Package: biosigner

Version: 1.15.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:biosigner.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings biosigner_1.15.0.tar.gz

StartedAt: 2020-01-16 02:14:05 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 02:19:49 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 344.0 seconds

RetCode: 0

Status:  OK

CheckDir: biosigner.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:biosigner.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings biosigner_1.15.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/biosigner.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 ‘biosigner/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘biosigner’ version ‘1.15.0’
* 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 ‘biosigner’ 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 ... NOTE
Namespace in Imports field not imported from: ‘MultiDataSet’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
biosign        89.368  4.425  99.863
plot           69.604  3.146  72.776
getMset        65.501  2.668  69.557
getSignatureLs  5.476  0.507   5.985
biosign-class   5.045  0.514   5.596
predict         5.121  0.437   5.558
getEset         4.938  0.465   5.405
show            4.923  0.456   5.379
* 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/biosigner.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 biosigner
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘biosigner’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
in method for ‘biosign’ with signature ‘x="MultiDataSet"’: no definition for class “MultiDataSet”
** 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 (biosigner)

name	user	system	elapsed
biosign-class	5.045	0.514	5.596
biosign	89.368	4.425	99.863
biosignMultiDataSet-class	0	0	0
biosigner-package	4.160	0.484	4.651
getAccuracyMN	4.118	0.389	4.523
getEset	4.938	0.465	5.405
getMset	65.501	2.668	69.557
getSignatureLs	5.476	0.507	5.985
plot	69.604	3.146	72.776
predict	5.121	0.437	5.558
show	4.923	0.456	5.379