Multiple platform build/check report for BioC 3.10 - CHECK report for DiffLogo on tokay1

Package: DiffLogo

Version: 2.10.0

Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DiffLogo.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings DiffLogo_2.10.0.tar.gz

StartedAt: 2020-04-15 02:41:22 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 02:42:16 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 54.5 seconds

RetCode: 0

Status: WARNINGS

CheckDir: DiffLogo.Rcheck

Warnings: 1

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DiffLogo.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings DiffLogo_2.10.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/DiffLogo.Rcheck'
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'DiffLogo/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'DiffLogo' version '2.10.0'
* 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 'DiffLogo' 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
* 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 ... 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 ... 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 ... WARNING
Documented arguments not in \usage in documentation object 'diffLogoTableConfiguration':
  '...'

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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.R'
 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 WARNING
See
  'C:/Users/biocbuild/bbs-3.10-bioc/meat/DiffLogo.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/DiffLogo_2.10.0.tar.gz && rm -rf DiffLogo.buildbin-libdir && mkdir DiffLogo.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DiffLogo.buildbin-libdir DiffLogo_2.10.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL DiffLogo_2.10.0.zip && rm DiffLogo_2.10.0.tar.gz DiffLogo_2.10.0.zip
###
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  % 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  740k  100  740k    0     0  18.5M      0 --:--:-- --:--:-- --:--:-- 20.6M

install for i386

* installing *source* package 'DiffLogo' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'DiffLogo'
    finding HTML links ... done
    ASN                                     html  
    Alphabet                                html  
    DNA                                     html  
    FULL_ALPHABET                           html  
    RNA                                     html  
    alignPwmSets                            html  
    baseDistributionPwm                     html  
    calculatePvalue                         html  
    createDiffLogoObject                    html  
    diffLogo                                html  
    diffLogoFromPwm                         html  
    diffLogoTable                           html  
    diffLogoTableConfiguration              html  
    differenceOfICs                         html  
    drawDiffLogoTable                       html  
    enrichDiffLogoObjectWithPvalues         html  
    enrichDiffLogoTableWithPvalues          html  
    extendPwmsFromAlignmentVector           html  
    getAlphabetFromCharacters               html  
    getAlphabetFromSequences                html  
    getPwmFromAlignment                     html  
    getPwmFromAlignmentFile                 html  
    getPwmFromFastaFile                     html  
    getPwmFromFile                          html  
    getPwmFromHomerFile                     html  
    getPwmFromPfmOrJasparFile               html  
    getPwmFromPwmFile                       html  
    getSequencesFromAlignmentFile           html  
    getSequencesFromFastaFile               html  
    informationContent                      html  
    localPwmAlignment                       html  
    lossOfAbsICDifferences                  html  
    multipleLocalPwmsAlignment              html  
    normalizePWM                            html  
    normalizedDifferenceOfProbabilities     html  
    prepareDiffLogoTable                    html  
    probabilities                           html  
    pwmDivergence                           html  
    pwmsDistanceMatrix                      html  
    reverseAlignmentVector                  html  
    seqLogo                                 html  
    shannonDivergence                       html  
    sumOfAbsICDifferences                   html  
    sumOfAbsProbabilityDifferences          html  
    sumProbabilities                        html  
    switchDirection                         html  
    twoSetsAveragePwmDivergenceFromAlignmentVector
                                            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 'DiffLogo' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DiffLogo' as DiffLogo_2.10.0.zip
* DONE (DiffLogo)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'DiffLogo' successfully unpacked and MD5 sums checked


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> 
> proc.time()
   user  system elapsed 
   0.25    0.01    0.25


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> 
> proc.time()
   user  system elapsed 
   0.25    0.03    0.26

name	user	system	elapsed
ASN	0	0	0
Alphabet	0	0	0
DNA	0	0	0
FULL_ALPHABET	0	0	0
RNA	0	0	0
calculatePvalue	0.05	0.00	0.04
createDiffLogoObject	0.08	0.02	0.13
diffLogo	0.06	0.00	0.06
diffLogoFromPwm	0.08	0.00	0.08
diffLogoTable	1.25	0.03	1.28
diffLogoTableConfiguration	0	0	0
differenceOfICs	0.37	0.00	0.37
drawDiffLogoTable	1.24	0.00	1.24
enrichDiffLogoObjectWithPvalues	0.20	0.01	0.22
enrichDiffLogoTableWithPvalues	3.83	0.00	3.83
extendPwmsFromAlignmentVector	0.03	0.00	0.03
getAlphabetFromCharacters	0	0	0
getAlphabetFromSequences	0	0	0
getPwmFromAlignment	0.47	0.04	0.50
getPwmFromAlignmentFile	0.02	0.00	0.01
getPwmFromFastaFile	0.01	0.00	0.02
getPwmFromFile	0.02	0.00	0.03
getPwmFromHomerFile	0	0	0
getPwmFromPfmOrJasparFile	0	0	0
getPwmFromPwmFile	0.01	0.00	0.01
getSequencesFromAlignmentFile	0	0	0
getSequencesFromFastaFile	0	0	0
informationContent	0.1	0.0	0.1
lossOfAbsICDifferences	0.07	0.00	0.08
multipleLocalPwmsAlignment	0.04	0.00	0.03
normalizePWM	0	0	0
normalizedDifferenceOfProbabilities	0.06	0.00	0.06
prepareDiffLogoTable	0.73	0.00	0.73
probabilities	0.06	0.00	0.07
seqLogo	0.05	0.00	0.04
shannonDivergence	0.06	0.00	0.06
sumOfAbsICDifferences	0.08	0.00	0.08
sumOfAbsProbabilityDifferences	0.08	0.00	0.08
sumProbabilities	0.06	0.00	0.06

name	user	system	elapsed
ASN	0	0	0
Alphabet	0	0	0
DNA	0	0	0
FULL_ALPHABET	0	0	0
RNA	0	0	0
calculatePvalue	0.03	0.00	0.04
createDiffLogoObject	0.08	0.00	0.07
diffLogo	0.06	0.01	0.08
diffLogoFromPwm	0.06	0.02	0.08
diffLogoTable	1.25	0.03	1.28
diffLogoTableConfiguration	0	0	0
differenceOfICs	0.39	0.00	0.39
drawDiffLogoTable	1.25	0.01	1.27
enrichDiffLogoObjectWithPvalues	0.22	0.00	0.22
enrichDiffLogoTableWithPvalues	3.46	0.02	3.47
extendPwmsFromAlignmentVector	0.01	0.02	0.03
getAlphabetFromCharacters	0	0	0
getAlphabetFromSequences	0	0	0
getPwmFromAlignment	0.45	0.03	0.49
getPwmFromAlignmentFile	0	0	0
getPwmFromFastaFile	0	0	0
getPwmFromFile	0.02	0.00	0.02
getPwmFromHomerFile	0	0	0
getPwmFromPfmOrJasparFile	0	0	0
getPwmFromPwmFile	0	0	0
getSequencesFromAlignmentFile	0	0	0
getSequencesFromFastaFile	0	0	0
informationContent	0.09	0.00	0.09
lossOfAbsICDifferences	0.08	0.00	0.08
multipleLocalPwmsAlignment	0.03	0.00	0.03
normalizePWM	0	0	0
normalizedDifferenceOfProbabilities	0.05	0.02	0.06
prepareDiffLogoTable	0.89	0.00	0.89
probabilities	0.07	0.00	0.08
seqLogo	0.07	0.00	0.06
shannonDivergence	0.06	0.00	0.07
sumOfAbsICDifferences	0.08	0.00	0.08
sumOfAbsProbabilityDifferences	0.08	0.00	0.07
sumProbabilities	0.06	0.00	0.07

CHECK report for DiffLogo on tokay1

Summary

Command output

Installation output

Tests output

Example timings