Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-11-20 12:06 -0500 (Wed, 20 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
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 1841/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
SARC 1.4.0 (landing page) Krutik Patel
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ||||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the SARC package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SARC.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: SARC |
Version: 1.4.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SARC.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SARC_1.4.0.tar.gz |
StartedAt: 2024-11-20 02:14:21 -0500 (Wed, 20 Nov 2024) |
EndedAt: 2024-11-20 02:24:02 -0500 (Wed, 20 Nov 2024) |
EllapsedTime: 580.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: SARC.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SARC.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SARC_1.4.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/SARC.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘SARC/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘SARC’ version ‘1.4.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 ‘SARC’ 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 ... NOTE File LICENSE is not mentioned in the DESCRIPTION file. * 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 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 addExonsGenes: no visible global function definition for ‘metadata’ addExonsGenes: no visible global function definition for ‘metadata<-’ anovaOnCNV: no visible global function definition for ‘metadata’ anovaOnCNV: no visible global function definition for ‘metadata<-’ cnvConfidence: no visible global function definition for ‘metadata’ cnvConfidence: no visible global function definition for ‘metadata<-’ pasteExonsGenes: no visible global function definition for ‘metadata’ pasteExonsGenes: no visible global function definition for ‘metadata<-’ phDunnetonCNV: no visible global function definition for ‘metadata’ phDunnetonCNV: no visible global function definition for ‘metadata<-’ plotCovPrep: no visible global function definition for ‘metadata’ plotCovPrep: no visible global function definition for ‘metadata<-’ prepAnova: no visible global function definition for ‘metadata’ prepAnova: no visible global function definition for ‘metadata<-’ regionGrangeMake: no visible global function definition for ‘metadata’ regionGrangeMake: no visible global function definition for ‘metadata<-’ regionMean: no visible global function definition for ‘metadata’ regionMean: no visible global function definition for ‘metadata<-’ regionQuantiles: no visible global function definition for ‘metadata’ regionQuantiles: no visible global function definition for ‘metadata<-’ regionSet: no visible global function definition for ‘sortSeqlevels’ regionSet: no visible global function definition for ‘metadata’ regionSet: no visible global function definition for ‘metadata<-’ regionSplit: no visible global function definition for ‘metadata’ regionSplit: no visible global function definition for ‘metadata<-’ setQDplot: no visible global function definition for ‘metadata’ setQDplot: no visible global function definition for ‘metadata<-’ setupCNVplot: no visible global function definition for ‘metadata’ setupCNVplot: no visible global function definition for ‘metadata<-’ Undefined global functions or variables: metadata metadata<- sortSeqlevels * 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 addExonsGenes 28.136 1.869 31.716 plotCNV 20.324 0.700 21.169 pasteExonsGenes 20.225 0.654 20.997 setupCNVplot 19.610 0.834 20.617 * 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 ‘/Users/biocbuild/bbs-3.20-bioc/meat/SARC.Rcheck/00check.log’ for details.
SARC.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SARC ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘SARC’ ... ** 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 (SARC)
SARC.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 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. > #test SARC unit tests > #unit test check > library(testthat) > library(SARC) Loading required package: RaggedExperiment Loading required package: GenomicRanges Loading required package: stats4 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 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 Loading required package: GenomeInfoDb > test_check(package = "SARC") Error in x$.self$finalize() : attempt to apply non-function [1] "All CNVs are fine for further evaluation" [ FAIL 0 | WARN 0 | SKIP 0 | PASS 28 ] Warning message: call dbDisconnect() when finished working with a connection > > proc.time() user system elapsed 43.223 1.950 45.523
SARC.Rcheck/SARC-Ex.timings
name | user | system | elapsed | |
addExonsGenes | 28.136 | 1.869 | 31.716 | |
anovaOnCNV | 0.717 | 0.086 | 0.808 | |
cnvConfidence | 0.360 | 0.024 | 0.386 | |
pasteExonsGenes | 20.225 | 0.654 | 20.997 | |
plotCNV | 20.324 | 0.700 | 21.169 | |
plotCovPrep | 0.212 | 0.007 | 0.223 | |
prepAnova | 0.783 | 0.052 | 0.847 | |
regionGrangeMake | 1.221 | 0.138 | 1.368 | |
regionMean | 0.567 | 0.014 | 0.586 | |
regionQuantiles | 0.601 | 0.107 | 0.720 | |
regionSet | 0.261 | 0.010 | 0.273 | |
regionSplit | 0.322 | 0.074 | 0.400 | |
seeDist | 0.591 | 0.069 | 0.662 | |
setQDplot | 0.620 | 0.018 | 0.641 | |
setupCNVplot | 19.610 | 0.834 | 20.617 | |
test_cnv | 0.001 | 0.001 | 0.002 | |
test_cnv2 | 0.000 | 0.001 | 0.002 | |
test_cov | 0.064 | 0.001 | 0.066 | |