Package: SparseSignatures

Version: 1.0.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SparseSignatures.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SparseSignatures_1.0.3.tar.gz

StartedAt: 2018-10-17 00:11:51 -0400 (Wed, 17 Oct 2018)

EndedAt: 2018-10-17 00:17:59 -0400 (Wed, 17 Oct 2018)

EllapsedTime: 368.1 seconds

RetCode: 0

Status:  OK

CheckDir: SparseSignatures.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:SparseSignatures.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SparseSignatures_1.0.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/SparseSignatures.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SparseSignatures/DESCRIPTION’ ... OK
* this is package ‘SparseSignatures’ version ‘1.0.3’
* package encoding: UTF-8
* 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 ‘SparseSignatures’ 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
import.counts.data: no visible global function definition for ‘.’
patient.plot: no visible binding for global variable ‘Context’
patient.plot: no visible binding for global variable ‘alt’
patient.plot: no visible binding for global variable ‘N’
signatures.plot: no visible binding for global variable ‘Context’
signatures.plot: no visible binding for global variable ‘alt’
signatures.plot: no visible binding for global variable ‘value’
Undefined global functions or variables:
  . Context N alt value
* 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 or elapsed time > 5s
                     user system elapsed
nmf.LassoK         51.935  0.635  53.230
signatures.plot     5.014  0.010   5.115
import.counts.data  2.321  0.918   5.306
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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-3.7-bioc/meat/SparseSignatures.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 SparseSignatures
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘SparseSignatures’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (SparseSignatures)

R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> Sys.setenv("R_TESTS" = "")
> 
> library(testthat)
> library(SparseSignatures)
Loading required package: NMF
Loading required package: pkgmaker
Loading required package: registry

Attaching package: 'pkgmaker'

The following object is masked from 'package:base':

    isFALSE

Loading required package: rngtools
Loading required package: cluster
NMF - BioConductor layer [OK] | Shared memory capabilities [NO: synchronicity] | Cores 23/24
  To enable shared memory capabilities, try: install.extras('
NMF
')

Attaching package: 'NMF'

The following object is masked from 'package:testthat':

    compare

> 
> test_check("SparseSignatures")
Performing the discovery of the signatures by NMF with Lasso... 
Performing a total of 5 iterations... 
Progress 20%... 
Progress 40%... 
Progress 60%... 
Progress 80%... 
Progress 100%... 
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 10 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 64.645   1.193  66.681 

name	user	system	elapsed
as.alpha	0.004	0.002	0.009
as.alpha.in.range	0.006	0.002	0.008
as.beta	0.002	0.001	0.004
as.beta.in.range	0.006	0.002	0.009
as.loglik.progression	0.003	0.001	0.004
as.loglik.progression.in.range	0.007	0.002	0.009
as.mean.squared.error	0.009	0.002	0.010
as.starting.beta	0.003	0.001	0.004
as.starting.beta.in.range	0.006	0.002	0.008
import.counts.data	2.321	0.918	5.306
nmf.LassoK	51.935	0.635	53.230
patient.plot	1.013	0.005	1.039
signatures.plot	5.014	0.010	5.115