Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-04-22 13:19 -0400 (Tue, 22 Apr 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4831 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six" | 4573 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4599 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4553 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4570 |
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 2339/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
zitools 1.2.0 (landing page) Carlotta Meyring
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | NA | ||||||||||
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: 1.2.0 |
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_1.2.0.tar.gz |
StartedAt: 2025-04-21 22:22:12 -0400 (Mon, 21 Apr 2025) |
EndedAt: 2025-04-21 22:24:43 -0400 (Mon, 21 Apr 2025) |
EllapsedTime: 151.4 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_1.2.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/zitools.Rcheck’ * using R version 4.5.0 RC (2025-04-04 r88126) * using platform: aarch64-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 Ventura 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘zitools/DESCRIPTION’ ... OK * this is package ‘zitools’ version ‘1.2.0’ * 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-3.21-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-arm64/Resources/library’ * installing *source* package ‘zitools’ ... ** this is package ‘zitools’ version ‘1.2.0’ ** 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 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" Copyright (C) 2025 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. > 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 12.670 1.917 14.600
zitools.Rcheck/zitools-Ex.timings
name | user | system | elapsed | |
MissingValueHeatmap | 0.001 | 0.001 | 0.001 | |
assays | 1.396 | 0.266 | 1.661 | |
boxplot | 1.294 | 0.208 | 1.501 | |
colData | 0.901 | 0.228 | 1.138 | |
colMeans2 | 0.891 | 0.213 | 1.107 | |
colMedians | 0.825 | 0.180 | 1.006 | |
cor | 1.132 | 0.213 | 1.344 | |
cov | 0.822 | 0.186 | 1.009 | |
deinflatedcounts | 0.875 | 0.263 | 1.155 | |
heatmap | 0.929 | 0.327 | 1.260 | |
inputcounts | 1.240 | 0.275 | 1.521 | |
inputdata | 0.847 | 0.293 | 1.140 | |
log1p | 0.817 | 0.207 | 1.024 | |
log2p | 0.803 | 0.177 | 0.980 | |
mean | 1.190 | 0.244 | 1.438 | |
median | 0.880 | 0.312 | 1.192 | |
model | 0.912 | 0.223 | 1.142 | |
otu_table | 0.882 | 0.162 | 1.045 | |
plot | 1.202 | 0.267 | 1.469 | |
plus | 1.594 | 0.426 | 2.031 | |
quantile | 1.099 | 0.154 | 1.253 | |
resample_deinflatedcounts | 0.762 | 0.160 | 0.926 | |
rowData | 0.796 | 0.111 | 0.907 | |
rowQuantiles | 0.876 | 0.167 | 1.044 | |
rowSds | 1.131 | 0.166 | 1.297 | |
rowVars | 0.878 | 0.189 | 1.067 | |
rowWeightedMeans | 0.828 | 0.233 | 1.061 | |
rowWeightedSds | 1.127 | 0.156 | 1.282 | |
sample_data | 0.807 | 0.137 | 0.946 | |
sd | 0.833 | 0.158 | 0.992 | |
show | 0.854 | 0.176 | 1.032 | |
slash | 1.140 | 0.118 | 1.257 | |
subset_feature | 0.816 | 0.109 | 0.925 | |
subset_sample | 0.814 | 0.116 | 0.930 | |
t | 0.836 | 0.121 | 0.958 | |
tax_table | 1.170 | 0.157 | 1.327 | |
times | 0.849 | 0.221 | 1.071 | |
var | 0.828 | 0.148 | 0.976 | |
weighted.mean | 1.138 | 0.141 | 1.280 | |
weightedVar | 0.804 | 0.146 | 0.950 | |
weights | 0.811 | 0.150 | 0.961 | |
zi2deseq2 | 0.902 | 0.130 | 1.032 | |
zi2phyloseq | 1.181 | 0.225 | 1.407 | |
ziMain | 0.794 | 0.130 | 0.925 | |