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This page was generated on 2021-10-21 12:05:33 -0400 (Thu, 21 Oct 2021).

CHECK results for SEtools on merida1

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? 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 1769/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SEtools 1.7.0  (landing page)
Pierre-Luc Germain
Snapshot Date: 2021-10-20 14:50:05 -0400 (Wed, 20 Oct 2021)
git_url: https://git.bioconductor.org/packages/SEtools
git_branch: master
git_last_commit: cd35cc2
git_last_commit_date: 2021-05-19 12:46:08 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    NA  

Summary

Package: SEtools
Version: 1.7.0
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_1.7.0.tar.gz
StartedAt: 2021-10-21 09:11:32 -0400 (Thu, 21 Oct 2021)
EndedAt: 2021-10-21 09:16:27 -0400 (Thu, 21 Oct 2021)
EllapsedTime: 294.5 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_1.7.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/SEtools.Rcheck’
* using R version 4.1.1 Patched (2021-08-22 r80813)
* 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 ‘1.7.0’
* 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

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SEtools
###
##############################################################################
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* 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-heatmap0.2750.0090.284
aggSE0.2730.0100.284
castSE0.0480.0010.049
crossHm0.3390.0030.342
getBreaks0.0010.0000.001
log2FC0.0020.0000.002
meltSE0.0360.0010.036
mergeSEs0.7630.0040.767
resetAllSEtoolsOptions000
scale20.0010.0000.000
se2xls0.0080.0000.008
sortRows0.0030.0010.004