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This page was generated on 2024-04-16 14:51:28 -0400 (Tue, 16 Apr 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4676
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 24/429HostnameOS / ArchINSTALLBUILDCHECK
benchmarkfdrData2019 1.16.0  (landing page)
Stephanie Hicks
Snapshot Date: 2024-04-16 07:30:02 -0400 (Tue, 16 Apr 2024)
git_url: https://git.bioconductor.org/packages/benchmarkfdrData2019
git_branch: RELEASE_3_18
git_last_commit: 80fb82d
git_last_commit_date: 2023-10-24 09:19:45 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published

CHECK results for benchmarkfdrData2019 on nebbiolo2


To the developers/maintainers of the benchmarkfdrData2019 package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: benchmarkfdrData2019
Version: 1.16.0
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:benchmarkfdrData2019.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings benchmarkfdrData2019_1.16.0.tar.gz
StartedAt: 2024-04-16 11:02:19 -0400 (Tue, 16 Apr 2024)
EndedAt: 2024-04-16 11:10:38 -0400 (Tue, 16 Apr 2024)
EllapsedTime: 498.9 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-3.18-bioc/R/bin/R CMD check --install=check:benchmarkfdrData2019.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings benchmarkfdrData2019_1.16.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-data-experiment/meat/benchmarkfdrData2019.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘benchmarkfdrData2019/DESCRIPTION’ ... OK
* this is package ‘benchmarkfdrData2019’ version ‘1.16.0’
* 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 loading without being on the library search path ... OK
* checking startup messages can be suppressed ... 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 ...
  ‘benchmarkfdrData2019.Rmd’ using ‘UTF-8’... OK
 OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-data-experiment/meat/benchmarkfdrData2019.Rcheck/00check.log’
for details.



Installation output

benchmarkfdrData2019.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL benchmarkfdrData2019
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (benchmarkfdrData2019)

Tests output


Example timings

benchmarkfdrData2019.Rcheck/benchmarkfdrData2019-Ex.timings

nameusersystemelapsed
chipseq-cbp0.0420.0040.046
chipseq-h3k4me30.0390.0000.039
gsa-human0.0400.0000.041
gsa-mouse0.0310.0080.039
gwas-bmi0.0300.0080.039
microbiome-baxter0.0380.0040.042
microbiome-enigma0.0370.0040.040
microbiome-goodrich0.0360.0040.040
microbiome-papa0.0410.0000.042
microbiome-schubert0.0410.0000.041
polyester-insilico0.0410.0000.042
rnaseq-brain0.0430.0000.043
rnaseq-mir200c0.0450.0000.046
scrnaseq-human0.0450.0000.045
scrnaseq-mouse0.0520.0040.057
sims-informative-cosine0.0430.0040.047
sims-informative-cubic0.0480.0000.048
sims-informative-sine0.0430.0040.047
sims-informative-step0.0450.0040.049
sims-null0.0570.0200.076
sims-uasettings-250.0270.0080.035
sims-uasettings-t0.0270.0080.035
sims-uasettings0.0350.0000.035
sims-varyinginfo-discrete0.0340.0040.037
sims-varyinginfo-smooth0.0350.0040.040
sims-varyingntests0.0380.0000.038
sims-varyingpi0-t0.0390.0000.040
sims-varyingpi00.0370.0000.037
yeast-insilico0.0380.0000.037