Package: DiscoRhythm

Version: 1.2.1

Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:DiscoRhythm.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings DiscoRhythm_1.2.1.tar.gz

StartedAt: 2020-04-15 06:27:08 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 06:30:43 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 215.6 seconds

RetCode: 0

Status:  OK

CheckDir: DiscoRhythm.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:DiscoRhythm.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings DiscoRhythm_1.2.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/DiscoRhythm.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DiscoRhythm/DESCRIPTION’ ... OK
* this is package ‘DiscoRhythm’ version ‘1.2.1’
* 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 for sufficient/correct file permissions ... 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
* 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 ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
discoBatch 34.66   1.04  28.109
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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
  ‘/home/biocbuild/bbs-3.10-bioc/meat/DiscoRhythm.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL DiscoRhythm
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* 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
** 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
* DONE (DiscoRhythm)

R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 
 10.348   0.384  11.010 

name	user	system	elapsed
discoApp	0.000	0.000	0.001
discoBatch	34.660	1.040	28.109
discoCheckInput	0.056	0.000	0.057
discoDFtoSE	0.036	0.000	0.036
discoDesignSummary	0.032	0.000	0.032
discoGetSimu	0.02	0.00	0.02
discoODAexclusionMatrix	0	0	0
discoODAs	1.508	0.004	1.707
discoPCA	0.068	0.000	0.070
discoParseMeta	0.004	0.000	0.004
discoPeriodDetection	0.224	0.000	0.226
discoQC	0.2	0.0	0.2
lmCSmat	0.000	0.000	0.001
lmCSmatNoNA	0	0	0
sincos	0	0	0