Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-09-24 12:06 -0400 (Wed, 24 Sep 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4827 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4614 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4558 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4560 |
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 2333/2334 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
zitools 1.3.0 (landing page) Carlotta Meyring
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | WARNINGS | ||||||||||
To the developers/maintainers of the zitools package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/zitools.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: zitools |
Version: 1.3.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:zitools.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings zitools_1.3.0.tar.gz |
StartedAt: 2025-09-24 01:05:21 -0400 (Wed, 24 Sep 2025) |
EndedAt: 2025-09-24 01:10:36 -0400 (Wed, 24 Sep 2025) |
EllapsedTime: 315.3 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: zitools.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:zitools.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings zitools_1.3.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/zitools.Rcheck’ * using R version 4.5.1 Patched (2025-09-10 r88807) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 14.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘zitools/DESCRIPTION’ ... OK * this is package ‘zitools’ version ‘1.3.0’ * 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 ‘zitools’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE License stub is invalid DCF. * 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 ... NOTE calcWeights: no visible global function definition for ‘predict’ omit_str_zero: no visible global function definition for ‘predict’ Undefined global functions or variables: predict Consider adding importFrom("stats", "predict") to your NAMESPACE file. * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... WARNING Codoc mismatches from Rd file 'rowQuantiles.Rd': \S4method{rowQuantiles}{Zi} Code: function(x, rows = NULL, cols = NULL, probs = seq(from = 0, to = 1, by = 0.25), na.rm = FALSE, type = 7L, digits = 7L, ..., useNames = TRUE, drop = TRUE) Docs: function(x, rows = NULL, cols = NULL, probs = seq(from = 0, to = 1, by = 0.25), na.rm = TRUE, type = 7L, ..., useNames = TRUE, drop = TRUE) Argument names in code not in docs: digits Mismatches in argument names: Position: 7 Code: digits Docs: ... Position: 8 Code: ... Docs: useNames Position: 9 Code: useNames Docs: drop Mismatches in argument default values: Name: 'na.rm' Code: FALSE Docs: TRUE \S4method{colQuantiles}{Zi} Code: function(x, rows = NULL, cols = NULL, probs = seq(from = 0, to = 1, by = 0.25), na.rm = FALSE, type = 7L, digits = 7L, ..., useNames = TRUE, drop = TRUE) Docs: function(x, rows = NULL, cols = NULL, probs = seq(from = 0, to = 1, by = 0.25), na.rm = TRUE, type = 7L, ..., useNames = TRUE, drop = TRUE) Argument names in code not in docs: digits Mismatches in argument names: Position: 7 Code: digits Docs: ... Position: 8 Code: ... Docs: useNames Position: 9 Code: useNames Docs: drop Mismatches in argument default values: Name: 'na.rm' Code: FALSE Docs: TRUE * 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 sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * 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, 2 NOTEs See ‘/Users/biocbuild/bbs-3.22-bioc/meat/zitools.Rcheck/00check.log’ for details.
zitools.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL zitools ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘zitools’ ... ** this is package ‘zitools’ version ‘1.3.0’ ** using staged installation ** R ** data ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘weights’ in package ‘zitools’ Creating a new generic function for ‘weightedSd’ in package ‘zitools’ Creating a generic function for ‘cov’ from package ‘stats’ in package ‘zitools’ ** 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 (zitools)
zitools.Rcheck/tests/testthat.Rout
R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" Copyright (C) 2025 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. > library(testthat) > library(zitools) Attaching package: 'zitools' The following objects are masked from 'package:stats': heatmap, weights > > test_check("zitools") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 9 ] > > > proc.time() user system elapsed 18.780 3.549 22.334
zitools.Rcheck/zitools-Ex.timings
name | user | system | elapsed | |
MissingValueHeatmap | 0.002 | 0.001 | 0.003 | |
assays | 2.234 | 0.527 | 2.762 | |
boxplot | 2.070 | 0.719 | 2.804 | |
colData | 1.479 | 0.585 | 2.064 | |
colMeans2 | 1.462 | 0.615 | 2.124 | |
colMedians | 2.059 | 0.629 | 2.692 | |
cor | 1.438 | 0.560 | 2.011 | |
cov | 1.458 | 0.506 | 1.967 | |
deinflatedcounts | 1.450 | 0.486 | 1.937 | |
heatmap | 1.999 | 0.577 | 2.578 | |
inputcounts | 1.436 | 0.594 | 2.034 | |
inputdata | 1.451 | 0.574 | 2.031 | |
log1p | 2.013 | 0.555 | 2.569 | |
log2p | 1.452 | 0.608 | 2.063 | |
mean | 1.461 | 0.622 | 2.091 | |
median | 1.458 | 0.655 | 2.119 | |
model | 1.969 | 0.528 | 2.498 | |
otu_table | 1.466 | 0.518 | 1.985 | |
plot | 1.444 | 0.375 | 1.820 | |
plus | 3.496 | 1.261 | 4.764 | |
quantile | 1.436 | 0.567 | 2.005 | |
resample_deinflatedcounts | 1.463 | 0.573 | 2.039 | |
rowData | 1.953 | 0.563 | 2.521 | |
rowQuantiles | 1.379 | 0.501 | 1.882 | |
rowSds | 1.410 | 0.535 | 1.947 | |
rowVars | 1.373 | 0.399 | 1.773 | |
rowWeightedMeans | 1.882 | 0.500 | 2.382 | |
rowWeightedSds | 1.350 | 0.556 | 1.909 | |
sample_data | 1.401 | 0.453 | 1.856 | |
sd | 1.383 | 0.547 | 1.933 | |
show | 1.864 | 0.555 | 2.422 | |
slash | 1.371 | 0.599 | 1.973 | |
subset_feature | 1.353 | 0.477 | 1.829 | |
subset_sample | 1.346 | 0.370 | 1.716 | |
t | 1.752 | 0.505 | 2.257 | |
tax_table | 1.250 | 0.319 | 1.568 | |
times | 1.279 | 0.418 | 1.697 | |
var | 1.756 | 0.438 | 2.195 | |
weighted.mean | 1.253 | 0.531 | 1.789 | |
weightedVar | 1.287 | 0.476 | 1.765 | |
weights | 1.278 | 0.273 | 1.551 | |
zi2deseq2 | 1.942 | 0.545 | 2.488 | |
zi2phyloseq | 1.325 | 0.502 | 1.826 | |
ziMain | 1.274 | 0.449 | 1.723 | |