apparently no vignettes.
Perhaps the 'VignetteBuilder' information is missing from the
DESCRIPTION file?
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 2 NOTEs
See
  'F:/biocbuild/bbs-3.19-bioc/meat/funtooNorm.Rcheck/00check.log'
for details.


Installation output

funtooNorm.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL funtooNorm
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.19-bioc/R/library'
* installing *source* package 'funtooNorm' ...
** using staged installation
** R
** 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 (funtooNorm)

Tests output


Example timings

funtooNorm.Rcheck/funtooNorm-Ex.timings

nameusersystemelapsed
SampleSet-class000
agreement000
fromRGChannelSet14.83 0.8019.62
funtooNorm23.49 1.3624.83
getGRanges6.480.597.08
getNormBeta28.01 1.7029.61
getNormM23.05 1.7524.79
getRawBeta6.410.536.92
getSnpM24.54 1.3525.92
plotValidationGraph24.25 1.0625.31
show-SampleSet-method4.950.595.55