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This page was generated on 2021-10-15 15:06:53 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the singscore package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/singscore.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 1781/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
singscore 1.12.0 (landing page) Dharmesh D. Bhuva
| 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: singscore |
Version: 1.12.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:singscore.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings singscore_1.12.0.tar.gz |
StartedAt: 2021-10-15 00:06:08 -0400 (Fri, 15 Oct 2021) |
EndedAt: 2021-10-15 00:10:55 -0400 (Fri, 15 Oct 2021) |
EllapsedTime: 287.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: singscore.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:singscore.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings singscore_1.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/singscore.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 ‘singscore/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘singscore’ version ‘1.12.0’ * 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 ... 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 ‘singscore’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ...It is recommended to use ‘given’ instead of ‘middle’. 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 plotDispersion: no visible binding for global variable ‘Score’ plotDispersion: no visible binding for global variable ‘Dispersion’ plotDispersion: no visible binding for global variable ‘Class’ plotDispersion: no visible binding for global variable ‘SampleText’ plotDispersion: no visible binding for global variable ‘SampleLabel’ plotRankDensity_intl: no visible binding for global variable ‘Ranks’ plotRankDensity_intl: no visible binding for global variable ‘upDown’ plotRankDensity_intl: no visible binding for global variable ‘..density..’ plotRankDensity_intl: no visible binding for global variable ‘EntrezID’ plotScoreLandscape: no visible binding for global variable ‘sc1’ plotScoreLandscape: no visible binding for global variable ‘sc2’ projectScoreLandscape: no visible binding for global variable ‘SampleText’ projectScoreLandscape: no visible binding for global variable ‘Class’ projectScoreLandscape: no visible binding for global variable ‘SampleLabel’ Undefined global functions or variables: ..density.. Class Dispersion EntrezID Ranks SampleLabel SampleText Score sc1 sc2 upDown * 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 R/sysdata.rda ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * 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/singscore.Rcheck/00check.log’ for details.
singscore.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL singscore ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’ * installing *source* package ‘singscore’ ... ** using staged installation It is recommended to use ‘given’ instead of ‘middle’. It is recommended to use ‘given’ instead of ‘middle’. ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (singscore)
singscore.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. > library(testthat) > library(singscore) > > test_check("singscore") [ FAIL 0 | WARN 41 | SKIP 0 | PASS 138 ] > > proc.time() user system elapsed 22.009 0.874 22.895
singscore.Rcheck/singscore-Ex.timings
name | user | system | elapsed | |
generateNull | 1.782 | 0.025 | 1.809 | |
getPvals | 0.157 | 0.002 | 0.160 | |
getStableGenes | 0.297 | 0.026 | 0.324 | |
multiScore | 0.023 | 0.000 | 0.023 | |
plotDispersion | 1.217 | 0.085 | 1.305 | |
plotNull | 0.860 | 0.014 | 0.876 | |
plotRankDensity | 0.238 | 0.027 | 0.265 | |
plotScoreLandscape | 0.182 | 0.018 | 0.200 | |
rankGenes | 0.130 | 0.013 | 0.143 | |
simpleScore | 0.016 | 0.001 | 0.017 | |