Back to Multiple platform build/check report for BioC 3.14
ABC[D]EFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2022-01-17 13:05:01 -0500 (Mon, 17 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4328
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4077
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4138
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

CHECK results for diffUTR on nebbiolo2


To the developers/maintainers of the diffUTR package:
- Please 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 How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 511/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
diffUTR 1.2.0  (landing page)
Pierre-Luc Germain
Snapshot Date: 2022-01-16 01:55:05 -0500 (Sun, 16 Jan 2022)
git_url: https://git.bioconductor.org/packages/diffUTR
git_branch: RELEASE_3_14
git_last_commit: feef7a8
git_last_commit_date: 2021-10-26 13:09:41 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: diffUTR
Version: 1.2.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:diffUTR.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings diffUTR_1.2.0.tar.gz
StartedAt: 2022-01-16 07:28:11 -0500 (Sun, 16 Jan 2022)
EndedAt: 2022-01-16 07:33:40 -0500 (Sun, 16 Jan 2022)
EllapsedTime: 329.1 seconds
RetCode: 0
Status:   OK  
CheckDir: diffUTR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:diffUTR.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings diffUTR_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/diffUTR.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘diffUTR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘diffUTR’ version ‘1.2.0’
* 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 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
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 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
  ‘/home/biocbuild/bbs-3.14-bioc/meat/diffUTR.Rcheck/00check.log’
for details.



Installation output

diffUTR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL diffUTR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/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
DEUwrappers2.4370.0362.473
addNormalizedAssays0.080.000.08
countFeatures1.7870.1831.971
deuBinPlot0.9870.0191.008
diffSplice20.2980.0040.302
geneBinHeatmap2.5370.0362.572
geneLevelStats1.1310.0041.135
plotTopGenes0.9380.0270.965
prepareBins1.5230.0271.552
simesAggregation0.0010.0000.001