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This page was generated on 2022-01-14 13:05:49 -0500 (Fri, 14 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4327
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4076
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4137
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for SparseSignatures on nebbiolo2


To the developers/maintainers of the SparseSignatures package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SparseSignatures.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1843/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SparseSignatures 2.4.0  (landing page)
Luca De Sano
Snapshot Date: 2022-01-13 01:55:04 -0500 (Thu, 13 Jan 2022)
git_url: https://git.bioconductor.org/packages/SparseSignatures
git_branch: RELEASE_3_14
git_last_commit: 54424a2
git_last_commit_date: 2021-10-26 12:43:44 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: SparseSignatures
Version: 2.4.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:SparseSignatures.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings SparseSignatures_2.4.0.tar.gz
StartedAt: 2022-01-13 09:43:29 -0500 (Thu, 13 Jan 2022)
EndedAt: 2022-01-13 09:50:05 -0500 (Thu, 13 Jan 2022)
EllapsedTime: 396.3 seconds
RetCode: 0
Status:   OK  
CheckDir: SparseSignatures.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:SparseSignatures.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings SparseSignatures_2.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/SparseSignatures.Rcheck’
* using R version 4.1.2 (2021-11-01)
* 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 ‘2.4.0’
* 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.trinucleotides.counts: no visible global function definition for
  ‘.’
patients.plot: no visible binding for global variable ‘Context’
patients.plot: no visible binding for global variable ‘alt’
patients.plot: no visible binding for global variable ‘patient’
patients.plot: no visible binding for global variable ‘value’
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 alt patient 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
lambdaRangeBetaEvaluation  79.691  0.467  80.159
lambdaRangeAlphaEvaluation 70.850  0.698  71.548
nmfLassoCV                 11.665  0.060  11.724
nmfLassoBootstrap          10.340  0.228  10.568
* 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-3.14-bioc/meat/SparseSignatures.Rcheck/00check.log’
for details.



Installation output

SparseSignatures.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL SparseSignatures
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘SparseSignatures’ ...
** using staged installation
** R
** data
** 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 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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 71/72
  To enable shared memory capabilities, try: install.extras('
NMF
')

Attaching package: 'NMF'

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

    compare

> 
> test_check("SparseSignatures")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ]
> 
> proc.time()
   user  system elapsed 
 10.439   0.441  10.857 

Example timings

SparseSignatures.Rcheck/SparseSignatures-Ex.timings

nameusersystemelapsed
import.trinucleotides.counts1.6940.2714.545
lambdaRangeAlphaEvaluation70.850 0.69871.548
lambdaRangeBetaEvaluation79.691 0.46780.159
nmfLasso4.7270.0204.746
nmfLassoBootstrap10.340 0.22810.568
nmfLassoCV11.665 0.06011.724
patients.plot0.8490.0040.853
sigAssignmentCV0.0570.0080.065
sigAssignmentEvaluation1.7920.0121.804
sigAssignmentLasso0.5610.0000.561
signatures.plot1.4660.0001.466
startingBetaEstimation3.6960.0123.709