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This page was generated on 2024-02-20 11:36:25 -0500 (Tue, 20 Feb 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" 4690
palomino4Windows Server 2022 Datacenterx644.3.2 (2023-10-31 ucrt) -- "Eye Holes" 4443
lconwaymacOS 12.7.1 Montereyx86_644.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" 4464
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

Package 2006/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SparseSignatures 2.12.0  (landing page)
Luca De Sano
Snapshot Date: 2024-02-19 14:05:07 -0500 (Mon, 19 Feb 2024)
git_url: https://git.bioconductor.org/packages/SparseSignatures
git_branch: RELEASE_3_18
git_last_commit: 761604b
git_last_commit_date: 2023-10-24 11:04:29 -0500 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for SparseSignatures on nebbiolo2


To the developers/maintainers of the SparseSignatures package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: SparseSignatures
Version: 2.12.0
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:SparseSignatures.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings SparseSignatures_2.12.0.tar.gz
StartedAt: 2024-02-20 02:48:48 -0500 (Tue, 20 Feb 2024)
EndedAt: 2024-02-20 02:59:51 -0500 (Tue, 20 Feb 2024)
EllapsedTime: 662.7 seconds
RetCode: 0
Status:   OK  
CheckDir: SparseSignatures.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:SparseSignatures.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings SparseSignatures_2.12.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/SparseSignatures.Rcheck’
* using R version 4.3.2 Patched (2023-11-13 r85521)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘SparseSignatures/DESCRIPTION’ ... OK
* this is package ‘SparseSignatures’ version ‘2.12.0’
* 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 loading without being on the library search path ... 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  91.707  0.436  92.143
lambdaRangeAlphaEvaluation 82.461  0.647  83.109
nmfLassoCV                 13.364  0.008  13.373
nmfLassoBootstrap          12.567  0.104  12.671
nmfLasso                    5.428  0.004   5.431
* 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 ...
  ‘v1_introduction.rmd’ using ‘UTF-8’... OK
  ‘v2_using_the_package.rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/SparseSignatures.Rcheck/00check.log’
for details.



Installation output

SparseSignatures.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL SparseSignatures
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-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 4.3.2 Patched (2023-11-13 r85521) -- "Eye Holes"
Copyright (C) 2023 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: registry
Loading required package: rngtools
Loading required package: cluster
NMF - BioConductor layer [OK] | Shared memory capabilities [NO: bigmemory] | Cores 2/2
  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 
 11.497   0.930  12.454 

Example timings

SparseSignatures.Rcheck/SparseSignatures-Ex.timings

nameusersystemelapsed
import.trinucleotides.counts2.5490.1922.733
lambdaRangeAlphaEvaluation82.461 0.64783.109
lambdaRangeBetaEvaluation91.707 0.43692.143
nmfLasso5.4280.0045.431
nmfLassoBootstrap12.567 0.10412.671
nmfLassoCV13.364 0.00813.373
patients.plot1.1060.0401.146
sigAssignmentCV0.0840.0000.084
sigAssignmentEvaluation2.1160.0012.116
sigAssignmentLasso0.6210.0030.625
signatures.plot2.0450.0522.097
startingBetaEstimation3.5800.0333.612