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This page was generated on 2021-10-15 15:06:09 -0400 (Fri, 15 Oct 2021).

CHECK results for les on tokay2

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? here 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 982/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
les 1.42.0  (landing page)
Julian Gehring
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/les
git_branch: RELEASE_3_13
git_last_commit: 9224538
git_last_commit_date: 2021-05-19 11:46:16 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: les
Version: 1.42.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:les.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings les_1.42.0.tar.gz
StartedAt: 2021-10-15 01:06:53 -0400 (Fri, 15 Oct 2021)
EndedAt: 2021-10-15 01:08:23 -0400 (Fri, 15 Oct 2021)
EllapsedTime: 89.8 seconds
RetCode: 0
Status:   OK  
CheckDir: les.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:les.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings les_1.42.0.tar.gz
###
##############################################################################
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/les.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'les/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'les' version '1.42.0'
* 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 '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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
les-package 11.12   0.03   11.15
ci           9.13   0.00    9.13
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
les-package 11.50      0   11.50
ci           9.25      0    9.25
* 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
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/les.Rcheck/00check.log'
for details.



Installation output

les.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/les_1.42.0.tar.gz && rm -rf les.buildbin-libdir && mkdir les.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=les.buildbin-libdir les_1.42.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL les_1.42.0.zip && rm les_1.42.0.tar.gz les_1.42.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 52847  100 52847    0     0   306k      0 --:--:-- --:--:-- --:--:--  309k

install for i386

* installing *source* package 'les' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'les'
    finding HTML links ... done
    Les-class                               html  
    Les                                     html  
    chi2                                    html  
    ci                                      html  
    estimate                                html  
    export                                  html  
    les-internal                            html  
    les-package                             html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/les.buildbin-libdir/00LOCK-les/00new/les/help/les.html
    plot                                    html  
    regions                                 html  
    spikeInData                             html  
    spikeInStat                             html  
    threshold                               html  
    weighting                               html  
** 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

install for x64

* installing *source* package 'les' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'les' as les_1.42.0.zip
* DONE (les)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'les' successfully unpacked and MD5 sums checked

Tests output


Example timings

les.Rcheck/examples_i386/les-Ex.timings

nameusersystemelapsed
Les-class000
Les0.030.000.03
chi22.860.032.89
ci9.130.009.13
estimate0.220.000.22
export000
les-package11.12 0.0311.15
plot0.220.030.25
regions0.190.000.19
threshold0.190.000.19
weighting0.010.000.02

les.Rcheck/examples_x64/les-Ex.timings

nameusersystemelapsed
Les-class000
Les0.020.000.01
chi22.720.042.75
ci9.250.009.25
estimate0.210.010.22
export000
les-package11.5 0.011.5
plot0.210.000.20
regions0.20.00.2
threshold0.190.000.19
weighting0.020.000.01