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BioC 3.5: CHECK report for OSAT on tokay2

This page was generated on 2017-08-16 13:21:43 -0400 (Wed, 16 Aug 2017).

Package 933/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OSAT 1.24.0
Li Yan
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/OSAT
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: OSAT
Version: 1.24.0
Command: rm -rf OSAT.buildbin-libdir OSAT.Rcheck && mkdir OSAT.buildbin-libdir OSAT.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=OSAT.buildbin-libdir OSAT_1.24.0.tar.gz >OSAT.Rcheck\00install.out 2>&1 && cp OSAT.Rcheck\00install.out OSAT-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=OSAT.buildbin-libdir --install="check:OSAT-install.out" --force-multiarch --no-vignettes --timings OSAT_1.24.0.tar.gz
StartedAt: 2017-08-16 01:44:38 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 01:45:32 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 53.6 seconds
RetCode: 0
Status:  OK  
CheckDir: OSAT.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf OSAT.buildbin-libdir OSAT.Rcheck && mkdir OSAT.buildbin-libdir OSAT.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=OSAT.buildbin-libdir OSAT_1.24.0.tar.gz >OSAT.Rcheck\00install.out 2>&1 && cp OSAT.Rcheck\00install.out OSAT-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=OSAT.buildbin-libdir --install="check:OSAT-install.out" --force-multiarch --no-vignettes --timings OSAT_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/OSAT.Rcheck'
* using R version 3.4.1 (2017-06-30)
* 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 '1.24.0'
* 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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 installed files from 'inst/doc' ... 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-3.5-bioc/meat/OSAT.Rcheck/00check.log'
for details.


OSAT.Rcheck/00install.out:


install for i386

* installing *source* package 'OSAT' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'OSAT' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'OSAT' as OSAT_1.24.0.zip
* DONE (OSAT)

OSAT.Rcheck/examples_i386/OSAT-Ex.timings:

nameusersystemelapsed
BeadChip-class000
BeadPlate-class0.010.000.01
MSAroboticPlate-class0.30.00.3
QC1.060.001.06
create.optimized.setup0.80.00.8
example.setup0.020.020.03
gContainer-class0.010.000.02
gExperimentSetup-class0.050.000.04
gSample-class0.010.000.02
gSlide-class000
get.experiment.setup0.740.010.75
multi.barplot0.010.000.02
multi.chisq.test0.030.000.03
optimal.block1.520.001.51
optimal.shuffle0.810.000.81

OSAT.Rcheck/examples_x64/OSAT-Ex.timings:

nameusersystemelapsed
BeadChip-class000
BeadPlate-class0.020.000.01
MSAroboticPlate-class0.440.000.43
QC1.260.001.27
create.optimized.setup0.880.000.88
example.setup0.010.010.03
gContainer-class0.020.000.01
gExperimentSetup-class0.050.000.05
gSample-class0.010.000.01
gSlide-class000
get.experiment.setup0.820.000.82
multi.barplot0.010.000.01
multi.chisq.test0.050.000.05
optimal.block1.730.001.73
optimal.shuffle0.850.000.84