Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2021-10-19 12:04:46 -0400 (Tue, 19 Oct 2021).

CHECK results for affycomp on riesling1

To the developers/maintainers of the affycomp package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/affycomp.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here 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 24/2060HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
affycomp 1.69.0  (landing page)
Rafael A. Irizarry
Snapshot Date: 2021-10-18 14:50:10 -0400 (Mon, 18 Oct 2021)
git_url: https://git.bioconductor.org/packages/affycomp
git_branch: master
git_last_commit: 52efea6
git_last_commit_date: 2021-05-19 11:33:13 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: affycomp
Version: 1.69.0
Command: D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:affycomp.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings affycomp_1.69.0.tar.gz
StartedAt: 2021-10-19 00:08:15 -0400 (Tue, 19 Oct 2021)
EndedAt: 2021-10-19 00:09:15 -0400 (Tue, 19 Oct 2021)
EllapsedTime: 59.7 seconds
RetCode: 0
Status:   OK  
CheckDir: affycomp.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:affycomp.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings affycomp_1.69.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.14-bioc/meat/affycomp.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '1.69.0'
* 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 ... OK
* checking installed package size ... NOTE
  installed size is  7.5Mb
  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: 3 NOTEs
See
  'D:/biocbuild/bbs-3.14-bioc/meat/affycomp.Rcheck/00check.log'
for details.



Installation output

affycomp.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/affycomp_1.69.0.tar.gz && rm -rf affycomp.buildbin-libdir && mkdir affycomp.buildbin-libdir && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=affycomp.buildbin-libdir affycomp_1.69.0.tar.gz && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL affycomp_1.69.0.zip && rm affycomp_1.69.0.tar.gz affycomp_1.69.0.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
  2 7136k    2  197k    0     0   918k      0  0:00:07 --:--:--  0:00:07  914k
 57 7136k   57 4077k    0     0  3350k      0  0:00:02  0:00:01  0:00:01 3347k
100 7136k  100 7136k    0     0  4748k      0  0:00:01  0:00:01 --:--:-- 4744k

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  
    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_1.69.0.zip
* DONE (affycomp)
* installing to library 'D:/biocbuild/bbs-3.14-bioc/R/library'
package 'affycomp' successfully unpacked and MD5 sums checked

Tests output


Example timings

affycomp.Rcheck/examples_i386/affycomp-Ex.timings

nameusersystemelapsed
SD0.450.020.47
affycomp.compfigs.auxiliary0.230.000.23
affycomp.figures.auxiliary0.340.050.39
affycomp.table0.220.010.23
affycompPlot0.520.050.56

affycomp.Rcheck/examples_x64/affycomp-Ex.timings

nameusersystemelapsed
SD0.360.020.38
affycomp.compfigs.auxiliary0.20.00.2
affycomp.figures.auxiliary0.290.060.36
affycomp.table0.180.030.21
affycompPlot0.460.020.48