Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:54 -0400 (Fri, 15 Oct 2021).
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. |
Package 1813/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
SparseSignatures 2.2.0 (landing page) Luca De Sano
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: SparseSignatures |
Version: 2.2.0 |
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_2.2.0.tar.gz |
StartedAt: 2021-10-15 00:16:37 -0400 (Fri, 15 Oct 2021) |
EndedAt: 2021-10-15 00:28:05 -0400 (Fri, 15 Oct 2021) |
EllapsedTime: 688.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: SparseSignatures.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running 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_2.2.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/SparseSignatures.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘SparseSignatures/DESCRIPTION’ ... OK * this is package ‘SparseSignatures’ version ‘2.2.0’ * 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 ... NOTE Found the following hidden files and directories: .git_fetch_output.txt .git_merge_output.txt These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * 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 LazyData ... 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 (user + system) or elapsed time > 5s user system elapsed lambdaRangeBetaEvaluation 158.325 9.127 167.595 lambdaRangeAlphaEvaluation 145.062 8.933 154.166 nmfLassoCV 19.476 1.120 20.612 nmfLassoBootstrap 16.853 3.627 20.495 nmfLasso 10.152 0.431 10.598 startingBetaEstimation 5.132 0.064 5.197 * 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: 2 NOTEs See ‘/Users/biocbuild/bbs-3.13-bioc/meat/SparseSignatures.Rcheck/00check.log’ for details.
SparseSignatures.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL SparseSignatures ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/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)
SparseSignatures.Rcheck/tests/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin17.0 (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 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") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ] > > proc.time() user system elapsed 14.498 0.632 15.119
SparseSignatures.Rcheck/SparseSignatures-Ex.timings
name | user | system | elapsed | |
import.trinucleotides.counts | 0.000 | 0.001 | 0.000 | |
lambdaRangeAlphaEvaluation | 145.062 | 8.933 | 154.166 | |
lambdaRangeBetaEvaluation | 158.325 | 9.127 | 167.595 | |
nmfLasso | 10.152 | 0.431 | 10.598 | |
nmfLassoBootstrap | 16.853 | 3.627 | 20.495 | |
nmfLassoCV | 19.476 | 1.120 | 20.612 | |
patients.plot | 1.354 | 0.012 | 1.367 | |
sigAssignmentCV | 0.112 | 0.004 | 0.116 | |
sigAssignmentEvaluation | 3.774 | 0.182 | 3.961 | |
sigAssignmentLasso | 0.892 | 0.051 | 0.943 | |
signatures.plot | 2.359 | 0.018 | 2.380 | |
startingBetaEstimation | 5.132 | 0.064 | 5.197 | |