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CHECK report for AgiMicroRna on riesling1

This page was generated on 2021-01-25 12:38:20 -0500 (Mon, 25 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE AgiMicroRna PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 39/1938HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AgiMicroRna 2.41.0
Pedro Lopez-Romero
Snapshot Date: 2021-01-24 14:40:26 -0500 (Sun, 24 Jan 2021)
URL: https://git.bioconductor.org/packages/AgiMicroRna
Branch: master
Last Commit: 46b6c16
Last Changed Date: 2020-10-27 10:36:25 -0500 (Tue, 27 Oct 2020)
malbec2 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK [ WARNINGS ] OK 
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: AgiMicroRna
Version: 2.41.0
Command: D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:AgiMicroRna.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings AgiMicroRna_2.41.0.tar.gz
StartedAt: 2021-01-24 19:34:31 -0500 (Sun, 24 Jan 2021)
EndedAt: 2021-01-24 19:41:57 -0500 (Sun, 24 Jan 2021)
EllapsedTime: 445.9 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: AgiMicroRna.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:AgiMicroRna.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings AgiMicroRna_2.41.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.13-bioc/meat/AgiMicroRna.Rcheck'
* using R Under development (unstable) (2020-12-30 r79736)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'AgiMicroRna/DESCRIPTION' ... OK
* this is package 'AgiMicroRna' version '2.41.0'
* 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 whether package 'AgiMicroRna' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: cannot open file 'D:/biocbuild/bbs-3.13-bioc/meat/AgiMicroRna.buildbin-libdir/00LOCK-AgiMicroRna/00new/AgiMicroRna/help/dimnames<-.uRNAList.html': Invalid argument
See 'D:/biocbuild/bbs-3.13-bioc/meat/AgiMicroRna.Rcheck/00install.out' for details.
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
mvaMicroRna 18.64   0.18   18.86
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
mvaMicroRna 15.62   0.28   15.97
rmaMicroRna  5.10   0.05    5.14
* 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, 6 NOTEs
See
  'D:/biocbuild/bbs-3.13-bioc/meat/AgiMicroRna.Rcheck/00check.log'
for details.



Installation output

AgiMicroRna.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.4/BBS/3.13/bioc/src/contrib/AgiMicroRna_2.41.0.tar.gz && rm -rf AgiMicroRna.buildbin-libdir && mkdir AgiMicroRna.buildbin-libdir && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=AgiMicroRna.buildbin-libdir AgiMicroRna_2.41.0.tar.gz && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL AgiMicroRna_2.41.0.zip && rm AgiMicroRna_2.41.0.tar.gz AgiMicroRna_2.41.0.zip
###
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##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 26 1337k   26  356k    0     0  7915k      0 --:--:-- --:--:-- --:--:-- 7743k
100 1337k  100 1337k    0     0  23.3M      0 --:--:-- --:--:-- --:--:-- 22.9M

install for i386

* installing *source* package 'AgiMicroRna' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'AgiMicroRna'
    finding HTML links ... done
    HeatMapMicroRna                         html  
REDIRECT:topic	 HeatMapMicroRna -> HeatMapMicroRna.html [ SUCCESS ]
    PCAplotMicroRna                         html  
REDIRECT:topic	 PCAplotMicroRna -> PCAplotMicroRna.html [ SUCCESS ]
    RleMicroRna                             html  
REDIRECT:topic	 RleMicroRna -> RleMicroRna.html [ SUCCESS ]
    basicLimma                              html  
REDIRECT:topic	 basicLimma -> basicLimma.html [ SUCCESS ]
    boxplotMicroRna                         html  
REDIRECT:topic	 boxplotMicroRna -> boxplotMicroRna.html [ SUCCESS ]
    cvArray                                 html  
REDIRECT:topic	 cvArray -> cvArray.html [ SUCCESS ]
    dd.micro                                html  
REDIRECT:topic	 dd.micro -> dd.micro.html [ SUCCESS ]
    ddPROC                                  html  
REDIRECT:topic	 ddPROC -> ddPROC.html [ SUCCESS ]
    dim.uRNAList                            html  
REDIRECT:topic	 dim.uRNAList -> dim.uRNAList.html [ SUCCESS ]
REDIRECT:topic	 length.uRNAList -> dim.uRNAList.html [ SUCCESS ]
    dimnames.uRNAList                       html  
REDIRECT:topic	 dimnames.uRNAList -> dimnames.uRNAList.html [ SUCCESS ]
REDIRECT:topic	 dimnames<-.uRNAList -> dimnames.uRNAList.html [ FAIL ]
Rd warning: cannot open file 'D:/biocbuild/bbs-3.13-bioc/meat/AgiMicroRna.buildbin-libdir/00LOCK-AgiMicroRna/00new/AgiMicroRna/help/dimnames<-.uRNAList.html': Invalid argument
    esetMicroRna                            html  
REDIRECT:topic	 esetMicroRna -> esetMicroRna.html [ SUCCESS ]
    filterMicroRna                          html  
REDIRECT:topic	 filterMicroRna -> filterMicroRna.html [ SUCCESS ]
    getDecideTests                          html  
REDIRECT:topic	 getDecideTests -> getDecideTests.html [ SUCCESS ]
    hierclusMicroRna                        html  
REDIRECT:topic	 hierclusMicroRna -> hierclusMicroRna.html [ SUCCESS ]
    mvaBASIC                                html  
REDIRECT:topic	 mvaBASIC -> mvaBASIC.html [ SUCCESS ]
    mvaMicroRna                             html  
REDIRECT:topic	 mvaMicroRna -> mvaMicroRna.html [ SUCCESS ]
    plotDensityMicroRna                     html  
REDIRECT:topic	 plotDensityMicroRna -> plotDensityMicroRna.html [ SUCCESS ]
    pvalHistogram                           html  
REDIRECT:topic	 pvalHistogram -> pvalHistogram.html [ SUCCESS ]
    qcPlots                                 html  
REDIRECT:topic	 qcPlots -> qcPlots.html [ SUCCESS ]
    readMicroRnaAFE                         html  
REDIRECT:topic	 readMicroRnaAFE -> readMicroRnaAFE.html [ SUCCESS ]
    readTargets                             html  
REDIRECT:topic	 readTargets -> readTargets.html [ SUCCESS ]
    rmaMicroRna                             html  
REDIRECT:topic	 rmaMicroRna -> rmaMicroRna.html [ SUCCESS ]
    significantMicroRna                     html  
REDIRECT:topic	 significantMicroRna -> significantMicroRna.html [ SUCCESS ]
    summary.uRNAList                        html  
REDIRECT:topic	 summary.uRNAList -> summary.uRNAList.html [ SUCCESS ]
    targets.micro                           html  
REDIRECT:topic	 targets.micro -> targets.micro.html [ SUCCESS ]
    tgsMicroRna                             html  
REDIRECT:topic	 tgsMicroRna -> tgsMicroRna.html [ SUCCESS ]
    tgsNormalization                        html  
REDIRECT:topic	 tgsNormalization -> tgsNormalization.html [ SUCCESS ]
    uRNAList                                html  
REDIRECT:topic	 uRNAList-class -> uRNAList.html [ SUCCESS ]
REDIRECT:topic	 show,uRNAList-method -> uRNAList.html [ SUCCESS ]
REDIRECT:file	 uRNAList.html -> uRNAList.html [ SUCCESS ]
    writeEset                               html  
REDIRECT:topic	 writeEset -> writeEset.html [ SUCCESS ]
** 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

install for x64

* installing *source* package 'AgiMicroRna' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'AgiMicroRna' as AgiMicroRna_2.41.0.zip
* DONE (AgiMicroRna)
* installing to library 'D:/biocbuild/bbs-3.13-bioc/R/library'
package 'AgiMicroRna' successfully unpacked and MD5 sums checked

Tests output


Example timings

AgiMicroRna.Rcheck/examples_i386/AgiMicroRna-Ex.timings

nameusersystemelapsed
HeatMapMicroRna0.340.010.91
PCAplotMicroRna0.150.000.17
RleMicroRna0.890.080.97
basicLimma000
boxplotMicroRna0.620.000.62
cvArray000
filterMicroRna0.460.110.61
getDecideTests000
hierclusMicroRna0.030.000.05
mvaBASIC3.170.123.34
mvaMicroRna18.64 0.1818.86
plotDensityMicroRna1.000.011.01
pvalHistogram000
qcPlots000
readMicroRnaAFE000
rmaMicroRna3.190.023.20
significantMicroRna0.400.080.52
tgsMicroRna0.160.000.16
tgsNormalization000
uRNAList000
writeEset000

AgiMicroRna.Rcheck/examples_x64/AgiMicroRna-Ex.timings

nameusersystemelapsed
HeatMapMicroRna0.210.030.61
PCAplotMicroRna0.110.030.16
RleMicroRna0.530.050.58
basicLimma000
boxplotMicroRna0.330.050.38
cvArray000
filterMicroRna0.310.090.46
getDecideTests000
hierclusMicroRna0.030.020.06
mvaBASIC2.550.012.64
mvaMicroRna15.62 0.2815.97
plotDensityMicroRna1.080.021.09
pvalHistogram000
qcPlots000
readMicroRnaAFE000
rmaMicroRna5.100.055.14
significantMicroRna0.340.060.42
tgsMicroRna0.090.020.11
tgsNormalization000
uRNAList000
writeEset000