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CHECK report for icetea on machv2

This page was generated on 2020-10-17 11:58:42 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE icetea PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 848/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
icetea 1.6.1
Vivek Bhardwaj
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/icetea
Branch: RELEASE_3_11
Last Commit: 618e6b3
Last Changed Date: 2020-10-13 07:43:21 -0400 (Tue, 13 Oct 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: icetea
Version: 1.6.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:icetea.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings icetea_1.6.1.tar.gz
StartedAt: 2020-10-17 02:06:53 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 02:16:20 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 566.8 seconds
RetCode: 0
Status:  OK 
CheckDir: icetea.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:icetea.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings icetea_1.6.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/icetea.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘icetea/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘icetea’ version ‘1.6.1’
* 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 ‘icetea’ 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
detectTSS,CapSet : <anonymous>: no visible binding for global variable
  ‘filter’
Undefined global functions or variables:
  filter
Consider adding
  importFrom("stats", "filter")
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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
detectTSS   19.750  1.804  20.781
annotateTSS 14.652  0.422  15.306
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/icetea.Rcheck/00check.log’
for details.



Installation output

icetea.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL icetea
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘icetea’ ...
** using staged installation
** R
** 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 (icetea)

Tests output

icetea.Rcheck/tests/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-apple-darwin17.0 (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(icetea)
> 
> test_check("icetea")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 17 | SKIPPED: 0 | WARNINGS: 2 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 57.575   2.633  62.169 

Example timings

icetea.Rcheck/icetea-Ex.timings

nameusersystemelapsed
annotateTSS14.652 0.42215.306
demultiplexFASTQ2.9780.0693.054
detectDiffTSS0.0010.0010.002
detectTSS19.750 1.80420.781
exampleCSobject0.1680.0240.192
exportTSS0.2760.0290.306
filterDuplicates2.2230.2672.493
fitDiffTSS0.0010.0000.000
getGeneCounts2.9890.1083.098
getNormFactors2.0670.5301.693
mapCaps0.0000.0010.000
newCapSet0.0880.0150.105
plotReadStats0.5120.0570.570
plotTSSprecision3.3180.2493.741
sampleInfo0.1720.0080.179
splitBAM_byIndex0.3650.0590.424
splitBAM_byRepindex0.2880.0500.340