Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2021-10-19 12:04:46 -0400 (Tue, 19 Oct 2021).

CHECK results for airpart on riesling1

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? 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 39/2060HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
airpart 1.1.4  (landing page)
Wancen Mu
Snapshot Date: 2021-10-18 14:50:10 -0400 (Mon, 18 Oct 2021)
git_url: https://git.bioconductor.org/packages/airpart
git_branch: master
git_last_commit: fb9467c
git_last_commit_date: 2021-10-17 22:12:42 -0400 (Sun, 17 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: airpart
Version: 1.1.4
Command: D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:airpart.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings airpart_1.1.4.tar.gz
StartedAt: 2021-10-19 00:08:15 -0400 (Tue, 19 Oct 2021)
EndedAt: 2021-10-19 00:16:02 -0400 (Tue, 19 Oct 2021)
EllapsedTime: 466.7 seconds
RetCode: 0
Status:   OK  
CheckDir: airpart.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:airpart.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings airpart_1.1.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.14-bioc/meat/airpart.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 'airpart/DESCRIPTION' ... OK
* this is package 'airpart' version '1.1.4'
* 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 ... NOTE
allelicRatio: no visible global function definition for 'pchisq'
allelicRatio: no visible global function definition for 'p.adjust'
Undefined global functions or variables:
  p.adjust pchisq
Consider adding
  importFrom("stats", "p.adjust", "pchisq")
to your NAMESPACE file.
* 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  5.61   0.00    5.61
makeStep      5.05   0.00    5.04
consensusPart 1.66   0.03   10.89
fusedLasso    1.10   0.04    5.37
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
allelicRatio  5.50   0.08    5.58
consensusPart 1.64   0.07   10.41
fusedLasso    1.11   0.01    5.45
* 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 NOTE
See
  'D:/biocbuild/bbs-3.14-bioc/meat/airpart.Rcheck/00check.log'
for details.



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_1.1.4.tar.gz && rm -rf airpart.buildbin-libdir && mkdir airpart.buildbin-libdir && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=airpart.buildbin-libdir airpart_1.1.4.tar.gz && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL airpart_1.1.4.zip && rm airpart_1.1.4.tar.gz airpart_1.1.4.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 31130  100 31130    0     0  78611      0 --:--:-- --:--:-- --:--:-- 78611

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_1.1.4.zip
* DONE (airpart)
* installing to library 'D:/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 4.1.1 (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(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=15660 on localhost:11418 at 00:12:59.738
starting worker pid=6716 on localhost:11418 at 00:12:59.754
model-based optimal number of clusters: 3 
[ FAIL 0 | WARN 18 | SKIP 0 | PASS 12 ]
> 
> proc.time()
   user  system elapsed 
  11.90    0.25   22.06 

airpart.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(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=1336 on localhost:11281 at 00:13:23.516
starting worker pid=11456 on localhost:11281 at 00:13:23.516
model-based optimal number of clusters: 3 
[ FAIL 0 | WARN 18 | SKIP 0 | PASS 12 ]
> 
> proc.time()
   user  system elapsed 
  13.03    0.59   23.93 

Example timings

airpart.Rcheck/examples_i386/airpart-Ex.timings

nameusersystemelapsed
allelicRatio5.610.005.61
cellQC0.480.000.49
consensusPart 1.66 0.0310.89
estDisp1.290.001.30
extractResult3.490.003.48
featureQC1.370.001.38
fusedLasso1.100.045.37
geneCluster0.340.000.35
makeForest4.160.004.15
makeHeatmap3.610.043.66
makeOffByOneAdjMat0.120.000.13
makeSimulatedData0.220.030.25
makeStep5.050.005.04
makeViolin3.720.003.72
preprocess0.280.050.33
summaryAllelicRatio0.530.000.53
wilcoxExt1.310.001.31

airpart.Rcheck/examples_x64/airpart-Ex.timings

nameusersystemelapsed
allelicRatio5.500.085.58
cellQC0.490.010.50
consensusPart 1.64 0.0710.41
estDisp1.250.001.25
extractResult3.310.003.31
featureQC1.450.001.45
fusedLasso1.110.015.45
geneCluster0.380.000.38
makeForest4.010.004.01
makeHeatmap3.440.023.46
makeOffByOneAdjMat0.140.000.14
makeSimulatedData0.220.010.23
makeStep4.980.004.99
makeViolin4.150.004.14
preprocess0.320.020.34
summaryAllelicRatio0.550.000.55
wilcoxExt1.230.011.25