Multiple platform build/check report for BioC 3.12 - CHECK report for periodicDNA on tokay1

Package: periodicDNA

Version: 1.0.0

Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:periodicDNA.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings periodicDNA_1.0.0.tar.gz

StartedAt: 2021-05-06 05:28:08 -0400 (Thu, 06 May 2021)

EndedAt: 2021-05-06 05:37:00 -0400 (Thu, 06 May 2021)

EllapsedTime: 532.2 seconds

RetCode: 0

Status: OK

CheckDir: periodicDNA.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:periodicDNA.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings periodicDNA_1.0.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/periodicDNA.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'periodicDNA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'periodicDNA' version '1.0.0'
* 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 'periodicDNA' 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
getPeriodicity         19.24   1.14   22.39
getPeriodicityTrack     8.56   1.10    9.66
plotPeriodicityResults  8.28   0.22    8.50
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
getPeriodicity         17.15   0.95   18.11
plotPeriodicityResults  7.69   0.17    7.86
getPeriodicityTrack     6.16   0.17    6.33
* 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

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###
### Running command:
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###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/periodicDNA_1.0.0.tar.gz && rm -rf periodicDNA.buildbin-libdir && mkdir periodicDNA.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=periodicDNA.buildbin-libdir periodicDNA_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL periodicDNA_1.0.0.zip && rm periodicDNA_1.0.0.tar.gz periodicDNA_1.0.0.zip
###
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  % 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 2761k  100 2761k    0     0  44.8M      0 --:--:-- --:--:-- --:--:-- 45.7M

install for i386

* installing *source* package 'periodicDNA' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'periodicDNA'
    finding HTML links ... done
    ce11_ATACseq                            html  
    ce11_TSSs                               html  
    ce11_WW_10bp                            html  
    ce11_all_REs                            html  
    ce11_proms                              html  
    ce11_proms_seqs                         html  
    getPeriodicity                          html  
    getPeriodicityTrack                     html  
    getPeriodicityWithIterations            html  
    plotAggregateCoverage                   html  
    plotPeriodicityResults                  html  
    setUpBPPARAM                            html  
    theme_ggplot2                           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 'periodicDNA' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'periodicDNA' as periodicDNA_1.0.0.zip
* DONE (periodicDNA)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'periodicDNA' successfully unpacked and MD5 sums checked


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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(periodicDNA)
Loading required package: Biostrings
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

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

    windows

Loading required package: XVector

Attaching package: 'Biostrings'

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

    strsplit

Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: BSgenome
Loading required package: rtracklayer
Loading required package: BiocParallel
> library(BiocParallel)
> register(setUpBPPARAM(1), default = TRUE)
> 
> test_check("periodicDNA")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 6 ]
> 
> proc.time()
   user  system elapsed 
  53.23    3.62   56.82


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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(periodicDNA)
Loading required package: Biostrings
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

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

    windows

Loading required package: XVector

Attaching package: 'Biostrings'

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

    strsplit

Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: BSgenome
Loading required package: rtracklayer
Loading required package: BiocParallel
> library(BiocParallel)
> register(setUpBPPARAM(1), default = TRUE)
> 
> test_check("periodicDNA")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 6 ]
> 
> proc.time()
   user  system elapsed 
  47.71    2.17   49.87

name	user	system	elapsed
ce11_ATACseq	0.12	0.03	0.16
ce11_TSSs	0.06	0.09	0.16
ce11_WW_10bp	0.08	0.01	0.10
ce11_all_REs	0.21	0.07	0.26
ce11_proms	0.09	0.00	0.09
ce11_proms_seqs	0.06	0.07	0.13
getPeriodicity	19.24	1.14	22.39
getPeriodicityTrack	8.56	1.10	9.66
getPeriodicityWithIterations	4.01	0.04	4.06
plotAggregateCoverage	4.32	0.53	4.85
plotPeriodicityResults	8.28	0.22	8.50
setUpBPPARAM	0	0	0
theme_ggplot2	0.11	0.02	0.12

name	user	system	elapsed
ce11_ATACseq	0.06	0.04	0.10
ce11_TSSs	0.10	0.03	0.13
ce11_WW_10bp	0.07	0.00	0.06
ce11_all_REs	0.15	0.02	0.17
ce11_proms	0.05	0.02	0.06
ce11_proms_seqs	0.05	0.00	0.05
getPeriodicity	17.15	0.95	18.11
getPeriodicityTrack	6.16	0.17	6.33
getPeriodicityWithIterations	2.70	0.03	2.73
plotAggregateCoverage	3.36	0.02	3.38
plotPeriodicityResults	7.69	0.17	7.86
setUpBPPARAM	0	0	0
theme_ggplot2	0.21	0.00	0.20

CHECK report for periodicDNA on tokay1

Summary

Command output

Installation output

Tests output

Example timings