BioC 3.6: CHECK report for SigCheck on tokay1

Package: SigCheck

Version: 2.9.0

Command: rm -rf SigCheck.buildbin-libdir SigCheck.Rcheck && mkdir SigCheck.buildbin-libdir SigCheck.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SigCheck.buildbin-libdir SigCheck_2.9.0.tar.gz >SigCheck.Rcheck\00install.out 2>&1 && cp SigCheck.Rcheck\00install.out SigCheck-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=SigCheck.buildbin-libdir --install="check:SigCheck-install.out" --force-multiarch --no-vignettes --timings SigCheck_2.9.0.tar.gz

StartedAt: 2017-08-16 02:28:48 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 02:41:03 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 734.4 seconds

RetCode: 0

Status:  OK

CheckDir: SigCheck.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf SigCheck.buildbin-libdir SigCheck.Rcheck && mkdir SigCheck.buildbin-libdir SigCheck.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SigCheck.buildbin-libdir SigCheck_2.9.0.tar.gz >SigCheck.Rcheck\00install.out 2>&1 && cp SigCheck.Rcheck\00install.out SigCheck-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=SigCheck.buildbin-libdir --install="check:SigCheck-install.out" --force-multiarch --no-vignettes --timings SigCheck_2.9.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/SigCheck.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 'SigCheck/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SigCheck' version '2.9.0'
* 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 'SigCheck' 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
sigCheckKnown: no visible binding for global variable 'knownSignatures'
Undefined global functions or variables:
  knownSignatures
* 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
Examples with CPU or elapsed time > 5s
                   user system elapsed
sigCheckAll      116.08   5.14  121.22
sigCheckKnown     61.97   2.17   64.14
sigCheckPermuted  19.98   0.63   20.61
sigCheckPlot      14.58   0.67   15.25
sigCheck          12.45   1.64   14.09
sigCheckRandom     9.58   0.33    9.91
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
sigCheckAll      127.89   4.69  132.57
sigCheckKnown     66.83   1.37   68.22
sigCheckPermuted  15.81   0.55   16.36
sigCheck          14.94   0.66   15.59
sigCheckPlot      13.45   0.56   14.02
sigCheckRandom    10.92   0.44   11.36
* 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-3.6-bioc/meat/SigCheck.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'SigCheck' ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import 'BiocGenerics::var' by 'stats::var' when loading 'MLInterfaces'
Creating a new generic function for 'signature' in package 'SigCheck'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import 'BiocGenerics::var' by 'stats::var' when loading 'MLInterfaces'

install for x64

* installing *source* package 'SigCheck' ...
** testing if installed package can be loaded
Warning: replacing previous import 'BiocGenerics::var' by 'stats::var' when loading 'MLInterfaces'
* MD5 sums
packaged installation of 'SigCheck' as SigCheck_2.9.0.zip
* DONE (SigCheck)

name	user	system	elapsed
SigCheckObject-class	0	0	0
classifyResults	0.09	0.00	0.09
knownSignatures	0.03	0.03	0.06
nkiResults	0.04	0.02	0.06
sigCheck	12.45	1.64	14.09
sigCheckAll	116.08	5.14	121.22
sigCheckKnown	61.97	2.17	64.14
sigCheckPermuted	19.98	0.63	20.61
sigCheckPlot	14.58	0.67	15.25
sigCheckRandom	9.58	0.33	9.91

name	user	system	elapsed
SigCheckObject-class	0	0	0
classifyResults	0.09	0.00	0.10
knownSignatures	0.05	0.01	0.06
nkiResults	0.06	0.00	0.07
sigCheck	14.94	0.66	15.59
sigCheckAll	127.89	4.69	132.57
sigCheckKnown	66.83	1.37	68.22
sigCheckPermuted	15.81	0.55	16.36
sigCheckPlot	13.45	0.56	14.02
sigCheckRandom	10.92	0.44	11.36