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BioC 3.4: CHECK report for OSAT on moscato1

This page was generated on 2016-09-21 03:44:15 -0700 (Wed, 21 Sep 2016).

Package 853/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OSAT 1.21.0
Li Yan
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/OSAT
Last Changed Rev: 117081 / Revision: 121152
Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / 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: 1.21.0
Command: rm -rf OSAT.buildbin-libdir OSAT.Rcheck && mkdir OSAT.buildbin-libdir OSAT.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=OSAT.buildbin-libdir OSAT_1.21.0.tar.gz >OSAT.Rcheck\00install.out 2>&1 && cp OSAT.Rcheck\00install.out OSAT-install.out && D:\biocbld\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_1.21.0.tar.gz
StartedAt: 2016-09-20 13:27:39 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 13:28:34 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 55.2 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 && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=OSAT.buildbin-libdir OSAT_1.21.0.tar.gz >OSAT.Rcheck\00install.out 2>&1 && cp OSAT.Rcheck\00install.out OSAT-install.out  && D:\biocbld\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_1.21.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/OSAT.Rcheck'
* using R version 3.3.1 (2016-06-21)
* 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 '1.21.0'
* 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
  'D:/biocbld/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_1.21.0.zip
* DONE (OSAT)

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

nameusersystemelapsed
BeadChip-class0.020.000.01
BeadPlate-class0.010.000.02
MSAroboticPlate-class0.310.000.31
QC1.070.001.06
create.optimized.setup1.060.001.06
example.setup0.040.000.05
gContainer-class0.000.020.01
gExperimentSetup-class0.070.000.06
gSample-class0.010.000.02
gSlide-class0.020.000.02
get.experiment.setup1.350.001.35
multi.barplot0.020.000.02
multi.chisq.test0.020.000.01
optimal.block1.820.001.83
optimal.shuffle1.080.001.08

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

nameusersystemelapsed
BeadChip-class0.040.000.04
BeadPlate-class000
MSAroboticPlate-class0.360.000.36
QC1.260.011.28
create.optimized.setup1.300.001.29
example.setup0.040.000.05
gContainer-class0.020.000.02
gExperimentSetup-class0.080.000.07
gSample-class0.010.000.02
gSlide-class000
get.experiment.setup1.30.01.3
multi.barplot0.010.000.01
multi.chisq.test0.040.000.03
optimal.block2.460.022.48
optimal.shuffle1.590.001.59