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CHECK report for affyQCReport on tokay1

This page was generated on 2020-08-07 11:57:02 -0400 (Fri, 07 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE affyQCReport PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 34/1882HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
affyQCReport 1.67.0
Craig Parman
Snapshot Date: 2020-08-06 14:50:46 -0400 (Thu, 06 Aug 2020)
URL: https://git.bioconductor.org/packages/affyQCReport
Branch: master
Last Commit: e1927bf
Last Changed Date: 2020-04-27 14:11:46 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: affyQCReport
Version: 1.67.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:affyQCReport.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings affyQCReport_1.67.0.tar.gz
StartedAt: 2020-08-06 23:48:31 -0400 (Thu, 06 Aug 2020)
EndedAt: 2020-08-06 23:51:32 -0400 (Thu, 06 Aug 2020)
EllapsedTime: 181.1 seconds
RetCode: 0
Status:  OK  
CheckDir: affyQCReport.Rcheck
Warnings: 0

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:affyQCReport.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings affyQCReport_1.67.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/affyQCReport.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 'affyQCReport/DESCRIPTION' ... OK
* this is package 'affyQCReport' version '1.67.0'
* 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 'affyQCReport' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'affy' 'Biobase' 'lattice'
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 ... 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
borderQC1: warning in axis(1, label = ArrayIndex, at = seq(1 - 0.5,
  length(ArrayIndex) - 0.5), cex = 0.2): partial argument match of
  'label' to 'labels'
borderQC2: warning in axis(1, label = ArrayIndex, at = seq(1 - 0.5,
  length(ArrayIndex) - 0.5), cex = 0.2): partial argument match of
  'label' to 'labels'
correlationPlot: warning in axis(2, label = as.list(pretty(c, 10)), at
  = seq(0, 1, by = (1/(length(pretty(c, 10)) - 1)))): partial argument
  match of 'label' to 'labels'
correlationPlot: warning in axis(4, label =
  as.list(attr(object@phenoData, which = "varLabels")[1:phenodepth]),
  at = seq(1 - 0.5, phenodepth - 0.5), las = 1): partial argument match
  of 'label' to 'labels'
signalDist: warning in legend(((temppar$xaxp[2] -
  temppar$xaxp[1])/temppar$xaxp[3]) * (temppar$xaxp[3] - 1) +
  temppar$xaxp[1], temppar$yaxp[2], as.character(ArrayIndex), lt =
  1:length(ArrayIndex), col = 1:length(ArrayIndex), cex = 0.5): partial
  argument match of 'lt' to 'lty'
affyQAReport: no visible global function definition for 'shortPathName'
Undefined global functions or variables:
  shortPathName
Consider adding
  importFrom("utils", "shortPathName")
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 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/affyQCReport.Rcheck/00check.log'
for details.



Installation output

affyQCReport.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/affyQCReport_1.67.0.tar.gz && rm -rf affyQCReport.buildbin-libdir && mkdir affyQCReport.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=affyQCReport.buildbin-libdir affyQCReport_1.67.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL affyQCReport_1.67.0.zip && rm affyQCReport_1.67.0.tar.gz affyQCReport_1.67.0.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
100 27774  100 27774    0     0   435k      0 --:--:-- --:--:-- --:--:--  459k

install for i386

* installing *source* package 'affyQCReport' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'affyQCReport'
    finding HTML links ... done
    QCReport                                html  
    affyQAReport                            html  
    borderQC1                               html  
    borderQC2                               html  
    correlationPlot                         html  
    signalDist                              html  
    titlePage                               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 'affyQCReport' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'affyQCReport' as affyQCReport_1.67.0.zip
* DONE (affyQCReport)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'affyQCReport' successfully unpacked and MD5 sums checked

Tests output


Example timings

affyQCReport.Rcheck/examples_i386/affyQCReport-Ex.timings

nameusersystemelapsed
QCReport000
affyQAReport000
borderQC10.410.050.45
borderQC20.300.050.34
correlationPlot2.570.082.66
signalDist2.140.252.40
titlePage0.440.030.46

affyQCReport.Rcheck/examples_x64/affyQCReport-Ex.timings

nameusersystemelapsed
QCReport000
affyQAReport000
borderQC11.170.021.19
borderQC20.250.020.27
correlationPlot2.680.152.83
signalDist2.390.192.57
titlePage0.390.000.39