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This page was generated on 2022-10-19 13:23:10 -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 les on merida1


To the developers/maintainers of the les package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/les.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 1018/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
les 1.46.0  (landing page)
Julian Gehring
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/les
git_branch: RELEASE_3_15
git_last_commit: dccbe3a
git_last_commit_date: 2022-04-26 11:05:46 -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: les
Version: 1.46.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:les.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings les_1.46.0.tar.gz
StartedAt: 2022-10-19 03:57:57 -0400 (Wed, 19 Oct 2022)
EndedAt: 2022-10-19 03:59:27 -0400 (Wed, 19 Oct 2022)
EllapsedTime: 89.3 seconds
RetCode: 0
Status:   OK  
CheckDir: les.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:les.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings les_1.46.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/les.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 ‘les/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘les’ version ‘1.46.0’
* 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 ‘les’ 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 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 ... NOTE
Package in Depends field not imported from: ‘fdrtool’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' call which should be '::': ‘stats:::lm.wfit’
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘calcSingle’ ‘cdfDuplicates’ ‘checkState’ ‘diagSquare’ ‘fitGsri’
  ‘gsri’ ‘itLinReg’ ‘mcsapply’ ‘modGrenander’ ‘qrSlope’ ‘reg2log’
  ‘seSlopeWeight’ ‘setState’ ‘slopeWeight’ ‘wcdf2’ ‘wcdfGrenander’
  ‘xvalWeight’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function call to a different package:
  .C("C_isomean", ..., PACKAGE = "fdrtool")
Call with DUP:
   .C("C_isomean", as.double(rawslope), as.double(dx), as.integer(n), 
       ghat = double(n), PACKAGE = "fdrtool", DUP = FALSE)
DUP is no longer supported and will be ignored.
* checking R code for possible problems ... OK
* 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
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
les-package 22.617  0.123  23.575
ci          16.710  0.067  16.800
chi2         5.132  0.285   5.423
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.15-bioc/meat/les.Rcheck/00check.log’
for details.



Installation output

les.Rcheck/00install.out

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


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

Tests output


Example timings

les.Rcheck/les-Ex.timings

nameusersystemelapsed
Les-class0.0030.0000.003
Les0.0320.0050.037
chi25.1320.2855.423
ci16.710 0.06716.800
estimate0.3810.0230.405
export0.0000.0000.001
les-package22.617 0.12323.575
plot0.4150.0090.425
regions0.3930.0130.407
threshold0.3710.0110.383
weighting0.0170.0020.019