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This page was generated on 2021-09-18 12:06:19 -0400 (Sat, 18 Sep 2021).

CHECK results for proActiv on riesling1

To the developers/maintainers of the proActiv package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/proActiv.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 1420/2029HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
proActiv 1.3.4  (landing page)
Joseph Lee
Snapshot Date: 2021-09-17 14:50:09 -0400 (Fri, 17 Sep 2021)
git_url: https://git.bioconductor.org/packages/proActiv
git_branch: master
git_last_commit: a0df319
git_last_commit_date: 2021-06-23 06:28:09 -0400 (Wed, 23 Jun 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: proActiv
Version: 1.3.4
Command: D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:proActiv.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings proActiv_1.3.4.tar.gz
StartedAt: 2021-09-18 02:29:06 -0400 (Sat, 18 Sep 2021)
EndedAt: 2021-09-18 02:40:28 -0400 (Sat, 18 Sep 2021)
EllapsedTime: 681.4 seconds
RetCode: 0
Status:   OK  
CheckDir: proActiv.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:proActiv.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings proActiv_1.3.4.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.14-bioc/meat/proActiv.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 'proActiv/DESCRIPTION' ... OK
* this is package 'proActiv' version '1.3.4'
* 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 'proActiv' 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 LazyData ... 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
preparePromoterAnnotation 14.25   0.07   14.33
integrateProactiv          6.08   0.03    6.11
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
preparePromoterAnnotation 15.53   0.04   15.56
integrateProactiv          6.56   0.03    6.59
* 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

proActiv.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/proActiv_1.3.4.tar.gz && rm -rf proActiv.buildbin-libdir && mkdir proActiv.buildbin-libdir && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=proActiv.buildbin-libdir proActiv_1.3.4.tar.gz && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL proActiv_1.3.4.zip && rm proActiv_1.3.4.tar.gz proActiv_1.3.4.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
 83 3469k   83 2912k    0     0  3681k      0 --:--:-- --:--:-- --:--:-- 3676k
100 3469k  100 3469k    0     0  3846k      0 --:--:-- --:--:-- --:--:-- 3842k

install for i386

* installing *source* package 'proActiv' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'proActiv'
    finding HTML links ... done
    PromoterAnnotation-class                html  
    boxplotPromoters                        html  
    calculateJunctionReadCounts             html  
    calculatePromoterReadCounts             html  
    getAbsolutePromoterActivity             html  
    getAlternativePromoters                 html  
    getGeneExpression                       html  
    getRelativePromoterActivity             html  
    integrateProactiv                       html  
    normalizePromoterReadCounts             html  
    plotHeatmap                             html  
    plotPCA                                 html  
    preparePromoterAnnotation               html  
    proActiv                                html  
    promoterAnnotation.gencode.v34.subset   html  
    reexports                               html  
*** copying figures
** 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 'proActiv' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'proActiv' as proActiv_1.3.4.zip
* DONE (proActiv)
* installing to library 'D:/biocbuild/bbs-3.14-bioc/R/library'
package 'proActiv' successfully unpacked and MD5 sums checked

Tests output

proActiv.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(proActiv)

Attaching package: 'proActiv'

The following object is masked from 'package:stats':

    filter

> 
> test_check("proActiv")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 22 ]
> 
> proc.time()
   user  system elapsed 
 107.06    0.70  118.48 

proActiv.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(proActiv)

Attaching package: 'proActiv'

The following object is masked from 'package:stats':

    filter

> 
> test_check("proActiv")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 22 ]
> 
> proc.time()
   user  system elapsed 
 119.39    1.09  133.26 

Example timings

proActiv.Rcheck/examples_i386/proActiv-Ex.timings

nameusersystemelapsed
PromoterAnnotation-class0.040.000.04
boxplotPromoters2.600.022.61
getAlternativePromoters3.780.043.83
integrateProactiv6.080.036.11
plotHeatmap2.410.022.42
plotPCA2.230.002.24
preparePromoterAnnotation14.25 0.0714.33
proActiv2.660.002.65

proActiv.Rcheck/examples_x64/proActiv-Ex.timings

nameusersystemelapsed
PromoterAnnotation-class0.030.000.03
boxplotPromoters2.850.092.94
getAlternativePromoters4.310.024.33
integrateProactiv6.560.036.59
plotHeatmap2.640.012.66
plotPCA2.470.002.47
preparePromoterAnnotation15.53 0.0415.56
proActiv2.330.012.34