Package: SigCheck

Version: 2.19.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SigCheck.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SigCheck_2.19.0.tar.gz

StartedAt: 2020-01-16 08:53:45 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 09:04:20 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 635.7 seconds

RetCode: 0

Status:  OK

CheckDir: SigCheck.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SigCheck.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SigCheck_2.19.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/SigCheck.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SigCheck/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SigCheck’ version ‘2.19.0’
* 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 for sufficient/correct file permissions ... 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
* 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 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
sigCheckAll      168.892 31.929 204.729
sigCheckKnown     77.410 15.872  93.285
sigCheck          21.454  3.701  25.400
sigCheckPermuted  20.397  3.794  24.545
sigCheckPlot      18.665  3.761  22.429
sigCheckRandom    13.834  2.367  16.203
* 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
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/SigCheck.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL SigCheck
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘SigCheck’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (SigCheck)

name	user	system	elapsed
SigCheckObject-class	0.006	0.001	0.007
classifyResults	0.054	0.004	0.058
knownSignatures	0.029	0.006	0.035
nkiResults	0.028	0.005	0.034
sigCheck	21.454	3.701	25.400
sigCheckAll	168.892	31.929	204.729
sigCheckKnown	77.410	15.872	93.285
sigCheckPermuted	20.397	3.794	24.545
sigCheckPlot	18.665	3.761	22.429
sigCheckRandom	13.834	2.367	16.203