Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-24 13:05:50 -0500 (Mon, 24 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4080
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4141
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 a4Base on tokay2


To the developers/maintainers of the a4Base package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/a4Base.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 2/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
a4Base 1.42.0  (landing page)
Laure Cougnaud
Snapshot Date: 2022-01-23 01:55:04 -0500 (Sun, 23 Jan 2022)
git_url: https://git.bioconductor.org/packages/a4Base
git_branch: RELEASE_3_14
git_last_commit: d7296e2
git_last_commit_date: 2021-10-26 11:58:47 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 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: a4Base
Version: 1.42.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:a4Base.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings a4Base_1.42.0.tar.gz
StartedAt: 2022-01-23 15:02:09 -0500 (Sun, 23 Jan 2022)
EndedAt: 2022-01-23 15:07:48 -0500 (Sun, 23 Jan 2022)
EllapsedTime: 339.3 seconds
RetCode: 0
Status:   OK  
CheckDir: a4Base.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:a4Base.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings a4Base_1.42.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/a4Base.Rcheck'
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'a4Base/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'a4Base' version '1.42.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: 'JavaGD'
* 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 'a4Base' can be installed ... OK
* checking installed package size ... OK
* checking package 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 ... 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 examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
spectralMap     11.56   0.76   12.33
plotLogRatio     5.43   0.21    5.64
computeLogRatio  5.22   0.19    5.41
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
spectralMap     12.53   0.53   13.08
computeLogRatio  5.11   0.11    5.29
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/a4Base.Rcheck/00check.log'
for details.



Installation output

a4Base.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/a4Base_1.42.0.tar.gz && rm -rf a4Base.buildbin-libdir && mkdir a4Base.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=a4Base.buildbin-libdir a4Base_1.42.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL a4Base_1.42.0.zip && rm a4Base_1.42.0.tar.gz a4Base_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
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  368k  100  368k    0     0  1248k      0 --:--:-- --:--:-- --:--:-- 1248k

install for i386

* installing *source* package 'a4Base' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'a4Base'
    finding HTML links ... done
    ExpressionSetWithComputation-class      html  
    finding level-2 HTML links ... done

    a4palette                               html  
    addQuantilesColors                      html  
    boxPlot                                 html  
    combineTwoExpressionSet                 html  
    computeLogRatio                         html  
    createExpressionSet                     html  
    filterVarInt                            html  
    heatmap.expressionSet                   html  
    histPvalue                              html  
    histpvalueplotter                       html  
    lassoReg                                html  
    limmaReg                                html  
    limmaTwoLevels                          html  
    logReg                                  html  
    nlcvTT                                  html  
    oaColors                                html  
    oaPalette                               html  
    plot1gene                               html  
    plotComb2Samples                        html  
    plotCombMultSamples                     html  
    plotCombination2genes                   html  
    plotLogRatio                            html  
    probabilitiesPlot                       html  
    probe2gene                              html  
    profilesPlot                            html  
    propDEgenes-methods                     html  
    propDEgenes                             html  
    propdegenescalculation                  html  
    replicates                              html  
    spectralMap-methods                     html  
    spectralMap                             html  
    tTest                                   html  
    topTable-methods                        html  
    volcanoPlot-methods                     html  
    volcanoPlot                             html  
    volcanoplotter                          html  
** building package indices
** 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 'a4Base' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'a4Base' as a4Base_1.42.0.zip
* DONE (a4Base)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'a4Base' successfully unpacked and MD5 sums checked

Tests output


Example timings

a4Base.Rcheck/examples_i386/a4Base-Ex.timings

nameusersystemelapsed
a4palette0.020.000.03
addQuantilesColors2.920.163.08
boxPlot3.080.043.12
combineTwoExpressionSet000
computeLogRatio5.220.195.41
createExpressionSet0.050.000.04
filterVarInt2.080.082.16
heatmap.expressionSet000
histPvalue2.400.082.49
histpvalueplotter1.950.092.04
lassoReg2.490.242.81
logReg000
nlcvTT000
plot1gene2.390.042.44
plotComb2Samples2.390.052.46
plotCombMultSamples3.880.164.03
plotCombination2genes3.390.043.43
plotLogRatio5.430.215.64
probabilitiesPlot000
probe2gene2.080.092.17
profilesPlot2.170.052.22
propdegenescalculation2.300.112.41
replicates000
spectralMap11.56 0.7612.33
tTest3.340.133.46
volcanoPlot2.800.042.85

a4Base.Rcheck/examples_x64/a4Base-Ex.timings

nameusersystemelapsed
a4palette0.010.000.01
addQuantilesColors1.990.042.03
boxPlot2.370.072.44
combineTwoExpressionSet000
computeLogRatio5.110.115.29
createExpressionSet0.070.000.06
filterVarInt3.060.133.19
heatmap.expressionSet000
histPvalue2.110.042.16
histpvalueplotter1.560.021.58
lassoReg1.700.031.73
logReg000
nlcvTT000
plot1gene1.600.051.64
plotComb2Samples2.290.042.35
plotCombMultSamples2.830.082.92
plotCombination2genes3.250.143.39
plotLogRatio4.790.074.86
probabilitiesPlot000
probe2gene2.230.042.28
profilesPlot1.960.102.05
propdegenescalculation1.560.061.62
replicates000
spectralMap12.53 0.5313.08
tTest2.670.082.75
volcanoPlot2.630.052.67