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CHECK report for benchmarkfdrData2019 on malbec1

This page was generated on 2021-05-06 14:10:05 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the benchmarkfdrData2019 package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 25/398HostnameOS / ArchINSTALLBUILDCHECK
benchmarkfdrData2019 1.4.0  (landing page)
Stephanie Hicks
Snapshot Date: 2021-05-06 09:00:13 -0400 (Thu, 06 May 2021)
URL: https://git.bioconductor.org/packages/benchmarkfdrData2019
Branch: RELEASE_3_12
Last Commit: 98823f5
Last Changed Date: 2020-10-27 10:30:09 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: benchmarkfdrData2019
Version: 1.4.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:benchmarkfdrData2019.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings benchmarkfdrData2019_1.4.0.tar.gz
StartedAt: 2021-05-06 11:36:13 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 11:41:14 -0400 (Thu, 06 May 2021)
EllapsedTime: 301.0 seconds
RetCode: 0
Status:   OK  
CheckDir: benchmarkfdrData2019.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:benchmarkfdrData2019.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings benchmarkfdrData2019_1.4.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-data-experiment/meat/benchmarkfdrData2019.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘benchmarkfdrData2019/DESCRIPTION’ ... OK
* this is package ‘benchmarkfdrData2019’ version ‘1.4.0’
* 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 ... NOTE
Found the following non-portable file paths:
  benchmarkfdrData2019/inst/scripts/make-data/Simulations/simulations-varyinginformativeness-discrete.Rmd
  benchmarkfdrData2019/inst/scripts/make-data/Simulations/simulations-varyinginformativeness-smooth.Rmd
  benchmarkfdrData2019/inst/scripts/make-data/YeastInSilico/yeast-simulation-bimodalalternative-highpi0.Rmd

Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘benchmarkfdrData2019’ 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
Package in Depends field not imported from: ‘SummarizedExperiment’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* 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 files in ‘vignettes’ ... OK
* checking examples ... 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-3.12-data-experiment/meat/benchmarkfdrData2019.Rcheck/00check.log’
for details.



Installation output

benchmarkfdrData2019.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL benchmarkfdrData2019
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘benchmarkfdrData2019’ ...
** 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
snapshotDate(): 2020-10-27
** testing if installed package can be loaded from final location
snapshotDate(): 2020-10-27
** testing if installed package keeps a record of temporary installation path
* DONE (benchmarkfdrData2019)

Tests output


Example timings

benchmarkfdrData2019.Rcheck/benchmarkfdrData2019-Ex.timings

nameusersystemelapsed
chipseq-cbp1.6720.0162.006
chipseq-h3k4me31.4840.0281.814
gsa-human1.0960.0001.356
gsa-mouse1.0920.0201.379
gwas-bmi1.0600.0201.401
microbiome-baxter1.1120.0201.403
microbiome-enigma1.2520.0201.544
microbiome-goodrich1.2640.0321.559
microbiome-papa1.2840.0201.570
microbiome-schubert1.1400.0201.438
polyester-insilico1.2280.0121.510
rnaseq-brain1.3080.0241.604
rnaseq-mir200c1.2880.0161.573
scrnaseq-human1.2160.0121.504
scrnaseq-mouse1.1440.0161.427
sims-informative-cosine1.1160.0241.417
sims-informative-cubic1.1400.0281.436
sims-informative-sine1.1480.0081.428
sims-informative-step1.2120.0241.499
sims-null1.3040.0201.590
sims-uasettings-251.5520.0161.839
sims-uasettings-t1.3240.0201.608
sims-uasettings1.2560.0281.555
sims-varyinginfo-discrete1.2080.0201.529
sims-varyinginfo-smooth1.6160.0201.970
sims-varyingntests1.0920.0201.379
sims-varyingpi0-t1.0680.0281.355
sims-varyingpi01.0800.0121.359
yeast-insilico1.0680.0161.351