Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-10-15 15:06:25 -0400 (Fri, 15 Oct 2021).

CHECK results for tomoda on tokay2

To the developers/maintainers of the tomoda package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/tomoda.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
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raw results

Package 1933/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
tomoda 1.2.0  (landing page)
Wendao Liu
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/tomoda
git_branch: RELEASE_3_13
git_last_commit: fa482a2
git_last_commit_date: 2021-05-19 12:56:18 -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: tomoda
Version: 1.2.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:tomoda.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings tomoda_1.2.0.tar.gz
StartedAt: 2021-10-15 06:45:03 -0400 (Fri, 15 Oct 2021)
EndedAt: 2021-10-15 06:55:56 -0400 (Fri, 15 Oct 2021)
EllapsedTime: 653.1 seconds
RetCode: 0
Status:   OK  
CheckDir: tomoda.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:tomoda.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings tomoda_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/tomoda.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 'tomoda/DESCRIPTION' ... OK
* this is package 'tomoda' version '1.2.0'
* package encoding: UTF-8
* 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 'tomoda' 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 ... 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
findPeakGene   63.94   0.07   64.00
geneCorHeatmap 34.34   0.04   34.39
geneEmbedPlot  29.69   0.32   30.00
expHeatmap     26.08   0.40   26.49
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
findPeakGene   70.98   0.10   71.08
geneCorHeatmap 35.56   0.67   36.24
geneEmbedPlot  31.58   0.00   31.60
expHeatmap     26.25   0.03   26.29
* 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: OK


Installation output

tomoda.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/tomoda_1.2.0.tar.gz && rm -rf tomoda.buildbin-libdir && mkdir tomoda.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=tomoda.buildbin-libdir tomoda_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL tomoda_1.2.0.zip && rm tomoda_1.2.0.tar.gz tomoda_1.2.0.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  250k  100  250k    0     0   745k      0 --:--:-- --:--:-- --:--:--  748k

install for i386

* installing *source* package 'tomoda' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'tomoda'
    finding HTML links ... done
    corHeatmap                              html  
    createTomo                              html  
    embedPlot                               html  
    expHeatmap                              html  
    findPeak                                html  
    findPeakGene                            html  
    geneCorHeatmap                          html  
    geneEmbedPlot                           html  
    hierarchClust                           html  
    kmeansClust                             html  
    linePlot                                html  
    normalizeTomo                           html  
    runPCA                                  html  
    runTSNE                                 html  
    runUMAP                                 html  
    scaleTomo                               html  
    tomoMatrix                              html  
    tomoSummarizedExperiment                html  
    zh.data                                 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 'tomoda' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'tomoda' as tomoda_1.2.0.zip
* DONE (tomoda)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'tomoda' successfully unpacked and MD5 sums checked

Tests output

tomoda.Rcheck/tests_i386/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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.

> library(testthat)
> library(tomoda)
> 
> test_check("tomoda")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 43 ]
> 
> proc.time()
   user  system elapsed 
  37.64    1.90   39.53 

tomoda.Rcheck/tests_x64/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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.

> library(testthat)
> library(tomoda)
> 
> test_check("tomoda")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 43 ]
> 
> proc.time()
   user  system elapsed 
  43.39    0.96   52.31 

Example timings

tomoda.Rcheck/examples_i386/tomoda-Ex.timings

nameusersystemelapsed
corHeatmap1.630.221.84
createTomo1.560.051.61
embedPlot3.810.143.95
expHeatmap26.08 0.4026.49
findPeak000
findPeakGene63.94 0.0764.00
geneCorHeatmap34.34 0.0434.39
geneEmbedPlot29.69 0.3230.00
hierarchClust1.250.001.25
kmeansClust1.090.061.15
linePlot1.460.031.49
normalizeTomo0.20.00.2
runPCA1.360.031.39
runTSNE1.690.021.70
runUMAP1.400.001.41
scaleTomo0.540.000.53
tomoMatrix0.540.000.55
tomoSummarizedExperiment0.670.040.72

tomoda.Rcheck/examples_x64/tomoda-Ex.timings

nameusersystemelapsed
corHeatmap2.200.052.25
createTomo1.750.031.78
embedPlot3.430.003.43
expHeatmap26.25 0.0326.29
findPeak000
findPeakGene70.98 0.1071.08
geneCorHeatmap35.56 0.6736.24
geneEmbedPlot31.58 0.0031.60
hierarchClust2.280.012.30
kmeansClust1.960.021.97
linePlot1.570.001.58
normalizeTomo0.190.000.19
runPCA1.020.001.01
runTSNE1.230.031.27
runUMAP1.810.021.83
scaleTomo0.710.000.70
tomoMatrix0.780.010.80
tomoSummarizedExperiment0.700.020.72