Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:08:47 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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 SEtools on machv2


To the developers/maintainers of the SEtools package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SEtools.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? 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 1776/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SEtools 1.8.0  (landing page)
Pierre-Luc Germain
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/SEtools
git_branch: RELEASE_3_14
git_last_commit: 30a597c
git_last_commit_date: 2021-10-26 12:54:06 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: SEtools
Version: 1.8.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SEtools.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SEtools_1.8.0.tar.gz
StartedAt: 2022-04-12 18:28:44 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 18:34:05 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 320.8 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: SEtools.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SEtools.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SEtools_1.8.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/SEtools.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SEtools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SEtools’ version ‘1.8.0’
* 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 ‘SEtools’ 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
castSE : <anonymous>: warning in sparseMatrix(i = as.integer(rowNames),
  j = as.integer(colNames), x = x[[y]], dim =
  c(length(levels(rowNames)), length(levels(colNames))), dimnames =
  list(levels(rowNames), levels(colNames))): partial argument match of
  'dim' to 'dims'
* 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 ... WARNING
Undocumented arguments in documentation object 'SE-heatmap'
  ‘annorow_title_side’
Documented arguments not in \usage in documentation object 'SE-heatmap':
  ‘annorows_title_side’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 WARNING, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/SEtools.Rcheck/00check.log’
for details.



Installation output

SEtools.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SEtools
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘SEtools’ ...
** 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 (SEtools)

Tests output


Example timings

SEtools.Rcheck/SEtools-Ex.timings

nameusersystemelapsed
SE-heatmap0.2420.0060.248
aggSE0.2920.0120.305
castSE0.0450.0010.046
crossHm0.2210.0010.223
getBreaks0.0010.0000.001
log2FC0.0020.0010.002
meltSE0.0360.0010.040
mergeSEs0.1760.0100.185
resetAllSEtoolsOptions0.0010.0010.001
scale20.0010.0000.001
se2xls0.0080.0010.008
sortRows0.0040.0020.005