Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:05 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 1813/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
RTCGA 1.36.0 (landing page) Marcin Kosinski
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the RTCGA package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RTCGA.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. |
Package: RTCGA |
Version: 1.36.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:RTCGA.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings RTCGA_1.36.0.tar.gz |
StartedAt: 2024-12-20 05:29:55 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 05:32:58 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 182.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: RTCGA.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:RTCGA.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings RTCGA_1.36.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/RTCGA.Rcheck' * using R version 4.4.2 (2024-10-31 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.3.0 GNU Fortran (GCC) 13.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'RTCGA/DESCRIPTION' ... OK * this is package 'RTCGA' version '1.36.0' * 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 whether package 'RTCGA' 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 code 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 whether startup messages can be suppressed ... 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 availableDates: no visible binding for global variable '.' downloadTCGA: no visible binding for global variable '.' ggbiplot: no visible binding for global variable 'xvar' ggbiplot: no visible binding for global variable 'yvar' ggbiplot: no visible global function definition for 'muted' ggbiplot: no visible binding for global variable 'varname' ggbiplot: no visible binding for global variable 'angle' ggbiplot: no visible binding for global variable 'hjust' read.mutations: no visible binding for global variable '.' read.rnaseq: no visible binding for global variable '.' survivalTCGA: no visible binding for global variable 'times' whichDateToUse: no visible binding for global variable '.' Undefined global functions or variables: . angle hjust muted times varname xvar yvar * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Unknown packages 'RTCGA.rnaseq.20160128', 'RTCGA.clinical.20160128', 'RTCGA.mutations.20160128', 'RTCGA.CNV.20160128', 'RTCGA.RPPA.20160128', 'RTCGA.mRNA.20160128', 'RTCGA.miRNASeq.20160128', 'RTCGA.methylation.20160128' in Rd xrefs * 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 files in 'vignettes' ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed boxplotTCGA 16.16 1.48 18.20 expressionsTCGA 10.64 1.78 14.16 heatmapTCGA 8.66 0.53 9.18 kmTCGA 7.33 0.23 7.78 survivalTCGA 7.27 0.17 7.43 * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'testthat.R' OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... 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 'F:/biocbuild/bbs-3.20-bioc/meat/RTCGA.Rcheck/00check.log' for details.
RTCGA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL RTCGA ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'RTCGA' ... ** using staged installation ** R ** 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 (RTCGA)
RTCGA.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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(RTCGA) Welcome to the RTCGA (version: 1.36.0). Read more about the project under https://rtcga.github.io/RTCGA/ > library(RTCGA.rnaseq) > library(Biobase) Loading required package: BiocGenerics Attaching package: 'BiocGenerics' 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, aperm, 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, saveRDS, setdiff, table, tapply, union, unique, unsplit, which.max, which.min Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. > library(GenomicRanges) Loading required package: stats4 Loading required package: S4Vectors Attaching package: 'S4Vectors' The following object is masked from 'package:utils': findMatches The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: IRanges Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows Loading required package: GenomeInfoDb > #library(RTCGA.CNV) > #library(RTCGA.PANCAN12) > > test_check("RTCGA") trying URL 'https://gdac.broadinstitute.org/runs/stddata__2015_06_01/data/ACC/20150601//gdac.broadinstitute.org_ACC.Merge_Clinical.Level_1.2015060100.0.0.tar.gz' Content type 'application/x-gzip' length 151456 bytes (147 KB) ================================================== downloaded 147 KB trying URL 'https://gdac.broadinstitute.org/runs/stddata__2015_06_01/data/ACC/20150601//gdac.broadinstitute.org_ACC.Merge_Clinical.Level_1.2015060100.0.0.tar.gz' Content type 'application/x-gzip' length 151456 bytes (147 KB) ================================================== downloaded 147 KB [ FAIL 0 | WARN 0 | SKIP 0 | PASS 11 ] > > proc.time() user system elapsed 11.28 1.21 14.59
RTCGA.Rcheck/RTCGA-Ex.timings
name | user | system | elapsed | |
RTCGA-package | 0 | 0 | 0 | |
boxplotTCGA | 16.16 | 1.48 | 18.20 | |
checkTCGA | 0.14 | 0.06 | 1.27 | |
convertTCGA | 2.00 | 0.30 | 2.29 | |
datasetsTCGA | 0 | 0 | 0 | |
downloadTCGA | 0.01 | 0.02 | 0.44 | |
expressionsTCGA | 10.64 | 1.78 | 14.16 | |
heatmapTCGA | 8.66 | 0.53 | 9.18 | |
infoTCGA | 0.81 | 0.00 | 1.11 | |
installTCGA | 0 | 0 | 0 | |
kmTCGA | 7.33 | 0.23 | 7.78 | |
mutationsTCGA | 3.84 | 0.18 | 4.02 | |
pcaTCGA | 0 | 0 | 0 | |
readTCGA | 0.00 | 0.01 | 0.02 | |
survivalTCGA | 7.27 | 0.17 | 7.43 | |
theme_RTCGA | 2.49 | 0.07 | 2.55 | |