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BioC 3.0: CHECK report for Rnits on moscato1

This page was generated on 2015-04-10 09:51:00 -0700 (Fri, 10 Apr 2015).

Package 763/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rnits 1.0.0
Dipen P. Sangurdekar
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/Rnits
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: Rnits
Version: 1.0.0
Command: rm -rf Rnits.buildbin-libdir Rnits.Rcheck && mkdir Rnits.buildbin-libdir Rnits.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Rnits.buildbin-libdir Rnits_1.0.0.tar.gz >Rnits.Rcheck\00install.out 2>&1 && cp Rnits.Rcheck\00install.out Rnits-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=Rnits.buildbin-libdir --install="check:Rnits-install.out" --force-multiarch --no-vignettes --timings Rnits_1.0.0.tar.gz
StartedAt: 2015-04-10 05:07:53 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 05:10:14 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 140.9 seconds
RetCode: 0
Status:  OK  
CheckDir: Rnits.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf Rnits.buildbin-libdir Rnits.Rcheck && mkdir Rnits.buildbin-libdir Rnits.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Rnits.buildbin-libdir Rnits_1.0.0.tar.gz >Rnits.Rcheck\00install.out 2>&1 && cp Rnits.Rcheck\00install.out Rnits-install.out  && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=Rnits.buildbin-libdir --install="check:Rnits-install.out" --force-multiarch --no-vignettes --timings Rnits_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/Rnits.Rcheck'
* using R version 3.1.3 (2015-03-09)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Rnits/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Rnits' version '1.0.0'
* 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 'Rnits' 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
plotResults,Rnits: no visible global function definition for 'aes'
plotResults,Rnits: no visible binding for global variable 'Time'
plotResults,Rnits: no visible binding for global variable 'value'
plotResults,Rnits: no visible global function definition for
  'geom_point'
plotResults,Rnits: no visible binding for global variable 'Sample'
plotResults,Rnits: no visible global function definition for
  'geom_smooth'
plotResults,Rnits: no visible global function definition for 'ylab'
plotResults,Rnits: no visible global function definition for 'theme_bw'
plotResults,Rnits: no visible global function definition for 'theme'
plotResults,Rnits: no visible global function definition for
  'scale_color_brewer'
plotResults,Rnits: no visible global function definition for
  'facet_wrap'
* 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' ... [18s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
calculateGCV-methods 6.62   0.03    6.85
** running examples for arch 'x64' ... [25s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
calculateGCV-methods 10.15   0.03   10.24
* 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

NOTE: There was 1 note.
See
  'D:/biocbld/bbs-3.0-bioc/meat/Rnits.Rcheck/00check.log'
for details.

Rnits.Rcheck/00install.out:


install for i386

* installing *source* package 'Rnits' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Creating a generic function for 'summary' from package 'base' in package 'Rnits'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'Rnits' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Rnits' as Rnits_1.0.0.zip
* DONE (Rnits)

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

nameusersystemelapsed
build.Rnits0.740.030.78
calculateGCV-methods6.620.036.85
fit-methods0.440.000.44
getCID-methods0.480.000.48
getFitModel-methods0.430.000.43
getLR-methods0.430.020.45
getPval-methods0.470.000.47
getStat-methods0.470.000.47
plotResults-methods0.480.000.48
summarizeProbes-methods0.470.000.47
summary-methods0.470.000.47
timeAlign-methods3.290.003.29
topData-methods0.450.010.47

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

nameusersystemelapsed
build.Rnits1.080.021.10
calculateGCV-methods10.15 0.0310.24
fit-methods0.630.010.64
getCID-methods0.620.000.63
getFitModel-methods0.780.000.78
getLR-methods0.630.000.62
getPval-methods0.650.000.66
getStat-methods0.640.000.64
plotResults-methods0.750.000.75
summarizeProbes-methods0.620.000.62
summary-methods0.860.020.87
timeAlign-methods2.890.012.91
topData-methods0.560.000.56