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CHECK report for affycomp on tokay1

This page was generated on 2021-05-06 12:29:50 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the affycomp package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 25/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
affycomp 1.66.0  (landing page)
Rafael A. Irizarry
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/affycomp
Branch: RELEASE_3_12
Last Commit: 388d01a
Last Changed Date: 2020-10-27 10:22:30 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: affycomp
Version: 1.66.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:affycomp.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings affycomp_1.66.0.tar.gz
StartedAt: 2021-05-06 00:18:32 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 00:20:22 -0400 (Thu, 06 May 2021)
EllapsedTime: 110.7 seconds
RetCode: 0
Status:   WARNINGS   
CheckDir: affycomp.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:affycomp.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings affycomp_1.66.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/affycomp.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'affycomp/DESCRIPTION' ... OK
* this is package 'affycomp' version '1.66.0'
* 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 'affycomp' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpyY3FCX/R.INSTALLdb829efb4b/affycomp/man/mas5.assessment.Rd:10: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.12-bioc/meat/affycomp.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
  installed size is  7.4Mb
  sub-directories of 1Mb or more:
    data   7.0Mb
* 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' call to 'splines' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'Biobase' 'methods'
  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
affycomp.figure2b: warning in affycomp.compfig2b(list(l), method.name =
  l$method.name, add.legend = FALSE, main = main): partial argument
  match of 'method.name' to 'method.names'
affycompPlot: warning in vector(mode = "character", len = N): partial
  argument match of 'len' to 'length'
tableAll: warning in vector(mode = "character", len = N): partial
  argument match of 'len' to 'length'
tableOverallSNR: warning in vector(mode = "character", len = N):
  partial argument match of 'len' to 'length'
tableRanks: warning in vector(mode = "character", len = N): partial
  argument match of 'len' to 'length'
.onAttach: no visible global function definition for 'addVigs2WinMenu'
affycomp.compfig2: no visible global function definition for 'lines'
affycomp.compfig2: no visible global function definition for 'legend'
affycomp.compfig2b: no visible global function definition for 'lines'
affycomp.compfig2b: no visible global function definition for 'legend'
affycomp.compfig3: no visible global function definition for 'boxplot'
affycomp.compfig4a: no visible global function definition for 'lines'
affycomp.compfig4a: no visible global function definition for 'legend'
affycomp.compfig4b: no visible global function definition for 'lines'
affycomp.compfig4b: no visible global function definition for 'legend'
affycomp.compfig4b: no visible global function definition for 'abline'
affycomp.compfig4c: no visible global function definition for 'lines'
affycomp.compfig4c: no visible global function definition for 'legend'
affycomp.compfig4c: no visible global function definition for 'abline'
affycomp.compfig5a: no visible global function definition for 'lines'
affycomp.compfig5a: no visible global function definition for 'legend'
affycomp.compfig5b: no visible global function definition for 'lines'
affycomp.compfig5b: no visible global function definition for 'legend'
affycomp.compfig5cde: no visible global function definition for 'lines'
affycomp.compfig5cde: no visible global function definition for
  'legend'
affycomp.compfig7: no visible global function definition for 'boxplot'
affycomp.compfigs: no visible global function definition for 'par'
affycomp.compfigs: no visible global function definition for
  'dev.interactive'
affycomp.figure1: no visible global function definition for
  'topo.colors'
affycomp.figure1: no visible global function definition for
  'heat.colors'
affycomp.figure1: no visible global function definition for 'points'
affycomp.figure1: no visible global function definition for 'text'
affycomp.figure1b: no visible global function definition for
  'topo.colors'
affycomp.figure1b: no visible global function definition for
  'heat.colors'
affycomp.figure1b: no visible global function definition for 'points'
affycomp.figure1b: no visible global function definition for 'text'
affycomp.figure3: no visible global function definition for 'abline'
affycomp.figure3: no visible global function definition for 'points'
affycomp.figure4a: no visible global function definition for 'lines'
affycomp.figure4b: no visible global function definition for 'abline'
affycomp.figure6a: no visible global function definition for 'matplot'
affycomp.figure6a: no visible global function definition for 'lines'
affycomp.figure6a: no visible global function definition for 'abline'
affycomp.figure6b: no visible global function definition for 'lines'
affycomp.figure6b: no visible global function definition for 'abline'
affycomp.figure7: no visible global function definition for 'lm'
affycomp.figure7: no visible global function definition for 'lines'
affycomp.figure7: no visible global function definition for 'abline'
affycomp.figures: no visible global function definition for 'par'
affycomp.figures: no visible global function definition for
  'dev.interactive'
assessDilution: no visible global function definition for 'exprs'
assessDilution: no visible global function definition for 'pData'
assessDilution : <anonymous>: no visible global function definition for
  'cor'
assessDilution : <anonymous>: no visible binding for global variable
  'sd'
assessDilution: no visible global function definition for 'lm'
assessDilution: no visible global function definition for 'median'
assessDilution: no visible global function definition for 'cor'
assessFC: no visible global function definition for 'exprs'
assessFC: no visible global function definition for 'pData'
assessFC: no visible global function definition for 'quantile'
assessFC: no visible global function definition for 'lm'
assessFC2: no visible global function definition for 'exprs'
assessFC2: no visible global function definition for 'pData'
assessLS: no visible global function definition for 'exprs'
assessLS: no visible global function definition for 'pData'
assessLS: no visible global function definition for 'featureNames'
assessLS: no visible global function definition for 'lm'
assessLS: no visible global function definition for 'cor'
assessMA: no visible global function definition for 'exprs'
assessMA: no visible global function definition for 'pData'
assessMA2: no visible global function definition for 'exprs'
assessMA2: no visible global function definition for 'pData'
assessMA2: no visible global function definition for 'featureNames'
assessMA2: no visible binding for global variable 'median'
assessSD: no visible global function definition for 'exprs'
assessSD: no visible global function definition for 'assayDataElement'
assessSD: no visible global function definition for 'pData'
assessSD : <anonymous>: no visible binding for global variable 'sd'
assessSD: no visible global function definition for 'cor'
assessSignal: no visible global function definition for 'exprs'
assessSignal: no visible global function definition for 'pData'
assessSignal: no visible global function definition for 'featureNames'
assessSignal: no visible global function definition for 'lm'
assessSpikeIn2: no visible global function definition for 'exprs'
assessSpikeInSD: no visible global function definition for 'pData'
assessSpikeInSD: no visible global function definition for
  'featureNames'
assessSpikeInSD: no visible global function definition for 'esApply'
assessSpikeInSD: no visible binding for global variable 'sd'
assessSpikeInSD: no visible global function definition for 'loess'
exprset.log: no visible global function definition for 'exprs'
exprset.log: no visible global function definition for 'exprs<-'
getData: no visible global function definition for 'data'
read.dilution: no visible global function definition for 'read.csv'
read.dilution: no visible global function definition for 'sampleNames'
read.dilution: no visible global function definition for 'new'
read.spikein: no visible global function definition for 'read.csv'
read.spikein: no visible global function definition for 'sampleNames'
read.spikein: no visible global function definition for 'new'
remove.hgu133a.xhyb: no visible global function definition for
  'featureNames'
tableMA2 : myauc: no visible global function definition for 'approx'
tableMA2: no visible global function definition for 'IQR'
tableMA2: no visible global function definition for 'quantile'
tableOverallSNR: no visible global function definition for 'median'
tableOverallSNR: no visible global function definition for 'IQR'
tableOverallSNR: no visible global function definition for 'quantile'
tableSD: no visible global function definition for 'IQR'
tableSpikeInSD: no visible global function definition for 'quantile'
Undefined global functions or variables:
  IQR abline addVigs2WinMenu approx assayDataElement boxplot cor data
  dev.interactive esApply exprs exprs<- featureNames heat.colors legend
  lines lm loess matplot median new pData par points quantile read.csv
  sampleNames sd text topo.colors
Consider adding
  importFrom("grDevices", "dev.interactive", "heat.colors",
             "topo.colors")
  importFrom("graphics", "abline", "boxplot", "legend", "lines",
             "matplot", "par", "points", "text")
  importFrom("methods", "new")
  importFrom("stats", "IQR", "approx", "cor", "lm", "loess", "median",
             "quantile", "sd")
  importFrom("utils", "data", "read.csv")
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
** running examples for arch 'x64' ... OK
* 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, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/affycomp.Rcheck/00check.log'
for details.



Installation output

affycomp.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/affycomp_1.66.0.tar.gz && rm -rf affycomp.buildbin-libdir && mkdir affycomp.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=affycomp.buildbin-libdir affycomp_1.66.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL affycomp_1.66.0.zip && rm affycomp_1.66.0.tar.gz affycomp_1.66.0.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
  0 7135k    0  4135    0     0   276k      0  0:00:25 --:--:--  0:00:25  269k
100 7135k  100 7135k    0     0  75.0M      0 --:--:-- --:--:-- --:--:-- 74.9M

install for i386

* installing *source* package 'affycomp' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'affycomp'
    finding HTML links ... done
    SD                                      html  
    affycomp.compfigs.auxiliary             html  
    affycomp.figures.auxiliary              html  
    affycomp.table                          html  
    affycompPlot                            html  
    assessAll                               html  
    assessDilution                          html  
    assessSD                                html  
    assessSpikeIn                           html  
    assessSpikeIn2                          html  
    dilution.phenodata                      html  
    exprset.log                             html  
    hgu133a.spikein.phenodata               html  
    mas5.assessment                         html  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpyY3FCX/R.INSTALLdb829efb4b/affycomp/man/mas5.assessment.Rd:10: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
    readin                                  html  
    remove.hgu133a.xhyb                     html  
    spikein.phenodata                       html  
    xhyb                                    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 'affycomp' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'affycomp' as affycomp_1.66.0.zip
* DONE (affycomp)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'affycomp' successfully unpacked and MD5 sums checked

Tests output


Example timings

affycomp.Rcheck/examples_i386/affycomp-Ex.timings

nameusersystemelapsed
SD0.830.050.97
affycomp.compfigs.auxiliary0.500.000.71
affycomp.figures.auxiliary0.830.000.83
affycomp.table0.470.060.53
affycompPlot1.120.111.23

affycomp.Rcheck/examples_x64/affycomp-Ex.timings

nameusersystemelapsed
SD0.560.050.61
affycomp.compfigs.auxiliary0.290.050.33
affycomp.figures.auxiliary0.500.030.53
affycomp.table0.280.010.30
affycompPlot0.670.050.71