Back to Multiple platform build/check report for BioC 3.20:   simplified   long
[A]BCDEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2024-05-15 13:46:26 -0400 (Wed, 15 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4663
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4480
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

Package 35/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AgiMicroRna 2.55.0  (landing page)
Pedro Lopez-Romero
Snapshot Date: 2024-05-13 14:05:07 -0400 (Mon, 13 May 2024)
git_url: https://git.bioconductor.org/packages/AgiMicroRna
git_branch: devel
git_last_commit: 15a2ac5
git_last_commit_date: 2024-04-30 10:20:35 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  
kjohnson1macOS 13.6.6 Ventura / arm64see weekly results here

CHECK results for AgiMicroRna on kunpeng2


To the developers/maintainers of the AgiMicroRna package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: AgiMicroRna
Version: 2.54.0
Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:AgiMicroRna.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings AgiMicroRna_2.54.0.tar.gz
StartedAt: 2024-05-09 04:38:57 -0000 (Thu, 09 May 2024)
EndedAt: 2024-05-09 04:47:02 -0000 (Thu, 09 May 2024)
EllapsedTime: 485.0 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: AgiMicroRna.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:AgiMicroRna.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings AgiMicroRna_2.54.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/AgiMicroRna.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘AgiMicroRna/DESCRIPTION’ ... OK
* this is package ‘AgiMicroRna’ version ‘2.54.0’
* 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 code 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 loading without being on the library search path ... 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 ... WARNING


See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* 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 ... NOTE
checkRd: (-1) basicLimma.Rd:46: Escaped LaTeX specials: \_ \_
checkRd: (-1) basicLimma.Rd:47: Escaped LaTeX specials: \_ \_
checkRd: (-1) basicLimma.Rd:53: Escaped LaTeX specials: \$ \$
checkRd: (-1) basicLimma.Rd:54: Escaped LaTeX specials: \$
checkRd: (-1) basicLimma.Rd:58: Escaped LaTeX specials: \_ \_ \_ \_
checkRd: (-1) dd.micro.Rd:22: Escaped LaTeX specials: \$
checkRd: (-1) dd.micro.Rd:23: Escaped LaTeX specials: \$
checkRd: (-1) dd.micro.Rd:24: Escaped LaTeX specials: \$
checkRd: (-1) dd.micro.Rd:25: Escaped LaTeX specials: \$
checkRd: (-1) dd.micro.Rd:26: Escaped LaTeX specials: \$
checkRd: (-1) dd.micro.Rd:27: Escaped LaTeX specials: \$ \$
checkRd: (-1) dd.micro.Rd:28: Escaped LaTeX specials: \$ \$
checkRd: (-1) dd.micro.Rd:29: Escaped LaTeX specials: \$ \$
checkRd: (-1) dd.micro.Rd:30: Escaped LaTeX specials: \$ \$
checkRd: (-1) dd.micro.Rd:31: Escaped LaTeX specials: \$ \$
checkRd: (-1) dd.micro.Rd:32: Escaped LaTeX specials: \$ \$
checkRd: (-1) dd.micro.Rd:33: Escaped LaTeX specials: \$ \$
checkRd: (-1) dd.micro.Rd:34: Escaped LaTeX specials: \$ \$
checkRd: (-1) dd.micro.Rd:35: Escaped LaTeX specials: \$ \$
checkRd: (-1) filterMicroRna.Rd:56: Escaped LaTeX specials: \_
checkRd: (-1) filterMicroRna.Rd:57: Escaped LaTeX specials: \_
checkRd: (-1) readMicroRnaAFE.Rd:27: Escaped LaTeX specials: \$
checkRd: (-1) readMicroRnaAFE.Rd:28: Escaped LaTeX specials: \$
checkRd: (-1) readMicroRnaAFE.Rd:29: Escaped LaTeX specials: \$
checkRd: (-1) readMicroRnaAFE.Rd:30: Escaped LaTeX specials: \$
checkRd: (-1) readMicroRnaAFE.Rd:31: Escaped LaTeX specials: \$
checkRd: (-1) readMicroRnaAFE.Rd:32: Escaped LaTeX specials: \$ \$
checkRd: (-1) readMicroRnaAFE.Rd:33: Escaped LaTeX specials: \$ \$
checkRd: (-1) readMicroRnaAFE.Rd:34: Escaped LaTeX specials: \$ \$
checkRd: (-1) readMicroRnaAFE.Rd:35: Escaped LaTeX specials: \$ \$
checkRd: (-1) readMicroRnaAFE.Rd:36: Escaped LaTeX specials: \$ \$
checkRd: (-1) readMicroRnaAFE.Rd:37: Escaped LaTeX specials: \$ \$
checkRd: (-1) readMicroRnaAFE.Rd:38: Escaped LaTeX specials: \$ \$
checkRd: (-1) readMicroRnaAFE.Rd:39: Escaped LaTeX specials: \$ \$
checkRd: (-1) readMicroRnaAFE.Rd:40: Escaped LaTeX specials: \$ \$
checkRd: (-1) readMicroRnaAFE.Rd:44: Escaped LaTeX specials: \$
checkRd: (-1) readMicroRnaAFE.Rd:45: Escaped LaTeX specials: \$
checkRd: (-1) readMicroRnaAFE.Rd:46: Escaped LaTeX specials: \$
checkRd: (-1) readMicroRnaAFE.Rd:47: Escaped LaTeX specials: \$
checkRd: (-1) readMicroRnaAFE.Rd:48: Escaped LaTeX specials: \$
checkRd: (-1) readMicroRnaAFE.Rd:49: Escaped LaTeX specials: \$ \$
checkRd: (-1) readMicroRnaAFE.Rd:50: Escaped LaTeX specials: \$ \$
checkRd: (-1) readMicroRnaAFE.Rd:51: Escaped LaTeX specials: \$ \$
checkRd: (-1) readMicroRnaAFE.Rd:52: Escaped LaTeX specials: \$ \$
checkRd: (-1) readMicroRnaAFE.Rd:53: Escaped LaTeX specials: \$ \$
checkRd: (-1) readMicroRnaAFE.Rd:54: Escaped LaTeX specials: \$ \$
checkRd: (-1) readMicroRnaAFE.Rd:55: Escaped LaTeX specials: \$ \$
checkRd: (-1) readMicroRnaAFE.Rd:56: Escaped LaTeX specials: \$ \$
checkRd: (-1) readMicroRnaAFE.Rd:57: Escaped LaTeX specials: \$ \$
checkRd: (-1) significantMicroRna.Rd:41: Escaped LaTeX specials: \_
checkRd: (-1) significantMicroRna.Rd:59: Escaped LaTeX specials: \_
checkRd: (-1) uRNAList.Rd:18: Escaped LaTeX specials: \$
checkRd: (-1) uRNAList.Rd:19: Escaped LaTeX specials: \$
checkRd: (-1) uRNAList.Rd:20: Escaped LaTeX specials: \$
checkRd: (-1) uRNAList.Rd:21: Escaped LaTeX specials: \$
checkRd: (-1) uRNAList.Rd:22: Escaped LaTeX specials: \$
checkRd: (-1) uRNAList.Rd:23: Escaped LaTeX specials: \$ \$
checkRd: (-1) uRNAList.Rd:24: Escaped LaTeX specials: \$ \$
checkRd: (-1) uRNAList.Rd:25: Escaped LaTeX specials: \$ \$
checkRd: (-1) uRNAList.Rd:26: Escaped LaTeX specials: \$ \$
checkRd: (-1) uRNAList.Rd:27: Escaped LaTeX specials: \$ \$
checkRd: (-1) uRNAList.Rd:28: Escaped LaTeX specials: \$ \$
checkRd: (-1) uRNAList.Rd:29: Escaped LaTeX specials: \$ \$
checkRd: (-1) uRNAList.Rd:30: Escaped LaTeX specials: \$ \$
checkRd: (-1) uRNAList.Rd:31: Escaped LaTeX specials: \$ \$
* 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 ... NOTE


The \usage entries for S3 methods should use the \method markup and not
their full name.
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
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
mvaMicroRna 14.544  0.167  14.735
rmaMicroRna  5.017  0.104   5.131
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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, 7 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/AgiMicroRna.Rcheck/00check.log’
for details.


Installation output

AgiMicroRna.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL AgiMicroRna
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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
HeatMapMicroRna0.3960.0200.417
PCAplotMicroRna0.1870.0080.195
RleMicroRna1.0400.1001.142
basicLimma0.0000.0000.001
boxplotMicroRna0.3830.0060.391
cvArray0.0000.0000.001
filterMicroRna0.4190.0240.444
getDecideTests000
hierclusMicroRna0.030.000.03
mvaBASIC2.6710.0562.732
mvaMicroRna14.544 0.16714.735
plotDensityMicroRna0.7600.0040.765
pvalHistogram000
qcPlots000
readMicroRnaAFE000
rmaMicroRna5.0170.1045.131
significantMicroRna0.6860.0320.726
tgsMicroRna0.1200.0000.121
tgsNormalization0.0000.0000.001
uRNAList000
writeEset000