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 12:02 -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 1110/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
lipidr 2.20.0 (landing page) Ahmed Mohamed
| 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 lipidr package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/lipidr.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: lipidr |
Version: 2.20.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:lipidr.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings lipidr_2.20.0.tar.gz |
StartedAt: 2024-11-20 05:04:19 -0500 (Wed, 20 Nov 2024) |
EndedAt: 2024-11-20 05:08:09 -0500 (Wed, 20 Nov 2024) |
EllapsedTime: 229.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: lipidr.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:lipidr.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings lipidr_2.20.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/lipidr.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘lipidr/DESCRIPTION’ ... OK * this is package ‘lipidr’ version ‘2.20.0’ * 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 for sufficient/correct file permissions ... OK * checking whether package ‘lipidr’ 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 loading without being on the library search path ... 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 plot_results_volcano: no visible binding for global variable ‘AveExpr’ Undefined global functions or variables: AveExpr * 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 ‘spelling.R’ Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/lipidr.Rcheck/00check.log’ for details.
lipidr.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL lipidr ### ############################################################################## ############################################################################## * installing to library ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘lipidr’ ... ** using staged installation ** R ** data ** 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 (lipidr)
lipidr.Rcheck/tests/spelling.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu 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. > if (requireNamespace("spelling", quietly = TRUE)) { + spelling::spell_check_test( + vignettes = TRUE, error = FALSE, + skip_on_cran = TRUE + ) + } NULL > > proc.time() user system elapsed 0.088 0.061 0.137
lipidr.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu 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(lipidr) Loading required package: SummarizedExperiment Loading required package: MatrixGenerics Loading required package: matrixStats Attaching package: 'MatrixGenerics' The following objects are masked from 'package:matrixStats': colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts, colCummaxs, colCummins, colCumprods, colCumsums, colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, colWeightedMeans, colWeightedMedians, colWeightedSds, colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, rowWeightedMads, rowWeightedMeans, rowWeightedMedians, rowWeightedSds, rowWeightedVars 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 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")'. Attaching package: 'Biobase' The following object is masked from 'package:MatrixGenerics': rowMedians The following objects are masked from 'package:matrixStats': anyMissing, rowMedians > test_check("lipidr") [1] 18866.28 [ FAIL 0 | WARN 6 | SKIP 15 | PASS 373 ] ══ Skipped tests (15) ══════════════════════════════════════════════════════════ • On Bioconductor (12): 'test-mw.R:4:3', 'test-mw.R:13:3', 'test-mw.R:26:3', 'test-workflow.R:65:3', 'test-workflow.R:72:3', 'test-workflow.R:79:3', 'test-workflow.R:87:3', 'test-workflow.R:95:3', 'test-workflow.R:104:3', 'test-workflow.R:113:3', 'test-workflow.R:123:3', 'test-workflow.R:151:3' • empty test (3): 'test-manip.R:14:1', 'test-manip.R:17:1', 'test-readfiles.R:233:1' [ FAIL 0 | WARN 6 | SKIP 15 | PASS 373 ] > > proc.time() user system elapsed 30.883 2.705 32.915
lipidr.Rcheck/lipidr-Ex.timings
name | user | system | elapsed | |
add_sample_annotation | 1.251 | 0.019 | 1.292 | |
annotate_lipids | 0.073 | 0.007 | 0.080 | |
data_normalized | 0.027 | 0.003 | 0.030 | |
de_analysis | 0.399 | 0.002 | 0.401 | |
filter_by_cv | 0.042 | 0.002 | 0.044 | |
gen_lipidsets | 0.102 | 0.020 | 0.123 | |
impute_na | 0.339 | 0.002 | 0.345 | |
lipidDefaults | 0.003 | 0.001 | 0.004 | |
lipidnames_pattern | 0.001 | 0.000 | 0.001 | |
lipidr-data | 0.027 | 0.003 | 0.030 | |
lsea | 4.146 | 0.481 | 4.271 | |
mva | 1.467 | 0.059 | 1.526 | |
mw | 0 | 0 | 0 | |
non_parsed_molecules | 0.031 | 0.000 | 0.030 | |
normalize_istd | 0.482 | 0.009 | 0.491 | |
normalize_pqn | 0.453 | 0.000 | 0.453 | |
pipe | 0.044 | 0.001 | 0.045 | |
plot_chain_distribution | 0.664 | 0.002 | 0.666 | |
plot_lipidclass | 1.441 | 0.001 | 1.443 | |
plot_molecules | 2.703 | 0.004 | 2.707 | |
plot_samples | 1.552 | 0.003 | 1.556 | |
plot_trend | 0.289 | 0.003 | 0.292 | |
read_skyline | 0.279 | 0.006 | 0.285 | |
remove_non_parsed_molecules | 0.035 | 0.001 | 0.037 | |
set_attr | 0.032 | 0.001 | 0.034 | |
summarize_transitions | 0.407 | 0.006 | 0.413 | |
update_molecule_names | 0.146 | 0.001 | 0.147 | |
use_interactive_graphics | 0.095 | 0.006 | 0.101 | |