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CHECK report for DiscoRhythm on tokay2

This page was generated on 2020-10-17 11:56:28 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE DiscoRhythm PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 481/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DiscoRhythm 1.4.2
Matthew Carlucci
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/DiscoRhythm
Branch: RELEASE_3_11
Last Commit: b516c12
Last Changed Date: 2020-09-29 13:54:03 -0400 (Tue, 29 Sep 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: DiscoRhythm
Version: 1.4.2
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DiscoRhythm.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings DiscoRhythm_1.4.2.tar.gz
StartedAt: 2020-10-17 03:26:04 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 03:31:48 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 343.7 seconds
RetCode: 0
Status:  OK  
CheckDir: DiscoRhythm.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DiscoRhythm.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings DiscoRhythm_1.4.2.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/DiscoRhythm.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'DiscoRhythm/DESCRIPTION' ... OK
* this is package 'DiscoRhythm' version '1.4.2'
* 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 'DiscoRhythm' 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 ... NOTE
Namespace in Imports field not imported from: 'data.table'
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
discoApp: no visible binding for global variable '.discorhythm_ncores'
discoBatch: no visible binding for global variable 'discoODAres'
Undefined global functions or variables:
  .discorhythm_ncores discoODAres
* 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
discoBatch 30.2   3.45   35.88
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
discoBatch 22.55   2.44   26.36
* 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/DiscoRhythm.Rcheck/00check.log'
for details.



Installation output

DiscoRhythm.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/DiscoRhythm_1.4.2.tar.gz && rm -rf DiscoRhythm.buildbin-libdir && mkdir DiscoRhythm.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DiscoRhythm.buildbin-libdir DiscoRhythm_1.4.2.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL DiscoRhythm_1.4.2.zip && rm DiscoRhythm_1.4.2.tar.gz DiscoRhythm_1.4.2.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 1495k  100 1495k    0     0  19.8M      0 --:--:-- --:--:-- --:--:-- 22.1M

install for i386

* installing *source* package 'DiscoRhythm' ...
** 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 'DiscoRhythm'
    finding HTML links ... done
    DiscoRhythm-package                     html  
    PeriodDetection_range                   html  
    checkJTKperiod                          html  
    checkPeriod                             html  
    discoApp                                html  
    discoBatch                              html  
    discoCheckInput                         html  
    discoColors                             html  
    discoDFtoSE                             html  
    discoDesignSummary                      html  
    discoGetSimu                            html  
    discoODAexclusionMatrix                 html  
    discoODAid2name                         html  
    discoODAs                               html  
    discoPCA                                html  
    discoPCAgetOutliers                     html  
    discoParseMeta                          html  
    discoPeriodDetection                    html  
    discoQC                                 html  
    discoShinyHandler                       html  
    fisherExact                             html  
    inferFilteredDesign                     html  
    lmCSmat                                 html  
    lmCSmatNoNA                             html  
    sincos                                  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 'DiscoRhythm' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DiscoRhythm' as DiscoRhythm_1.4.2.zip
* DONE (DiscoRhythm)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'DiscoRhythm' successfully unpacked and MD5 sums checked

Tests output

DiscoRhythm.Rcheck/tests_i386/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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(DiscoRhythm)
> 
> test_check("DiscoRhythm")
== testthat results  ===========================================================
[ OK: 2 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
   9.78    0.87   10.67 

DiscoRhythm.Rcheck/tests_x64/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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(DiscoRhythm)
> 
> test_check("DiscoRhythm")
== testthat results  ===========================================================
[ OK: 2 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
   9.90    0.51   10.40 

Example timings

DiscoRhythm.Rcheck/examples_i386/DiscoRhythm-Ex.timings

nameusersystemelapsed
discoApp000
discoBatch30.20 3.4535.88
discoCheckInput0.080.000.08
discoDFtoSE0.030.000.03
discoDesignSummary0.050.000.05
discoGetSimu0.030.000.03
discoODAexclusionMatrix000
discoODAs1.750.002.39
discoPCA0.090.000.09
discoParseMeta000
discoPeriodDetection0.270.030.30
discoQC1.090.001.10
lmCSmat000
lmCSmatNoNA000
sincos000

DiscoRhythm.Rcheck/examples_x64/DiscoRhythm-Ex.timings

nameusersystemelapsed
discoApp000
discoBatch22.55 2.4426.36
discoCheckInput0.080.000.08
discoDFtoSE0.030.000.03
discoDesignSummary0.050.000.05
discoGetSimu0.020.000.02
discoODAexclusionMatrix000
discoODAs1.070.011.09
discoPCA0.050.000.05
discoParseMeta000
discoPeriodDetection0.160.000.15
discoQC0.150.000.16
lmCSmat000
lmCSmatNoNA000
sincos000