Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2025-01-16 12:10 -0500 (Thu, 16 Jan 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4746 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4489 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4517 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4469 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4387 |
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 2287/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
zitools 1.0.0 (landing page) Carlotta Meyring
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | ERROR | skipped | ||||||||||
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: 1.0.0 |
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_1.0.0.tar.gz |
StartedAt: 2025-01-15 13:33:19 -0500 (Wed, 15 Jan 2025) |
EndedAt: 2025-01-15 13:40:22 -0500 (Wed, 15 Jan 2025) |
EllapsedTime: 423.2 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_1.0.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/zitools.Rcheck’ * using R version 4.4.2 (2024-10-31) * 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 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘zitools/DESCRIPTION’ ... OK * this is package ‘zitools’ version ‘1.0.0’ * 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 Examples with CPU (user + system) or elapsed time > 5s user system elapsed plus 5.108 1.059 6.199 assays 4.583 0.612 5.227 * 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-3.20-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/4.4-arm64/Resources/library’ * installing *source* package ‘zitools’ ... ** 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 4.4.2 (2024-10-31) -- "Pile of Leaves" 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. > 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 35.681 4.687 40.365
zitools.Rcheck/zitools-Ex.timings
name | user | system | elapsed | |
MissingValueHeatmap | 0.003 | 0.002 | 0.005 | |
assays | 4.583 | 0.612 | 5.227 | |
boxplot | 2.765 | 0.675 | 3.455 | |
colData | 3.593 | 0.623 | 4.234 | |
colMeans2 | 3.555 | 0.631 | 4.240 | |
colMedians | 3.650 | 0.674 | 4.346 | |
cor | 2.575 | 0.508 | 3.094 | |
cov | 2.596 | 0.594 | 3.201 | |
deinflatedcounts | 2.630 | 0.499 | 3.153 | |
heatmap | 3.484 | 0.507 | 4.009 | |
inputcounts | 2.589 | 0.488 | 3.088 | |
inputdata | 2.605 | 0.577 | 3.201 | |
log1p | 2.637 | 0.642 | 3.395 | |
log2p | 3.491 | 0.566 | 4.079 | |
mean | 2.541 | 0.507 | 3.063 | |
median | 2.572 | 0.587 | 3.175 | |
model | 2.557 | 0.563 | 3.140 | |
otu_table | 3.492 | 0.582 | 4.074 | |
plot | 2.506 | 0.553 | 3.060 | |
plus | 5.108 | 1.059 | 6.199 | |
quantile | 3.370 | 0.291 | 3.661 | |
resample_deinflatedcounts | 2.507 | 0.297 | 2.804 | |
rowData | 2.574 | 0.550 | 3.124 | |
rowQuantiles | 2.544 | 0.287 | 2.831 | |
rowSds | 3.438 | 0.290 | 3.759 | |
rowVars | 2.490 | 0.414 | 2.905 | |
rowWeightedMeans | 2.541 | 0.434 | 2.974 | |
rowWeightedSds | 2.562 | 0.301 | 2.863 | |
sample_data | 2.624 | 0.484 | 3.108 | |
sd | 3.306 | 0.466 | 3.791 | |
show | 2.509 | 0.618 | 3.128 | |
slash | 2.526 | 0.415 | 2.941 | |
subset_feature | 2.555 | 0.300 | 2.854 | |
subset_sample | 3.486 | 0.607 | 4.092 | |
t | 2.543 | 0.390 | 2.934 | |
tax_table | 2.563 | 0.419 | 2.982 | |
times | 2.580 | 0.318 | 2.898 | |
var | 3.361 | 0.486 | 3.847 | |
weighted.mean | 2.502 | 0.424 | 2.926 | |
weightedVar | 2.531 | 0.341 | 2.882 | |
weights | 2.546 | 0.267 | 2.813 | |
zi2deseq2 | 3.721 | 0.298 | 4.018 | |
zi2phyloseq | 2.548 | 0.575 | 3.123 | |
ziMain | 2.512 | 0.453 | 2.996 | |