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CHECK report for OSAT on tokay2

This page was generated on 2020-10-17 11:57:20 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE OSAT PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1249/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OSAT 1.36.0
Li Yan
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/OSAT
Branch: RELEASE_3_11
Last Commit: cfb27f4
Last Changed Date: 2020-04-27 14:30:09 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: OSAT
Version: 1.36.0
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:OSAT.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings OSAT_1.36.0.tar.gz
StartedAt: 2020-10-17 06:41:36 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 06:42:58 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 81.5 seconds
RetCode: 0
Status:  OK  
CheckDir: OSAT.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:OSAT.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings OSAT_1.36.0.tar.gz
###
##############################################################################
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/OSAT.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'OSAT/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'OSAT' version '1.36.0'
* 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 'OSAT' 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
assign.sample.to.container: no visible global function definition for
  'head'
barplot.gExperimentSetup: no visible global function definition for
  'layout'
barplot.gExperimentSetup: no visible global function definition for
  'barplot'
barplot.gExperimentSetup: no visible global function definition for
  'gray'
barplot.gExperimentSetup: no visible global function definition for
  'points'
barplot.gExperimentSetup: no visible global function definition for
  'mtext'
multi.barplot: no visible global function definition for 'layout'
multi.barplot: no visible global function definition for 'barplot'
multi.barplot: no visible global function definition for 'gray'
multi.barplot: no visible global function definition for 'mtext'
show,gAssembly: no visible global function definition for 'head'
show,gAssembly: no visible global function definition for 'tail'
show,gContainer: no visible global function definition for 'head'
show,gContainer: no visible global function definition for 'tail'
show,gExperimentSetup: no visible global function definition for 'head'
show,gExperimentSetup: no visible global function definition for 'tail'
show,gPlate: no visible global function definition for 'head'
show,gPlate: no visible global function definition for 'tail'
show,gSample: no visible global function definition for 'head'
show,gSample: no visible global function definition for 'tail'
Undefined global functions or variables:
  barplot gray head layout mtext points tail
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "barplot", "layout", "mtext", "points")
  importFrom("utils", "head", "tail")
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
** 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 NOTE
See
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/OSAT.Rcheck/00check.log'
for details.



Installation output

OSAT.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/OSAT_1.36.0.tar.gz && rm -rf OSAT.buildbin-libdir && mkdir OSAT.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=OSAT.buildbin-libdir OSAT_1.36.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL OSAT_1.36.0.zip && rm OSAT_1.36.0.tar.gz OSAT_1.36.0.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  624k  100  624k    0     0  9395k      0 --:--:-- --:--:-- --:--:-- 10.1M

install for i386

* installing *source* package 'OSAT' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'OSAT'
    finding HTML links ... done
    BeadChip-class                          html  
    BeadPlate-class                         html  
    MSAroboticPlate-class                   html  
    QC                                      html  
    create.optimized.setup                  html  
    example.setup                           html  
    gArray-class                            html  
    gAssembly-class                         html  
    gContainer-class                        html  
    gExperimentSetup-class                  html  
    gPlate-class                            html  
    gSample-class                           html  
    gSlide-class                            html  
    get.experiment.setup                    html  
    multi.barplot                           html  
    multi.chisq.test                        html  
    optimal.block                           html  
    optimal.shuffle                         html  
    plot-methods                            html  
    predefined                              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 'OSAT' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'OSAT' as OSAT_1.36.0.zip
* DONE (OSAT)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'OSAT' successfully unpacked and MD5 sums checked

Tests output


Example timings

OSAT.Rcheck/examples_i386/OSAT-Ex.timings

nameusersystemelapsed
BeadChip-class000
BeadPlate-class0.020.000.01
MSAroboticPlate-class0.360.000.43
QC1.10.01.1
create.optimized.setup0.860.000.86
example.setup0.040.000.04
gContainer-class0.010.000.02
gExperimentSetup-class0.070.000.06
gSample-class0.010.000.01
gSlide-class0.050.000.05
get.experiment.setup0.950.000.95
multi.barplot0.020.000.02
multi.chisq.test0.010.000.01
optimal.block1.160.001.16
optimal.shuffle0.780.000.78

OSAT.Rcheck/examples_x64/OSAT-Ex.timings

nameusersystemelapsed
BeadChip-class0.010.000.02
BeadPlate-class000
MSAroboticPlate-class0.250.000.25
QC1.000.001.03
create.optimized.setup1.080.001.08
example.setup0.030.000.03
gContainer-class0.030.000.03
gExperimentSetup-class0.030.000.03
gSample-class000
gSlide-class0.030.000.03
get.experiment.setup1.10.01.1
multi.barplot0.010.000.01
multi.chisq.test0.000.010.02
optimal.block1.410.001.40
optimal.shuffle1.010.001.02