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This page was generated on 2022-04-13 12:06:27 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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 DiffLogo on tokay2


To the developers/maintainers of the DiffLogo package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DiffLogo.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 508/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DiffLogo 2.18.0  (landing page)
Hendrik Treutler
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/DiffLogo
git_branch: RELEASE_3_14
git_last_commit: 8ac0955
git_last_commit_date: 2021-10-26 12:22:35 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: DiffLogo
Version: 2.18.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DiffLogo.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings DiffLogo_2.18.0.tar.gz
StartedAt: 2022-04-12 18:38:34 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 18:39:34 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 60.3 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: DiffLogo.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DiffLogo.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings DiffLogo_2.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/DiffLogo.Rcheck'
* using R version 4.1.3 (2022-03-10)
* 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 '2.18.0'
* 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 ... WARNING
Warning: S4 exports specified in 'NAMESPACE' but not defined in package 'DiffLogo'
** 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 ... WARNING
Warning: S4 exports specified in 'NAMESPACE' but not defined in package 'DiffLogo'
** 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 ... NOTE
diffLogo: no visible global function definition for 'is'
preconditionTransformPWM: no visible global function definition for
  'is'
Undefined global functions or variables:
  is
Consider adding
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 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: 2 WARNINGs, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/DiffLogo.Rcheck/00check.log'
for details.



Installation output

DiffLogo.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/DiffLogo_2.18.0.tar.gz && rm -rf DiffLogo.buildbin-libdir && mkdir DiffLogo.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DiffLogo.buildbin-libdir DiffLogo_2.18.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL DiffLogo_2.18.0.zip && rm DiffLogo_2.18.0.tar.gz DiffLogo_2.18.0.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  743k  100  743k    0     0   951k      0 --:--:-- --:--:-- --:--:--  953k

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_2.18.0.zip
* DONE (DiffLogo)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'DiffLogo' successfully unpacked and MD5 sums checked

Tests output

DiffLogo.Rcheck/tests_i386/testthat.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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 
   0.26    0.06    0.31 

DiffLogo.Rcheck/tests_x64/testthat.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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 

Example timings

DiffLogo.Rcheck/examples_i386/DiffLogo-Ex.timings

nameusersystemelapsed
ASN000
Alphabet000
DNA000
FULL_ALPHABET000
RNA000
calculatePvalue0.040.000.05
createDiffLogoObject0.110.000.11
diffLogo0.100.000.09
diffLogoFromPwm0.070.000.08
diffLogoTable1.380.021.39
diffLogoTableConfiguration000
differenceOfICs0.370.000.38
drawDiffLogoTable1.350.001.34
enrichDiffLogoObjectWithPvalues0.230.000.24
enrichDiffLogoTableWithPvalues3.570.013.57
extendPwmsFromAlignmentVector0.030.000.03
getAlphabetFromCharacters0.020.000.02
getAlphabetFromSequences000
getPwmFromAlignment0.480.000.48
getPwmFromAlignmentFile000
getPwmFromFastaFile0.020.000.02
getPwmFromFile000
getPwmFromHomerFile0.010.000.01
getPwmFromPfmOrJasparFile000
getPwmFromPwmFile000
getSequencesFromAlignmentFile000
getSequencesFromFastaFile000
informationContent0.10.00.1
lossOfAbsICDifferences0.070.000.06
multipleLocalPwmsAlignment0.030.020.05
normalizePWM000
normalizedDifferenceOfProbabilities0.060.020.08
prepareDiffLogoTable0.780.000.78
probabilities0.050.010.06
seqLogo0.060.000.07
shannonDivergence0.080.000.07
sumOfAbsICDifferences0.080.000.08
sumOfAbsProbabilityDifferences0.070.000.08
sumProbabilities0.050.000.05

DiffLogo.Rcheck/examples_x64/DiffLogo-Ex.timings

nameusersystemelapsed
ASN000
Alphabet000
DNA000
FULL_ALPHABET000
RNA000
calculatePvalue0.040.000.03
createDiffLogoObject0.090.000.09
diffLogo0.090.000.10
diffLogoFromPwm0.080.000.07
diffLogoTable1.310.001.32
diffLogoTableConfiguration000
differenceOfICs0.390.000.39
drawDiffLogoTable1.250.021.26
enrichDiffLogoObjectWithPvalues0.210.000.21
enrichDiffLogoTableWithPvalues3.320.033.35
extendPwmsFromAlignmentVector0.040.000.04
getAlphabetFromCharacters000
getAlphabetFromSequences000
getPwmFromAlignment0.470.000.47
getPwmFromAlignmentFile0.020.000.02
getPwmFromFastaFile0.010.000.01
getPwmFromFile000
getPwmFromHomerFile000
getPwmFromPfmOrJasparFile000
getPwmFromPwmFile0.020.000.02
getSequencesFromAlignmentFile000
getSequencesFromFastaFile000
informationContent0.090.000.09
lossOfAbsICDifferences0.080.000.08
multipleLocalPwmsAlignment0.030.000.03
normalizePWM000
normalizedDifferenceOfProbabilities0.060.000.06
prepareDiffLogoTable0.820.020.83
probabilities0.060.000.06
seqLogo0.060.000.07
shannonDivergence0.060.000.06
sumOfAbsICDifferences0.080.000.08
sumOfAbsProbabilityDifferences0.060.000.06
sumProbabilities0.070.000.06