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CHECK report for benchmarkfdrData2019 on malbec2

This page was generated on 2021-01-14 15:58:57 -0500 (Thu, 14 Jan 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 25/385HostnameOS / ArchINSTALLBUILDCHECK
benchmarkfdrData2019 1.5.0
Stephanie Hicks
Snapshot Date: 2021-01-14 09:00:13 -0500 (Thu, 14 Jan 2021)
URL: https://git.bioconductor.org/packages/benchmarkfdrData2019
Branch: master
Last Commit: 259eb05
Last Changed Date: 2020-10-27 10:30:09 -0500 (Tue, 27 Oct 2020)
malbec2 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK  OK 

Summary

Package: benchmarkfdrData2019
Version: 1.5.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:benchmarkfdrData2019.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings benchmarkfdrData2019_1.5.0.tar.gz
StartedAt: 2021-01-14 11:42:38 -0500 (Thu, 14 Jan 2021)
EndedAt: 2021-01-14 11:48:06 -0500 (Thu, 14 Jan 2021)
EllapsedTime: 328.0 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-3.13-bioc/R/bin/R CMD check --install=check:benchmarkfdrData2019.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings benchmarkfdrData2019_1.5.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-data-experiment/meat/benchmarkfdrData2019.Rcheck’
* using R Under development (unstable) (2021-01-05 r79797)
* 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 ‘1.5.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
microbiome-enigma 1.369  0.016   6.865
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.13-data-experiment/meat/benchmarkfdrData2019.Rcheck/00check.log’
for details.



Installation output

benchmarkfdrData2019.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL benchmarkfdrData2019
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.13-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(): 2021-01-14
** testing if installed package can be loaded from final location
snapshotDate(): 2021-01-14
** testing if installed package keeps a record of temporary installation path
* DONE (benchmarkfdrData2019)

Tests output


Example timings

benchmarkfdrData2019.Rcheck/benchmarkfdrData2019-Ex.timings

nameusersystemelapsed
chipseq-cbp1.2930.0081.858
chipseq-h3k4me31.2600.0201.736
gsa-human1.1890.0161.580
gsa-mouse1.1580.0081.622
gwas-bmi1.2140.0041.679
microbiome-baxter1.1200.0131.591
microbiome-enigma1.3690.0166.865
microbiome-goodrich1.0310.0161.518
microbiome-papa1.2120.0241.720
microbiome-schubert1.2650.0081.781
polyester-insilico1.2230.0241.611
rnaseq-brain1.1940.0121.661
rnaseq-mir200c1.2270.0121.709
scrnaseq-human1.2650.0281.669
scrnaseq-mouse1.1900.0241.664
sims-informative-cosine1.3570.0161.866
sims-informative-cubic1.2740.0121.761
sims-informative-sine1.3210.0241.806
sims-informative-step1.2750.0161.574
sims-null1.2210.0121.701
sims-uasettings-251.2420.0161.622
sims-uasettings-t1.2290.0201.709
sims-uasettings1.1380.0241.623
sims-varyinginfo-discrete1.3720.0041.881
sims-varyinginfo-smooth1.1430.0401.540
sims-varyingntests1.2500.0361.743
sims-varyingpi0-t1.3110.0161.606
sims-varyingpi01.2130.0201.528
yeast-insilico1.2610.0121.735