BioC 3.1: CHECK report for Rnits on moscato2

Package: Rnits

Version: 1.2.0

Command: rm -rf Rnits.buildbin-libdir Rnits.Rcheck && mkdir Rnits.buildbin-libdir Rnits.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Rnits.buildbin-libdir Rnits_1.2.0.tar.gz >Rnits.Rcheck\00install.out 2>&1 && cp Rnits.Rcheck\00install.out Rnits-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=Rnits.buildbin-libdir --install="check:Rnits-install.out" --force-multiarch --no-vignettes --timings Rnits_1.2.0.tar.gz

StartedAt: 2015-10-09 05:44:23 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 05:46:14 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 111.3 seconds

RetCode: 0

Status:  OK

CheckDir: Rnits.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf Rnits.buildbin-libdir Rnits.Rcheck && mkdir Rnits.buildbin-libdir Rnits.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Rnits.buildbin-libdir Rnits_1.2.0.tar.gz >Rnits.Rcheck\00install.out 2>&1 && cp Rnits.Rcheck\00install.out Rnits-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=Rnits.buildbin-libdir --install="check:Rnits-install.out" --force-multiarch --no-vignettes --timings Rnits_1.2.0.tar.gz
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* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/Rnits.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-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 '1.2.0'
* 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 ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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' ... [17s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
calculateGCV-methods 6.45   0.06    6.52
** running examples for arch 'x64' ... [19s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
calculateGCV-methods 6.95   0.05    7.01
* 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: 2 NOTEs
See
  'E:/biocbld/bbs-3.1-bioc/meat/Rnits.Rcheck/00check.log'
for details.

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_1.2.0.zip
* DONE (Rnits)

name	user	system	elapsed
build.Rnits	0.62	0.00	0.62
calculateGCV-methods	6.45	0.06	6.52
fit-methods	0.43	0.02	0.46
getCID-methods	0.49	0.00	0.48
getFitModel-methods	0.40	0.00	0.41
getLR-methods	0.42	0.00	0.42
getPval-methods	0.36	0.00	0.36
getStat-methods	0.45	0.02	0.46
plotResults-methods	0.36	0.01	0.38
summarizeProbes-methods	0.41	0.00	0.40
summary-methods	0.42	0.00	0.43
timeAlign-methods	3.24	0.00	3.26
topData-methods	0.38	0.00	0.37

name	user	system	elapsed
build.Rnits	0.66	0.03	0.68
calculateGCV-methods	6.95	0.05	7.01
fit-methods	0.44	0.00	0.44
getCID-methods	0.45	0.00	0.45
getFitModel-methods	0.49	0.02	0.50
getLR-methods	0.46	0.00	0.47
getPval-methods	0.53	0.01	0.54
getStat-methods	0.76	0.00	0.76
plotResults-methods	0.61	0.00	0.61
summarizeProbes-methods	0.69	0.03	0.72
summary-methods	0.65	0.00	0.65
timeAlign-methods	3.26	0.02	3.28
topData-methods	0.69	0.01	0.70