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This page was generated on 2024-06-13 12:18 -0400 (Thu, 13 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4679
lconwaymacOS 12.7.1 Montereyx86_644.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" 4353
kjohnson3macOS 13.6.5 Venturaarm644.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" 4344
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 562/2239HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
diffUTR 1.13.0  (landing page)
Pierre-Luc Germain
Snapshot Date: 2024-06-12 14:00 -0400 (Wed, 12 Jun 2024)
git_url: https://git.bioconductor.org/packages/diffUTR
git_branch: devel
git_last_commit: 0ca783b
git_last_commit_date: 2024-04-30 11:34:21 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for diffUTR on nebbiolo2

To the developers/maintainers of the diffUTR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/diffUTR.git to reflect on this report. See Troubleshooting Build Report for more information.
- 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: diffUTR
Version: 1.13.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:diffUTR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings diffUTR_1.13.0.tar.gz
StartedAt: 2024-06-12 22:33:41 -0400 (Wed, 12 Jun 2024)
EndedAt: 2024-06-12 22:39:24 -0400 (Wed, 12 Jun 2024)
EllapsedTime: 342.6 seconds
RetCode: 0
Status:   OK  
CheckDir: diffUTR.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:diffUTR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings diffUTR_1.13.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/diffUTR.Rcheck’
* using R version 4.4.0 RC (2024-04-16 r86468)
* using platform: x86_64-pc-linux-gnu
* 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 ‘diffUTR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘diffUTR’ version ‘1.13.0’
* 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 ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘diffUTR’ 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 code 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 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
deuBinPlot: no visible binding for global variable 'x_start'
deuBinPlot: no visible binding for global variable 'x_end'
deuBinPlot: no visible binding for global variable 'y_start'
deuBinPlot: no visible binding for global variable 'y_end'
plotTopGenes: no visible binding for global variable 'sizeScore'
plotTopGenes: no visible binding for global variable 'q.value'
plotTopGenes: no visible binding for global variable 'density.ratio'
plotTopGenes: no visible binding for global variable 'geneMeanDensity'
plotTopGenes: no visible binding for global variable 'w.abs.coef'
plotTopGenes: no visible binding for global variable 'tmp'
plotTopGenes: no visible binding for global variable 'name'
Undefined global functions or variables:
  density.ratio geneMeanDensity name q.value sizeScore tmp w.abs.coef
  x_end x_start y_end y_start
* 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
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/diffUTR.Rcheck/00check.log’
for details.


Installation output

diffUTR.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL diffUTR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘diffUTR’ ...
** using staged installation
** R
** data
** 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 (diffUTR)

Tests output


Example timings

diffUTR.Rcheck/diffUTR-Ex.timings

nameusersystemelapsed
DEUwrappers0.9420.0751.016
addNormalizedAssays0.0810.0130.093
countFeatures1.0390.1011.140
deuBinPlot1.1540.0441.199
diffSplice20.2400.0160.256
geneBinHeatmap2.9580.2283.185
geneLevelStats0.7750.0120.787
plotTopGenes0.7000.0230.725
prepareBins0.9540.0430.999
simesAggregation0.0010.0010.002