Back to Multiple platform build/check report for BioC 3.12
[A]BCDEFGHIJKLMNOPQRSTUVWXYZ

CHECK report for AffyExpress on tokay1

This page was generated on 2020-09-20 10:15:02 -0400 (Sun, 20 Sep 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE AffyExpress PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 28/1912HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AffyExpress 1.55.0
Xuejun Arthur Li
Snapshot Date: 2020-09-19 14:40:23 -0400 (Sat, 19 Sep 2020)
URL: https://git.bioconductor.org/packages/AffyExpress
Branch: master
Last Commit: 900fba3
Last Changed Date: 2020-04-27 14:15:41 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK  OK  OK 
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: AffyExpress
Version: 1.55.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:AffyExpress.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings AffyExpress_1.55.0.tar.gz
StartedAt: 2020-09-20 00:17:55 -0400 (Sun, 20 Sep 2020)
EndedAt: 2020-09-20 00:20:11 -0400 (Sun, 20 Sep 2020)
EllapsedTime: 135.8 seconds
RetCode: 0
Status:  OK  
CheckDir: AffyExpress.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:AffyExpress.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings AffyExpress_1.55.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/AffyExpress.Rcheck'
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'AffyExpress/DESCRIPTION' ... OK
* this is package 'AffyExpress' version '1.55.0'
* 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 'AffyExpress' 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
* 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 ... OK
** 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 ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' calls in package code:
  'R2HTML' 'affyPLM' 'annaffy' 'gcrma' 'genefilter' 'simpleaffy'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  '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
AffyQA: warning in matrix(c(1, 3, 5, 7, 2, 4, 6, 7), nr = 4, ncol = 2):
  partial argument match of 'nr' to 'nrow'
AffyInteraction: no visible global function definition for 'pData'
AffyInteraction: no visible global function definition for 'annotation'
AffyInteraction: no visible global function definition for 'exprs'
AffyQA: no visible global function definition for 'pData'
AffyQA: no visible global function definition for 'cdfName'
AffyQA: no visible global function definition for 'cleancdfname'
AffyQA: no visible global function definition for 'setQCEnvironment'
AffyQA: no visible global function definition for 'qc.get.alpha1'
AffyQA: no visible global function definition for 'HTMLStart'
AffyQA: no visible global function definition for 'HTML'
AffyQA: no visible global function definition for 'as.title'
AffyQA: no visible global function definition for 'png'
AffyQA: no visible global function definition for 'text'
AffyQA: no visible global function definition for 'HTMLInsertGraph'
AffyQA: no visible global function definition for 'dev.off'
AffyQA: no visible global function definition for 'call.exprs'
AffyQA: no visible global function definition for 'layout'
AffyQA: no visible global function definition for 'par'
AffyQA: no visible global function definition for 'description'
AffyQA: no visible global function definition for 'description<-'
AffyQA: no visible global function definition for 'boxplot'
AffyQA: no visible global function definition for 'barplot'
AffyQA: no visible global function definition for 'avbg'
AffyQA: no visible global function definition for 'percent.present'
AffyQA: no visible global function definition for 'sfs'
AffyQA: no visible global function definition for 'spikeInProbes'
AffyQA: no visible global function definition for 'legend'
AffyQA: no visible global function definition for 'ratios'
AffyQA: no visible global function definition for 'AffyRNAdeg'
AffyQA: no visible global function definition for 'summaryAffyRNAdeg'
AffyQA: no visible global function definition for 'plotAffyRNAdeg'
AffyQA: no visible global function definition for 'rma'
AffyQA: no visible global function definition for 'cor'
AffyQA: no visible global function definition for 'exprs'
AffyQA: no visible global function definition for 'hclust'
AffyQA: no visible global function definition for 'as.dist'
AffyQA: no visible global function definition for 'sampleNames<-'
AffyQA: no visible global function definition for 'fitPLM'
AffyQA: no visible global function definition for 'image'
AffyQA: no visible global function definition for 'Mbox'
AffyQA: no visible global function definition for 'package.version'
AffyQA: no visible global function definition for 'HTMLStop'
AffyRegress: no visible global function definition for 'annotation'
AffyRegress: no visible global function definition for 'pData'
Filter: no visible global function definition for 'exprs'
Filter: no visible global function definition for 'kOverA'
Filter: no visible global function definition for 'filterfun'
Filter: no visible global function definition for 'genefilter'
Filter: no visible binding for global variable 'IQR'
Filter: no visible global function definition for 'quantile'
f.test: no visible global function definition for 'classifyTestsF'
f.test: no visible global function definition for 'pf'
get.f: no visible global function definition for 'classifyTestsF'
import.data: no visible global function definition for
  'read.AnnotatedDataFrame'
import.data: no visible global function definition for 'ReadAffy'
import.data: no visible global function definition for 'pData'
interaction.result2html: no visible global function definition for
  'aaf.handler'
interaction.result2html: no visible global function definition for
  'aafTableAnn'
interaction.result2html: no visible global function definition for
  'aafTable'
interaction.result2html: no visible global function definition for
  'saveHTML'
make.design: no visible global function definition for 'model.matrix'
make.design: no visible global function definition for 'as.formula'
permute.1: no visible global function definition for 'lmFit'
permute.1: no visible global function definition for 'contrasts.fit'
post.interaction: no visible global function definition for 'pData'
pre.process: no visible global function definition for 'gcrma'
pre.process: no visible global function definition for 'rma'
pre.process: no visible global function definition for 'exprs'
pre.process: no visible global function definition for 'par'
pre.process: no visible global function definition for 'hist'
pre.process: no visible global function definition for 'write.table'
regress: no visible global function definition for 'lmFit'
regress: no visible global function definition for 'contrasts.fit'
regress: no visible global function definition for 'eBayes'
regress: no visible global function definition for 'p.adjust'
result2html: no visible global function definition for 'aaf.handler'
result2html: no visible global function definition for 'aafTableAnn'
result2html: no visible global function definition for 'aafTable'
result2html: no visible global function definition for 'saveHTML'
Undefined global functions or variables:
  AffyRNAdeg HTML HTMLInsertGraph HTMLStart HTMLStop IQR Mbox ReadAffy
  aaf.handler aafTable aafTableAnn annotation as.dist as.formula
  as.title avbg barplot boxplot call.exprs cdfName classifyTestsF
  cleancdfname contrasts.fit cor description description<- dev.off
  eBayes exprs filterfun fitPLM gcrma genefilter hclust hist image
  kOverA layout legend lmFit model.matrix p.adjust pData
  package.version par percent.present pf plotAffyRNAdeg png
  qc.get.alpha1 quantile ratios read.AnnotatedDataFrame rma
  sampleNames<- saveHTML setQCEnvironment sfs spikeInProbes
  summaryAffyRNAdeg text write.table
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "barplot", "boxplot", "hist", "image", "layout",
             "legend", "par", "text")
  importFrom("stats", "IQR", "as.dist", "as.formula", "cor", "hclust",
             "model.matrix", "p.adjust", "pf", "quantile")
  importFrom("utils", "write.table")
to your NAMESPACE file.
* 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
AffyInteraction 6.64   0.25    7.35
Filter          5.57   0.08    5.64
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
AffyInteraction 7.72   0.15    7.87
Filter          6.70   0.03    6.73
* 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/AffyExpress.Rcheck/00check.log'
for details.



Installation output

AffyExpress.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/AffyExpress_1.55.0.tar.gz && rm -rf AffyExpress.buildbin-libdir && mkdir AffyExpress.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=AffyExpress.buildbin-libdir AffyExpress_1.55.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL AffyExpress_1.55.0.zip && rm AffyExpress_1.55.0.tar.gz AffyExpress_1.55.0.zip
###
##############################################################################
##############################################################################


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

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  465k  100  465k    0     0  17.2M      0 --:--:-- --:--:-- --:--:-- 19.7M

install for i386

* installing *source* package 'AffyExpress' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'AffyExpress'
    finding HTML links ... done
    AffyInteraction                         html  
    AffyQA                                  html  
    AffyRegress                             html  
    Filter                                  html  
    import.data                             html  
    interaction.result2html                 html  
    make.contrast                           html  
    make.design                             html  
    post.interaction                        html  
    pre.process                             html  
    regress                                 html  
    result2html                             html  
    select.sig.gene                         html  
    testData                                html  
** 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 'AffyExpress' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'AffyExpress' as AffyExpress_1.55.0.zip
* DONE (AffyExpress)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'AffyExpress' successfully unpacked and MD5 sums checked

Tests output


Example timings

AffyExpress.Rcheck/examples_i386/AffyExpress-Ex.timings

nameusersystemelapsed
AffyInteraction6.640.257.35
AffyQA000
AffyRegress4.260.034.41
Filter5.570.085.64
import.data000
interaction.result2html4.320.034.37
make.contrast0.020.000.02
make.design000
post.interaction4.20.04.2
pre.process4.100.004.09
regress4.100.024.11
result2html4.220.004.22
select.sig.gene4.090.014.11

AffyExpress.Rcheck/examples_x64/AffyExpress-Ex.timings

nameusersystemelapsed
AffyInteraction7.720.157.87
AffyQA000
AffyRegress4.690.034.72
Filter6.700.036.73
import.data000
interaction.result2html4.510.054.56
make.contrast0.020.000.01
make.design000
post.interaction4.300.094.39
pre.process4.240.004.24
regress4.890.024.90
result2html4.840.034.88
select.sig.gene4.940.034.98