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CHECK report for OSAT on tokay1

This page was generated on 2019-04-13 11:22:13 -0400 (Sat, 13 Apr 2019).

Package 1104/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OSAT 1.30.0
Li Yan
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/OSAT
Branch: RELEASE_3_8
Last Commit: dc662ac
Last Changed Date: 2018-10-30 11:41:49 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 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 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: OSAT
Version: 1.30.0
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:OSAT.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings OSAT_1.30.0.tar.gz
StartedAt: 2019-04-13 04:20:12 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 04:22:06 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 114.0 seconds
RetCode: 0
Status:  OK  
CheckDir: OSAT.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:OSAT.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings OSAT_1.30.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/OSAT.Rcheck'
* using R version 3.5.3 (2019-03-11)
* 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 '1.30.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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-3.8-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://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/OSAT_1.30.0.tar.gz && rm -rf OSAT.buildbin-libdir && mkdir OSAT.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=OSAT.buildbin-libdir OSAT_1.30.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL OSAT_1.30.0.zip && rm OSAT_1.30.0.tar.gz OSAT_1.30.0.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  627k  100  627k    0     0  13.0M      0 --:--:-- --:--:-- --:--:-- 14.2M

install for i386

* installing *source* package 'OSAT' ...
** 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
In R CMD INSTALL

install for x64

* installing *source* package 'OSAT' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'OSAT' as OSAT_1.30.0.zip
* DONE (OSAT)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'OSAT' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

OSAT.Rcheck/examples_i386/OSAT-Ex.timings

nameusersystemelapsed
BeadChip-class0.010.000.02
BeadPlate-class000
MSAroboticPlate-class0.220.000.24
QC0.920.000.92
create.optimized.setup0.790.000.79
example.setup0.020.020.04
gContainer-class0.020.000.01
gExperimentSetup-class0.040.000.05
gSample-class0.020.000.01
gSlide-class0.010.000.02
get.experiment.setup0.80.00.8
multi.barplot0.020.000.01
multi.chisq.test0.010.000.02
optimal.block1.360.001.36
optimal.shuffle0.720.000.72

OSAT.Rcheck/examples_x64/OSAT-Ex.timings

nameusersystemelapsed
BeadChip-class0.020.000.01
BeadPlate-class000
MSAroboticPlate-class0.240.000.23
QC1.450.001.46
create.optimized.setup0.950.000.95
example.setup0.030.000.04
gContainer-class0.030.000.03
gExperimentSetup-class0.050.000.04
gSample-class000
gSlide-class0.030.000.03
get.experiment.setup0.910.000.91
multi.barplot0.010.000.02
multi.chisq.test000
optimal.block1.630.011.64
optimal.shuffle0.840.000.84