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CHECK report for SparseSignatures on malbec2

This page was generated on 2020-10-17 11:55:49 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE SparseSignatures PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1704/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SparseSignatures 1.8.0
Luca De Sano
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/SparseSignatures
Branch: RELEASE_3_11
Last Commit: ad76117
Last Changed Date: 2020-04-27 15:15:44 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  NA 
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: SparseSignatures
Version: 1.8.0
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:SparseSignatures.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings SparseSignatures_1.8.0.tar.gz
StartedAt: 2020-10-17 05:42:32 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 05:49:10 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 398.4 seconds
RetCode: 0
Status:  OK 
CheckDir: SparseSignatures.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:SparseSignatures.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings SparseSignatures_1.8.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/SparseSignatures.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SparseSignatures/DESCRIPTION’ ... OK
* this is package ‘SparseSignatures’ version ‘1.8.0’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
nmf.LassoK         37.361  0.050  37.412
import.counts.data  2.645  0.866  65.788
* 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
  ‘/home/biocbuild/bbs-3.11-bioc/meat/SparseSignatures.Rcheck/00check.log’
for details.



Installation output

SparseSignatures.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL SparseSignatures
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘SparseSignatures’ ...
** using staged installation
** 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 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 (SparseSignatures)

Tests output

SparseSignatures.Rcheck/tests/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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
Loading required package: rngtools
Loading required package: cluster
NMF - BioConductor layer [OK] | Shared memory capabilities [NO: synchronicity] | Cores 19/20
  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 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 55.652   0.542  56.209 

Example timings

SparseSignatures.Rcheck/SparseSignatures-Ex.timings

nameusersystemelapsed
as.alpha0.0000.0030.004
as.alpha.in.range0.0070.0000.006
as.beta0.0030.0000.002
as.beta.in.range0.6180.0000.618
as.loglik.progression0.0020.0000.002
as.loglik.progression.in.range0.0050.0000.005
as.mean.squared.error0.0060.0000.006
as.starting.beta0.0020.0000.001
as.starting.beta.in.range0.0060.0000.005
import.counts.data 2.645 0.86665.788
nmf.LassoK37.361 0.05037.412
patient.plot0.4510.0040.455
signatures.plot2.3230.0002.323