Back to Multiple platform build/check report for BioC 3.11
ABCDEFGHIJK[L]MNOPQRSTUVWXYZ

CHECK report for les on machv2

This page was generated on 2020-10-17 11:58:47 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE les PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 933/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
les 1.38.0
Julian Gehring
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/les
Branch: RELEASE_3_11
Last Commit: 41b5bd6
Last Changed Date: 2020-04-27 14:23:00 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: les
Version: 1.38.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:les.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings les_1.38.0.tar.gz
StartedAt: 2020-10-17 02:27:37 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 02:29:01 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 83.7 seconds
RetCode: 0
Status:  OK 
CheckDir: les.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:les.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings les_1.38.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/les.Rcheck’
* using R version 4.0.3 (2020-10-10)
* 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 ‘1.38.0’
* 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 21.283  0.167  21.478
ci          16.322  0.090  16.898
chi2         5.761  0.311   6.077
* 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-3.11-bioc/meat/les.Rcheck/00check.log’
for details.



Installation output

les.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/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-class0.0030.0020.005
Les0.0230.0050.027
chi25.7610.3116.077
ci16.322 0.09016.898
estimate0.4280.0090.437
export0.0000.0000.001
les-package21.283 0.16721.478
plot0.3440.0210.366
regions0.4610.0170.477
threshold0.3630.0140.378
weighting0.0170.0030.020