Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-05-16 11:07:37 -0400 (Mon, 16 May 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4379
palomino3Windows Server 2022 Datacenterx644.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics" 4153
merida1macOS 10.14.6 Mojavex86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4220
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 ExiMiR on merida1


To the developers/maintainers of the ExiMiR package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ExiMiR.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 632/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ExiMiR 2.38.0  (landing page)
Sylvain Gubian
Snapshot Date: 2022-05-15 13:55:12 -0400 (Sun, 15 May 2022)
git_url: https://git.bioconductor.org/packages/ExiMiR
git_branch: RELEASE_3_15
git_last_commit: 0581159
git_last_commit_date: 2022-04-26 11:06:50 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: ExiMiR
Version: 2.38.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ExiMiR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ExiMiR_2.38.0.tar.gz
StartedAt: 2022-05-16 02:10:41 -0400 (Mon, 16 May 2022)
EndedAt: 2022-05-16 02:12:37 -0400 (Mon, 16 May 2022)
EllapsedTime: 115.6 seconds
RetCode: 0
Status:   OK  
CheckDir: ExiMiR.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ExiMiR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ExiMiR_2.38.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/ExiMiR.Rcheck’
* using R version 4.2.0 (2022-04-22)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ExiMiR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ExiMiR’ version ‘2.38.0’
* 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 ‘ExiMiR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘Biobase’
A package should be listed in only one of these fields.
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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 ... NOTE
Namespaces in Imports field not imported from:
  ‘Biobase’ ‘affyio’ ‘preprocessCore’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘Biobase’ ‘affy’ ‘limma’
  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 ... NOTE
NormiR.bgcorrect.methods: no visible global function definition for
  ‘bgcorrect.methods’
NormiR.pmcorrect.methods: no visible global function definition for
  ‘mm’
NormiR.pmcorrect.methods: no visible global function definition for
  ‘pmcorrect.methods’
NormiR.summary.methods: no visible global function definition for
  ‘generateExprSet.methods’
ReadExi: no visible global function definition for ‘readTargets’
ReadExi: no visible global function definition for ‘read.maimages’
ReadExi: no visible global function definition for ‘readGAL’
ReadExi: no visible global function definition for ‘getLayout’
ReadExi: no visible global function definition for ‘head’
bg.boxplot: no visible global function definition for ‘boxplot’
bg.correct.miR: no visible global function definition for ‘new’
bg.correct.miR: no visible global function definition for ‘exprs’
bg.correct.miR: no visible global function definition for ‘se.exprs’
bg.correct.miR: no visible global function definition for
  ‘backgroundCorrect.matrix’
bg.correct.miR: no visible global function definition for ‘exprs<-’
bg.correct.miR: no visible global function definition for ‘se.exprs<-’
bg.correct.miR: no visible global function definition for
  ‘bgcorrect.methods’
bg.correct.miR: no visible global function definition for ‘bg.correct’
bg.hist: no visible global function definition for ‘hist’
bg.image: no visible global function definition for ‘image’
by.samples.curve: no visible global function definition for ‘points’
by.samples.curve: no visible global function definition for ‘lines’
by.samples.figures: no visible global function definition for ‘dev.new’
by.samples.figures: no visible global function definition for ‘pdf’
by.samples.figures: no visible global function definition for ‘par’
by.samples.figures: no visible global function definition for ‘layout’
by.samples.figures: no visible global function definition for
  ‘dev.interactive’
by.samples.figures: no visible global function definition for ‘dev.off’
by.samples.legend: no visible global function definition for ‘points’
by.samples.legend: no visible global function definition for ‘text’
by.samples.legend: no visible global function definition for ‘legend’
create.gal.env: no visible global function definition for ‘multiassign’
createAB: no visible global function definition for ‘new’
createAB: no visible global function definition for ‘runif’
createAB: no visible global function definition for ‘notes<-’
createAB: no visible global function definition for ‘notes’
createAB: no visible global function definition for ‘pData<-’
get.bg.ab: no visible global function definition for ‘new’
get.bg.ab: no visible global function definition for ‘se.exprs’
get.bg.ab: no visible global function definition for ‘exprs’
get.bg.ab: no visible global function definition for ‘cdfName’
get.bg.ab: no visible global function definition for ‘phenoData’
get.bg.ab: no visible global function definition for ‘annotation’
get.bg.ab: no visible global function definition for ‘protocolData’
get.bg.ab: no visible global function definition for ‘description’
get.bg.ab: no visible global function definition for ‘notes’
has.bg: no visible global function definition for ‘notes’
is.dual: no visible global function definition for ‘notes’
is.from.createAB: no visible global function definition for ‘notes’
make.gal.env: no visible global function definition for ‘readGAL’
make.gal.env: no visible global function definition for ‘getLayout’
meannorm: no visible global function definition for ‘exprs’
meannorm: no visible global function definition for ‘sampleNames’
mediannorm: no visible global function definition for ‘exprs’
mediannorm: no visible global function definition for ‘sampleNames’
mediannorm: no visible binding for global variable ‘median’
norm.miR: no visible global function definition for ‘getCdfInfo’
norm.miR: no visible global function definition for ‘new’
norm.miR: no visible global function definition for ‘exprs’
norm.miR: no visible global function definition for
  ‘normalizeQuantiles’
norm.miR: no visible global function definition for ‘normalize’
norm.miR: no visible global function definition for ‘exprs<-’
read.annotation.fromfile: no visible global function definition for
  ‘read.maimages’
spikeinnorm: no visible global function definition for ‘getCdfInfo’
spikeinnorm: no visible global function definition for ‘exprs’
spikeinnorm: no visible global function definition for ‘sampleNames’
spikeinnorm: no visible global function definition for ‘median’
spikeinnorm: no visible global function definition for ‘cor’
spikeinnorm: no visible binding for global variable ‘sd’
spikeinnorm: no visible global function definition for ‘dev.new’
spikeinnorm: no visible global function definition for ‘pdf’
spikeinnorm: no visible global function definition for ‘dev.cur’
spikeinnorm: no visible global function definition for ‘layout’
spikeinnorm: no visible global function definition for ‘par’
spikeinnorm: no visible global function definition for ‘matplot’
spikeinnorm: no visible global function definition for ‘rainbow’
spikeinnorm: no visible global function definition for ‘axis’
spikeinnorm: no visible global function definition for ‘points’
spikeinnorm: no visible global function definition for ‘text’
spikeinnorm: no visible global function definition for ‘legend’
spikeinnorm: no visible global function definition for
  ‘dev.interactive’
spikeinnorm: no visible global function definition for ‘dev.off’
spikeinnorm: no visible global function definition for ‘rgb’
spikeinnorm: no visible global function definition for ‘heat.colors’
spikeinnorm: no visible global function definition for ‘image’
spikeinnorm: no visible binding for global variable ‘var’
spikeinnorm: no visible global function definition for ‘barplot’
spikeinnorm: no visible global function definition for ‘lm’
spikeinnorm: no visible global function definition for ‘predict’
spikeinnorm: no visible global function definition for ‘loess.smooth’
spikeinnorm: no visible global function definition for ‘approx’
summarize.miR: no visible global function definition for ‘mm’
summarize.miR: no visible global function definition for
  ‘computeExprSet’
Undefined global functions or variables:
  annotation approx axis backgroundCorrect.matrix barplot bg.correct
  bgcorrect.methods boxplot cdfName computeExprSet cor description
  dev.cur dev.interactive dev.new dev.off exprs exprs<-
  generateExprSet.methods getCdfInfo getLayout head heat.colors hist
  image layout legend lines lm loess.smooth matplot median mm
  multiassign new normalize normalizeQuantiles notes notes<- pData<-
  par pdf phenoData pmcorrect.methods points predict protocolData
  rainbow read.maimages readGAL readTargets rgb runif sampleNames sd
  se.exprs se.exprs<- text var
Consider adding
  importFrom("grDevices", "dev.cur", "dev.interactive", "dev.new",
             "dev.off", "heat.colors", "pdf", "rainbow", "rgb")
  importFrom("graphics", "axis", "barplot", "boxplot", "hist", "image",
             "layout", "legend", "lines", "matplot", "par", "points",
             "text")
  importFrom("methods", "new")
  importFrom("stats", "approx", "cor", "lm", "loess.smooth", "median",
             "predict", "runif", "sd", "var")
  importFrom("utils", "head")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
NormiR        24.895  0.249  25.177
summarize.miR 23.673  0.062  23.761
* 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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.15-bioc/meat/ExiMiR.Rcheck/00check.log’
for details.



Installation output

ExiMiR.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘ExiMiR’ ...
** using staged installation
** R
** data
** 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 (ExiMiR)

Tests output


Example timings

ExiMiR.Rcheck/ExiMiR-Ex.timings

nameusersystemelapsed
NormiR24.895 0.24925.177
ReadExi000
bg.correct.miR2.7140.0452.762
make.gal.env000
norm.miR0.8020.0790.882
summarize.miR23.673 0.06223.761