Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-27 11:44 -0400 (Tue, 27 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4421 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4415 |
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 180/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
BiocGenerics 0.51.0 (landing page) Hervé Pagès
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
To the developers/maintainers of the BiocGenerics package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BiocGenerics.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: BiocGenerics |
Version: 0.51.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BiocGenerics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BiocGenerics_0.51.0.tar.gz |
StartedAt: 2024-08-26 19:43:17 -0400 (Mon, 26 Aug 2024) |
EndedAt: 2024-08-26 19:43:40 -0400 (Mon, 26 Aug 2024) |
EllapsedTime: 22.2 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: BiocGenerics.Rcheck |
Warnings: 2 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BiocGenerics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BiocGenerics_0.51.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/BiocGenerics.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-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 Ventura 13.6.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘BiocGenerics/DESCRIPTION’ ... OK * this is package ‘BiocGenerics’ version ‘0.51.0’ * package encoding: UTF-8 * 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 ‘BiocGenerics’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking DESCRIPTION meta-information ... NOTE Packages listed in more than one of Depends, Imports, Suggests, Enhances: ‘methods’ ‘utils’ ‘graphics’ ‘stats’ A package should be listed in only one of these fields. * 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 ... NOTE 'library' or 'require' call to ‘RUnit’ in package code. Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. * 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 ... WARNING Missing link or links in Rd file 'as.data.frame.Rd': ‘[IRanges]{as.data.frame,IntegerRanges-method}’ Missing link or links in Rd file 'order.Rd': ‘[IRanges]{order,IntegerRanges-method}’ Missing link or links in Rd file 'type.Rd': ‘[DelayedArray]{type,ANY-method}’ ‘[Biostrings]{type,PairwiseAlignments-method}’ See section 'Cross-references' in the 'Writing R Extensions' manual. * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... WARNING Codoc mismatches from Rd file 'funprog.Rd': Reduce Code: function(f, x, init, right = FALSE, accumulate = FALSE, simplify = TRUE) Docs: function(f, x, init, right = FALSE, accumulate = FALSE) Argument names in code not in docs: simplify Codoc mismatches from Rd file 'xtabs.Rd': xtabs Code: function(formula = ~., data = parent.frame(), subset, sparse = FALSE, na.action, na.rm = FALSE, addNA = FALSE, exclude = if (!addNA) c(NA, NaN), drop.unused.levels = FALSE) Docs: function(formula = ~., data = parent.frame(), subset, sparse = FALSE, na.action, addNA = FALSE, exclude = if (!addNA) c(NA, NaN), drop.unused.levels = FALSE) Argument names in code not in docs: na.rm Mismatches in argument names: Position: 6 Code: na.rm Docs: addNA Position: 7 Code: addNA Docs: exclude Position: 8 Code: exclude Docs: drop.unused.levels * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘run_unitTests.R’ OK * checking PDF version of manual ... OK * DONE Status: 2 WARNINGs, 2 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/BiocGenerics.Rcheck/00check.log’ for details.
BiocGenerics.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BiocGenerics ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘BiocGenerics’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘aperm’ in package ‘BiocGenerics’ Creating a new generic function for ‘append’ in package ‘BiocGenerics’ Creating a new generic function for ‘as.data.frame’ in package ‘BiocGenerics’ Creating a new generic function for ‘cbind’ in package ‘BiocGenerics’ Creating a new generic function for ‘rbind’ in package ‘BiocGenerics’ Creating a new generic function for ‘do.call’ in package ‘BiocGenerics’ Creating a new generic function for ‘duplicated’ in package ‘BiocGenerics’ Creating a new generic function for ‘anyDuplicated’ in package ‘BiocGenerics’ Creating a new generic function for ‘eval’ in package ‘BiocGenerics’ Creating a new generic function for ‘pmax’ in package ‘BiocGenerics’ Creating a new generic function for ‘pmin’ in package ‘BiocGenerics’ Creating a new generic function for ‘pmax.int’ in package ‘BiocGenerics’ Creating a new generic function for ‘pmin.int’ in package ‘BiocGenerics’ Creating a new generic function for ‘Reduce’ in package ‘BiocGenerics’ Creating a new generic function for ‘Filter’ in package ‘BiocGenerics’ Creating a new generic function for ‘Find’ in package ‘BiocGenerics’ Creating a new generic function for ‘Map’ in package ‘BiocGenerics’ Creating a new generic function for ‘Position’ in package ‘BiocGenerics’ Creating a new generic function for ‘get’ in package ‘BiocGenerics’ Creating a new generic function for ‘mget’ in package ‘BiocGenerics’ Creating a new generic function for ‘grep’ in package ‘BiocGenerics’ Creating a new generic function for ‘grepl’ in package ‘BiocGenerics’ Creating a new generic function for ‘is.unsorted’ in package ‘BiocGenerics’ Creating a new generic function for ‘lapply’ in package ‘BiocGenerics’ Creating a new generic function for ‘sapply’ in package ‘BiocGenerics’ Creating a new generic function for ‘mapply’ in package ‘BiocGenerics’ Creating a new generic function for ‘match’ in package ‘BiocGenerics’ Creating a new generic function for ‘order’ in package ‘BiocGenerics’ Creating a new generic function for ‘paste’ in package ‘BiocGenerics’ Creating a new generic function for ‘rank’ in package ‘BiocGenerics’ Creating a new generic function for ‘rownames’ in package ‘BiocGenerics’ Creating a new generic function for ‘colnames’ in package ‘BiocGenerics’ Creating a new generic function for ‘union’ in package ‘BiocGenerics’ Creating a new generic function for ‘intersect’ in package ‘BiocGenerics’ Creating a new generic function for ‘setdiff’ in package ‘BiocGenerics’ Creating a new generic function for ‘table’ in package ‘BiocGenerics’ Creating a new generic function for ‘tapply’ in package ‘BiocGenerics’ Creating a new generic function for ‘unique’ in package ‘BiocGenerics’ Creating a new generic function for ‘unsplit’ in package ‘BiocGenerics’ Creating a new generic function for ‘var’ in package ‘BiocGenerics’ Creating a new generic function for ‘sd’ in package ‘BiocGenerics’ Creating a new generic function for ‘which.min’ in package ‘BiocGenerics’ Creating a new generic function for ‘which.max’ in package ‘BiocGenerics’ Creating a new generic function for ‘IQR’ in package ‘BiocGenerics’ Creating a new generic function for ‘mad’ in package ‘BiocGenerics’ Creating a new generic function for ‘xtabs’ in package ‘BiocGenerics’ Creating a new generic function for ‘basename’ in package ‘BiocGenerics’ Creating a new generic function for ‘dirname’ in package ‘BiocGenerics’ ** help *** installing help indices ** building package indices ** 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 (BiocGenerics)
BiocGenerics.Rcheck/tests/run_unitTests.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-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. > require("BiocGenerics") || stop("unable to load BiocGenerics package") 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 [1] TRUE > BiocGenerics:::.test() Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following object is masked from 'package:utils': findMatches The following objects are masked from 'package:base': I, expand.grid, unname RUNIT TEST PROTOCOL -- Mon Aug 26 19:43:34 2024 *********************************************** Number of test functions: 25 Number of errors: 0 Number of failures: 0 1 Test Suite : BiocGenerics RUnit Tests - 25 test functions, 0 errors, 0 failures Number of test functions: 25 Number of errors: 0 Number of failures: 0 > > proc.time() user system elapsed 0.718 0.035 0.749
BiocGenerics.Rcheck/BiocGenerics-Ex.timings
name | user | system | elapsed | |
BiocGenerics-package | 0.000 | 0.000 | 0.001 | |
Extremes | 0.002 | 0.001 | 0.003 | |
IQR | 0.000 | 0.000 | 0.001 | |
Ontology | 1.187 | 0.044 | 1.232 | |
annotation | 0.004 | 0.001 | 0.004 | |
aperm | 0.000 | 0.000 | 0.001 | |
append | 0.001 | 0.000 | 0.001 | |
as.data.frame | 0.001 | 0.000 | 0.001 | |
as.list | 0.006 | 0.002 | 0.007 | |
as.vector | 0.001 | 0.000 | 0.001 | |
boxplot | 0.045 | 0.004 | 0.048 | |
cbind | 0.007 | 0.001 | 0.007 | |
combine | 0.013 | 0.001 | 0.014 | |
dbconn | 0.015 | 0.002 | 0.017 | |
density | 0 | 0 | 0 | |
dims | 0.008 | 0.001 | 0.009 | |
do.call | 0 | 0 | 0 | |
duplicated | 0.001 | 0.001 | 0.002 | |
eval | 0.001 | 0.000 | 0.000 | |
evalq | 0 | 0 | 0 | |
fileName | 3.023 | 0.078 | 3.101 | |
format | 0.001 | 0.000 | 0.001 | |
funprog | 0.001 | 0.001 | 0.002 | |
get | 0.001 | 0.000 | 0.001 | |
grep | 0.001 | 0.000 | 0.001 | |
image | 0.008 | 0.002 | 0.010 | |
is.unsorted | 0.000 | 0.000 | 0.001 | |
lapply | 0.001 | 0.000 | 0.001 | |
mad | 0.001 | 0.000 | 0.000 | |
mapply | 0.000 | 0.000 | 0.001 | |
match | 0.002 | 0.000 | 0.002 | |
mean | 0.000 | 0.000 | 0.001 | |
normalize | 0.008 | 0.002 | 0.008 | |
nrow | 0.002 | 0.000 | 0.002 | |
order | 0.001 | 0.000 | 0.001 | |
organism_species | 0.064 | 0.004 | 0.069 | |
paste | 0.000 | 0.000 | 0.001 | |
path | 0.006 | 0.001 | 0.008 | |
plotMA | 0.748 | 0.022 | 0.771 | |
plotPCA | 0.555 | 0.010 | 0.566 | |
rank | 0.001 | 0.000 | 0.001 | |
relist | 0 | 0 | 0 | |
rep | 0.001 | 0.000 | 0.000 | |
residuals | 0 | 0 | 0 | |
row_colnames | 0.003 | 0.000 | 0.004 | |
score | 0.024 | 0.003 | 0.026 | |
sets | 0.002 | 0.000 | 0.002 | |
sort | 0.000 | 0.000 | 0.001 | |
start | 0.018 | 0.002 | 0.020 | |
strand | 0.023 | 0.003 | 0.026 | |
subset | 0.008 | 0.001 | 0.009 | |
t | 0.001 | 0.000 | 0.001 | |
table | 0.000 | 0.000 | 0.001 | |
tapply | 0.001 | 0.000 | 0.001 | |
testPackage | 0.102 | 0.002 | 0.105 | |
toTable | 0.023 | 0.001 | 0.024 | |
type | 0.057 | 0.005 | 0.064 | |
unique | 0.000 | 0.000 | 0.001 | |
unlist | 0.001 | 0.000 | 0.001 | |
unsplit | 0.001 | 0.000 | 0.001 | |
updateObject | 0.049 | 0.002 | 0.050 | |
var | 0.001 | 0.000 | 0.001 | |
weights | 0 | 0 | 0 | |
which | 0.045 | 0.004 | 0.048 | |
which.min | 0.013 | 0.001 | 0.015 | |
xtabs | 0.008 | 0.001 | 0.010 | |