Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:06:09 -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 airpart on tokay2


To the developers/maintainers of the airpart package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/airpart.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 39/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
airpart 1.2.0  (landing page)
Wancen Mu
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/airpart
git_branch: RELEASE_3_14
git_last_commit: 62f2b32
git_last_commit_date: 2021-10-26 13:08:14 -0400 (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: airpart
Version: 1.2.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:airpart.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings airpart_1.2.0.tar.gz
StartedAt: 2022-04-12 15:28:42 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 15:37:03 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 501.1 seconds
RetCode: 0
Status:   OK  
CheckDir: airpart.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:airpart.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings airpart_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/airpart.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 'airpart/DESCRIPTION' ... OK
* this is package 'airpart' 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 'airpart' 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
allelicRatio  7.80   0.11    7.94
makeStep      6.91   0.01    6.93
makeForest    6.39   0.00    6.39
makeHeatmap   5.98   0.28    7.58
makeViolin    5.26   0.00    5.28
consensusPart 2.25   0.02   16.11
fusedLasso    2.10   0.08    9.28
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
makeStep      8.17   0.00    8.17
allelicRatio  7.91   0.01    7.92
makeForest    6.87   0.00    6.87
makeHeatmap   5.64   0.03    5.68
makeViolin    5.34   0.00    5.35
extractResult 5.20   0.00    5.21
consensusPart 2.25   0.08   16.09
fusedLasso    1.83   0.08    8.73
* 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

airpart.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/airpart_1.2.0.tar.gz && rm -rf airpart.buildbin-libdir && mkdir airpart.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=airpart.buildbin-libdir airpart_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL airpart_1.2.0.zip && rm airpart_1.2.0.tar.gz airpart_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 31769  100 31769    0     0   262k      0 --:--:-- --:--:-- --:--:--  265k

install for i386

* installing *source* package 'airpart' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'airpart'
    finding HTML links ... done
    allelicRatio                            html  
    cellQC                                  html  
    consensusPart                           html  
    estDisp                                 html  
    extractResult                           html  
    featureQC                               html  
    fusedLasso                              html  
    geneCluster                             html  
    makeForest                              html  
    makeHeatmap                             html  
    makeOffByOneAdjMat                      html  
    makeSimulatedData                       html  
    makeStep                                html  
    makeViolin                              html  
    preprocess                              html  
    summaryAllelicRatio                     html  
    wilcoxExt                               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 'airpart' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'airpart' as airpart_1.2.0.zip
* DONE (airpart)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'airpart' successfully unpacked and MD5 sums checked

Tests output

airpart.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.

> library(testthat)
> library(airpart)
> 
> test_check("airpart")
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min


Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname

model-based optimal number of clusters: 3 
model-based optimal number of clusters: 3 
model-based optimal number of clusters: 3 
starting worker pid=11356 on localhost:11774 at 15:35:47.679
starting worker pid=3748 on localhost:11774 at 15:35:47.695
model-based optimal number of clusters: 3 
[ FAIL 0 | WARN 18 | SKIP 0 | PASS 12 ]

[ FAIL 0 | WARN 18 | SKIP 0 | PASS 12 ]
> 
> proc.time()
   user  system elapsed 
  18.04    1.50   40.54 

airpart.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.

> library(testthat)
> library(airpart)
> 
> test_check("airpart")
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min


Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname

model-based optimal number of clusters: 3 
model-based optimal number of clusters: 3 
model-based optimal number of clusters: 3 
starting worker pid=3928 on localhost:11735 at 15:36:29.586
starting worker pid=5768 on localhost:11735 at 15:36:29.789
model-based optimal number of clusters: 3 
[ FAIL 0 | WARN 18 | SKIP 0 | PASS 12 ]

[ FAIL 0 | WARN 18 | SKIP 0 | PASS 12 ]
> 
> proc.time()
   user  system elapsed 
  20.26    0.62   44.67 

Example timings

airpart.Rcheck/examples_i386/airpart-Ex.timings

nameusersystemelapsed
allelicRatio7.800.117.94
cellQC0.700.230.95
consensusPart 2.25 0.0216.11
estDisp1.950.001.95
extractResult4.890.004.89
featureQC2.540.122.66
fusedLasso2.100.089.28
geneCluster0.600.000.59
makeForest6.390.006.39
makeHeatmap5.980.287.58
makeOffByOneAdjMat0.210.000.20
makeSimulatedData0.340.000.34
makeStep6.910.016.93
makeViolin5.260.005.28
preprocess0.630.050.67
summaryAllelicRatio0.900.000.91
wilcoxExt1.960.031.99

airpart.Rcheck/examples_x64/airpart-Ex.timings

nameusersystemelapsed
allelicRatio7.910.017.92
cellQC0.700.020.72
consensusPart 2.25 0.0816.09
estDisp2.240.012.25
extractResult5.200.005.21
featureQC2.610.002.61
fusedLasso1.830.088.73
geneCluster0.610.000.61
makeForest6.870.006.87
makeHeatmap5.640.035.68
makeOffByOneAdjMat0.220.000.21
makeSimulatedData0.380.000.38
makeStep8.170.008.17
makeViolin5.340.005.35
preprocess0.550.000.54
summaryAllelicRatio0.950.000.96
wilcoxExt2.130.002.12