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BioC 3.4: CHECK report for OSAT on tokay1

This page was generated on 2017-04-15 16:17:19 -0400 (Sat, 15 Apr 2017).

Package 876/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OSAT 1.22.0
Li Yan
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/OSAT
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: OSAT
Version: 1.22.0
Command: rm -rf OSAT.buildbin-libdir OSAT.Rcheck && mkdir OSAT.buildbin-libdir OSAT.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=OSAT.buildbin-libdir OSAT_1.22.0.tar.gz >OSAT.Rcheck\00install.out 2>&1 && cp OSAT.Rcheck\00install.out OSAT-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=OSAT.buildbin-libdir --install="check:OSAT-install.out" --force-multiarch --no-vignettes --timings OSAT_1.22.0.tar.gz
StartedAt: 2017-04-14 23:55:12 -0400 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 23:55:52 -0400 (Fri, 14 Apr 2017)
EllapsedTime: 39.9 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-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=OSAT.buildbin-libdir OSAT_1.22.0.tar.gz >OSAT.Rcheck\00install.out 2>&1 && cp OSAT.Rcheck\00install.out OSAT-install.out  && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=OSAT.buildbin-libdir --install="check:OSAT-install.out" --force-multiarch --no-vignettes --timings OSAT_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.4-bioc/meat/OSAT.Rcheck'
* using R version 3.3.3 (2017-03-06)
* 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 '1.22.0'
* 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-3.4-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_1.22.0.zip
* DONE (OSAT)

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

nameusersystemelapsed
BeadChip-class000
BeadPlate-class0.020.020.03
MSAroboticPlate-class0.230.000.23
QC0.780.000.78
create.optimized.setup0.800.010.82
example.setup0.060.000.06
gContainer-class0.020.000.01
gExperimentSetup-class0.060.000.07
gSample-class0.010.000.01
gSlide-class000
get.experiment.setup0.80.00.8
multi.barplot0.000.020.01
multi.chisq.test0.000.010.02
optimal.block1.390.001.39
optimal.shuffle0.830.000.83

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

nameusersystemelapsed
BeadChip-class0.050.000.05
BeadPlate-class000
MSAroboticPlate-class0.420.000.42
QC1.250.001.25
create.optimized.setup1.350.001.35
example.setup0.030.000.03
gContainer-class0.010.000.01
gExperimentSetup-class0.070.000.07
gSample-class0.010.000.01
gSlide-class000
get.experiment.setup1.110.021.13
multi.barplot000
multi.chisq.test000
optimal.block1.760.001.76
optimal.shuffle0.970.000.96