Back to Multiple platform build/check report for BioC 3.14 |
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This page was generated on 2022-04-13 12:08:14 -0400 (Wed, 13 Apr 2022).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
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 |
To the developers/maintainers of the lipidr package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to [email protected]:packages/lipidr.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1003/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
lipidr 2.8.1 (landing page) Ahmed Mohamed
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: lipidr |
Version: 2.8.1 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:lipidr.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings lipidr_2.8.1.tar.gz |
StartedAt: 2022-04-12 14:48:46 -0400 (Tue, 12 Apr 2022) |
EndedAt: 2022-04-12 14:55:07 -0400 (Tue, 12 Apr 2022) |
EllapsedTime: 380.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: lipidr.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:lipidr.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings lipidr_2.8.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/lipidr.Rcheck’ * using R version 4.1.3 (2022-03-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘lipidr/DESCRIPTION’ ... OK * this is package ‘lipidr’ version ‘2.8.1’ * 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 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 ... OK * 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 plot_molecules 6.852 0.04 6.943 plot_heatmap 5.865 0.10 5.980 * 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 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: OK
lipidr.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL lipidr ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/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 4.1.3 (2022-03-10) -- "One Push-Up" Copyright (C) 2022 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin17.0 (64-bit) 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 0.297 0.073 0.343
lipidr.Rcheck/tests/testthat.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up" Copyright (C) 2022 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin17.0 (64-bit) 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, 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.max, which.min Loading required package: S4Vectors Attaching package: 'S4Vectors' 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 3 | SKIP 15 | PASS 370 ] ══ Skipped tests ═══════════════════════════════════════════════════════════════ • On Bioconductor (12) • empty test (3) [ FAIL 0 | WARN 3 | SKIP 15 | PASS 370 ] > > proc.time() user system elapsed 81.047 3.884 84.166
lipidr.Rcheck/lipidr-Ex.timings
name | user | system | elapsed | |
add_sample_annotation | 1.126 | 0.041 | 1.194 | |
annotate_lipids | 0.201 | 0.003 | 0.205 | |
data_normalized | 0.056 | 0.006 | 0.062 | |
de_analysis | 0.987 | 0.021 | 1.008 | |
filter_by_cv | 0.117 | 0.007 | 0.124 | |
gen_lipidsets | 0.283 | 0.027 | 0.311 | |
impute_na | 1.050 | 0.020 | 1.072 | |
lipidDefaults | 0.010 | 0.003 | 0.014 | |
lipidnames_pattern | 0.002 | 0.002 | 0.005 | |
lipidr-data | 0.041 | 0.004 | 0.045 | |
lsea | 3.812 | 0.630 | 3.701 | |
mva | 4.333 | 0.162 | 4.508 | |
mw | 0 | 0 | 0 | |
non_parsed_molecules | 0.072 | 0.005 | 0.077 | |
normalize_istd | 1.551 | 0.034 | 1.589 | |
normalize_pqn | 1.530 | 0.016 | 1.547 | |
pipe | 0.132 | 0.006 | 0.138 | |
plot_chain_distribution | 1.366 | 0.019 | 1.388 | |
plot_heatmap | 5.865 | 0.100 | 5.980 | |
plot_lipidclass | 3.832 | 0.050 | 3.888 | |
plot_molecules | 6.852 | 0.040 | 6.943 | |
plot_samples | 3.268 | 0.037 | 3.312 | |
plot_trend | 0.663 | 0.015 | 0.677 | |
read_skyline | 0.708 | 0.020 | 0.728 | |
remove_non_parsed_molecules | 0.111 | 0.006 | 0.116 | |
set_attr | 0.085 | 0.006 | 0.093 | |
summarize_transitions | 1.036 | 0.017 | 1.053 | |
update_molecule_names | 0.364 | 0.010 | 0.374 | |
use_interactive_graphics | 0.172 | 0.010 | 0.183 | |