Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:07:36 -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 AgiMicroRna on machv2


To the developers/maintainers of the AgiMicroRna package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/AgiMicroRna.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 37/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AgiMicroRna 2.44.0  (landing page)
Pedro Lopez-Romero
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/AgiMicroRna
git_branch: RELEASE_3_14
git_last_commit: 8b308ba
git_last_commit_date: 2021-10-26 11:54:33 -0400 (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  ERROR    OK    ERROR    ERROR  
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: AgiMicroRna
Version: 2.44.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:AgiMicroRna.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings AgiMicroRna_2.44.0.tar.gz
StartedAt: 2022-04-12 10:13:03 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 10:22:03 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 540.3 seconds
RetCode: 0
Status:   OK  
CheckDir: AgiMicroRna.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:AgiMicroRna.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings AgiMicroRna_2.44.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/AgiMicroRna.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 ‘AgiMicroRna/DESCRIPTION’ ... OK
* this is package ‘AgiMicroRna’ version ‘2.44.0’
* 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 ‘AgiMicroRna’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
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 ... 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 ... NOTE
Warning: no function found corresponding to methods exports from ‘AgiMicroRna’ for: ‘show’

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' calls to packages already attached by Depends:
  'affy' 'affycoretools' 'preprocessCore'
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  'codelink' 'gdata' 'geneplotter' 'gplots' 'gtools' 'marray'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'affy' 'affycoretools' 'limma' 'methods' 'preprocessCore'
  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 ... NOTE
Foreign function call to a different package:
  .Call("rma_c_complete_copy", ..., PACKAGE = "affy")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
DEG.print.info: no visible global function definition for 'is'
DEG.print.info: no visible global function definition for 'exprs'
HeatMapMicroRna: no visible binding for global variable 'var'
HeatMapMicroRna: no visible global function definition for 'rainbow'
HeatMapMicroRna: no visible global function definition for 'maPalette'
HeatMapMicroRna: no visible global function definition for 'heatmap.2'
HeatMapMicroRna: no visible global function definition for 'title'
MA.plot.miRNA: no visible global function definition for 'dev.new'
MA.plot.miRNA: no visible global function definition for 'points'
MA.plot.miRNA: no visible global function definition for 'fitted'
MA.plot.miRNA: no visible global function definition for 'loess'
MA.plot.miRNA: no visible global function definition for 'legend'
MA.plot.miRNA: no visible global function definition for 'title'
PCAplotMicroRna: no visible global function definition for 'is'
PCAplotMicroRna: no visible global function definition for 'exprs'
PCAplotMicroRna: no visible global function definition for 'na.omit'
PCAplotMicroRna: no visible global function definition for 'exprs<-'
PCAplotMicroRna: no visible global function definition for 'plotPCA'
PCAplotMicroRna: no visible global function definition for 'dev.new'
RleMicroRna: no visible binding for global variable 'median'
RleMicroRna: no visible global function definition for 'par'
RleMicroRna: no visible global function definition for 'boxplot'
RleMicroRna: no visible global function definition for 'points'
RleMicroRna: no visible global function definition for 'lines'
RleMicroRna: no visible global function definition for 'title'
RleMicroRna: no visible global function definition for 'abline'
basicLimma: no visible global function definition for 'is'
basicLimma: no visible global function definition for 'exprs'
basicLimma: no visible global function definition for 'lmFit'
basicLimma: no visible global function definition for 'contrasts.fit'
basicLimma: no visible global function definition for 'eBayes'
boxplotMicroRna: no visible global function definition for 'par'
boxplotMicroRna: no visible global function definition for 'boxplot'
boxplotMicroRna: no visible global function definition for 'points'
boxplotMicroRna: no visible global function definition for 'lines'
boxplotMicroRna: no visible global function definition for 'title'
cv.array: no visible binding for global variable 'median'
cvArray: no visible global function definition for 'is'
esetMicroRna: no visible global function definition for 'is'
esetMicroRna: no visible global function definition for 'new'
esetMicroRna: no visible global function definition for 'dev.new'
esetMicroRna: no visible global function definition for 'exprs'
filter.IsGeneDetected: no visible global function definition for 'is'
filter.control.miRNA: no visible global function definition for 'is'
filter.wellaboveNEG.miRNA: no visible global function definition for
  'is'
filter.wellaboveNEG.miRNA: no visible binding for global variable 'sd'
filterMicroRna: no visible global function definition for 'is'
filterMicroRna: no visible global function definition for 'dev.new'
getDecideTests: no visible global function definition for 'is'
getDecideTests: no visible global function definition for 'decideTests'
hierclusMicroRna: no visible binding for global variable 'var'
hierclusMicroRna: no visible global function definition for 'dist'
hierclusMicroRna: no visible global function definition for 'as.dist'
hierclusMicroRna: no visible global function definition for 'cor'
hierclusMicroRna: no visible global function definition for 'hclust'
hierclusMicroRna: no visible global function definition for 'title'
mvaBASIC: no visible binding for global variable 'median'
mvaBASIC: no visible global function definition for 'title'
mvaBASIC: no visible global function definition for 'abline'
mvaMicroRna: no visible binding for global variable 'median'
mvaMicroRna: no visible global function definition for 'points'
mvaMicroRna: no visible global function definition for 'fitted'
mvaMicroRna: no visible global function definition for 'loess'
mvaMicroRna: no visible global function definition for 'title'
mvaMicroRna: no visible global function definition for 'abline'
mvaMicroRna: no visible global function definition for 'legend'
plotDensityMicroRna: no visible global function definition for
  'rainbow'
plotDensityMicroRna: no visible global function definition for
  'density'
plotDensityMicroRna: no visible global function definition for 'lines'
plotDensityMicroRna: no visible global function definition for 'title'
plotDensityMicroRna: no visible global function definition for 'legend'
pvalHistogram: no visible global function definition for 'p.adjust'
pvalHistogram: no visible global function definition for 'hist'
pvalHistogram: no visible global function definition for 'dev.new'
qcPlots: no visible global function definition for 'is'
qcPlots: no visible global function definition for 'dev.new'
read.agiMicroRna: no visible global function definition for
  'read.columns'
read.agiMicroRna: no visible global function definition for 'new'
readMicroRnaAFE: no visible global function definition for 'is'
readTargets: no visible global function definition for 'read.table'
rmaMicroRna: no visible global function definition for 'is'
rmaMicroRna: no visible global function definition for
  'rma.background.correct'
rmaMicroRna: no visible global function definition for
  'normalizeBetweenArrays'
rmaMicroRna: no visible binding for global variable 'median'
significantMicroRna: no visible global function definition for 'is'
significantMicroRna: no visible global function definition for 'exprs'
significantMicroRna: no visible global function definition for
  'p.adjust'
tgsMicroRna: no visible global function definition for 'is'
tgsMicroRna: no visible global function definition for 'dev.new'
tgsNormalization: no visible global function definition for 'is'
tgsNormalization: no visible global function definition for 'dev.new'
tgsNormalization: no visible global function definition for
  'normalizeBetweenArrays'
write.LIST.miRNA: no visible global function definition for 'is'
write.LIST.miRNA: no visible global function definition for
  'write.table'
write.control.out.miRNA: no visible global function definition for 'is'
write.control.out.miRNA: no visible global function definition for
  'write.table'
write.filt.out.miRNA: no visible global function definition for 'is'
write.filt.out.miRNA: no visible global function definition for
  'write.table'
writeEset: no visible global function definition for 'is'
writeEset: no visible global function definition for 'exprs'
writeEset: no visible global function definition for 'featureNames'
writeEset: no visible global function definition for 'write.table'
show,uRNAList: no visible global function definition for 'slotNames'
show,uRNAList: no visible global function definition for 'slot'
Undefined global functions or variables:
  abline as.dist boxplot contrasts.fit cor decideTests density dev.new
  dist eBayes exprs exprs<- featureNames fitted hclust heatmap.2 hist
  is legend lines lmFit loess maPalette median na.omit new
  normalizeBetweenArrays p.adjust par plotPCA points rainbow
  read.columns read.table rma.background.correct sd slot slotNames
  title var write.table
Consider adding
  importFrom("grDevices", "dev.new", "rainbow")
  importFrom("graphics", "abline", "boxplot", "hist", "legend", "lines",
             "par", "points", "title")
  importFrom("methods", "is", "new", "slot", "slotNames")
  importFrom("stats", "as.dist", "cor", "density", "dist", "fitted",
             "hclust", "loess", "median", "na.omit", "p.adjust", "sd",
             "var")
  importFrom("utils", "read.table", "write.table")
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
mvaMicroRna 21.789  0.539  22.409
rmaMicroRna  7.166  0.415   7.586
mvaBASIC     5.012  0.158   5.181
* 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: 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/AgiMicroRna.Rcheck/00check.log’
for details.



Installation output

AgiMicroRna.Rcheck/00install.out

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


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

Tests output


Example timings

AgiMicroRna.Rcheck/AgiMicroRna-Ex.timings

nameusersystemelapsed
HeatMapMicroRna0.7350.0810.860
PCAplotMicroRna0.1550.0130.260
RleMicroRna1.7130.1231.838
basicLimma000
boxplotMicroRna0.5940.0360.631
cvArray0.0000.0000.001
filterMicroRna0.6580.0850.773
getDecideTests000
hierclusMicroRna0.0440.0060.051
mvaBASIC5.0120.1585.181
mvaMicroRna21.789 0.53922.409
plotDensityMicroRna1.2800.0291.315
pvalHistogram0.0000.0010.000
qcPlots0.0000.0010.001
readMicroRnaAFE0.0000.0000.001
rmaMicroRna7.1660.4157.586
significantMicroRna0.7910.0660.874
tgsMicroRna0.2060.0060.214
tgsNormalization000
uRNAList0.0010.0000.000
writeEset0.0010.0000.000