Dharmesh D. Bhuva
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/singscore |
| Branch: RELEASE_3_10 |
| Last Commit: e80a3f9 |
| Last Changed Date: 2019-10-29 13:11:10 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:47:24 -0400 (Wed, 15 Apr 2020).
| Package 1607/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| singscore 1.6.0 Dharmesh D. Bhuva
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: singscore |
| Version: 1.6.0 |
| 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_1.6.0.tar.gz |
| StartedAt: 2020-04-15 05:45:51 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 05:50:11 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 259.9 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_1.6.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/singscore.Rcheck’ * using R version 3.6.3 (2020-02-29) * using platform: x86_64-apple-darwin15.6.0 (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 ‘1.6.0’ * 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 ‘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 data for ASCII and uncompressed saves ... 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: 1 NOTE See ‘/Users/biocbuild/bbs-3.10-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/3.6/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 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
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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
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> library(testthat)
> library(singscore)
Loading required package: GSEABase
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which, which.max, which.min
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: XML
Loading required package: graph
Attaching package: 'graph'
The following object is masked from 'package:XML':
addNode
>
> test_check("singscore")
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 111 | SKIPPED: 0 | WARNINGS: 34 | FAILED: 0 ]
>
> proc.time()
user system elapsed
25.411 8.067 20.406
singscore.Rcheck/singscore-Ex.timings
| name | user | system | elapsed | |
| generateNull | 1.337 | 0.020 | 1.372 | |
| getPvals | 0.083 | 0.002 | 0.084 | |
| multiScore | 0.025 | 0.000 | 0.026 | |
| plotDispersion | 1.422 | 0.245 | 1.689 | |
| plotNull | 0.995 | 0.032 | 1.038 | |
| plotRankDensity | 0.268 | 0.002 | 0.272 | |
| plotScoreLandscape | 0.206 | 0.001 | 0.210 | |
| rankGenes | 0.092 | 0.002 | 0.093 | |
| simpleScore | 0.01 | 0.00 | 0.01 | |