Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-10-18 20:39 -0400 (Fri, 18 Oct 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4763 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4500 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4530 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4480 |
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 17/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
adductomicsR 1.20.0 (landing page) Josie Hayes
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | TIMEOUT | skipped | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
To the developers/maintainers of the adductomicsR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/adductomicsR.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: adductomicsR |
Version: 1.20.0 |
Command: E:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:adductomicsR.install-out.txt --library=E:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings adductomicsR_1.20.0.tar.gz |
StartedAt: 2024-10-16 22:42:14 -0400 (Wed, 16 Oct 2024) |
EndedAt: 2024-10-16 22:46:21 -0400 (Wed, 16 Oct 2024) |
EllapsedTime: 246.6 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: adductomicsR.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:adductomicsR.install-out.txt --library=E:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings adductomicsR_1.20.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'E:/biocbuild/bbs-3.19-bioc/meat/adductomicsR.Rcheck' * using R version 4.4.1 (2024-06-14 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'adductomicsR/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'adductomicsR' version '1.20.0' * 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 'adductomicsR' 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 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 ... OK * checking Rd files ... NOTE checkRd: (-1) peakRangeSum.Rd:39: Lost braces 39 | smoothed using the link{\code{smth.gaussian}} function of the smoother | ^ * 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 ... WARNING Documented arguments not in \usage in Rd file 'probPeaks.Rd': '...' Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter 'Writing R documentation files' in the 'Writing R Extensions' manual. * 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 rtDevModelling 11.70 1.01 46.25 outputPeakTable 5.52 1.93 7.86 * 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: 1 WARNING, 1 NOTE See 'E:/biocbuild/bbs-3.19-bioc/meat/adductomicsR.Rcheck/00check.log' for details.
adductomicsR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL adductomicsR ### ############################################################################## ############################################################################## * installing to library 'E:/biocbuild/bbs-3.19-bioc/R/library' * installing *source* package 'adductomicsR' ... ** using staged installation ** R ** 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 (adductomicsR)
adductomicsR.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 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(adductomicsR) Loading required package: adductData Loading required package: ExperimentHub 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, setdiff, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: AnnotationHub Loading required package: BiocFileCache Loading required package: dbplyr > library(adductData) > library(testthat) > > test_check("adductomicsR") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 2 ] > > proc.time() user system elapsed 12.01 2.23 14.50
adductomicsR.Rcheck/adductomicsR-Ex.timings
name | user | system | elapsed | |
IsotopicDistributionMod | 0.77 | 0.03 | 0.79 | |
adductQuant | 0 | 0 | 0 | |
digestMod | 0.02 | 0.00 | 0.01 | |
filterAdductTable | 0.01 | 0.00 | 0.02 | |
findPeaks | 0 | 0 | 0 | |
generateTargTable | 0.05 | 0.00 | 0.04 | |
loessWrapperMod | 0.23 | 0.01 | 0.28 | |
outputPeakTable | 5.52 | 1.93 | 7.86 | |
rtDevModelling | 11.70 | 1.01 | 46.25 | |
specSimPepId | 0 | 0 | 0 | |