Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:07 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 | |||||||||
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: 2024-12-20 11:30:27 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 11:37:54 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 446.8 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: x86_64-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 Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘zitools/DESCRIPTION’ ... OK * this is package ‘zitools’ version ‘1.0.0’ * 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 * 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-x86_64/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: 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 26.964 2.688 29.636
zitools.Rcheck/zitools-Ex.timings
name | user | system | elapsed | |
MissingValueHeatmap | 0.002 | 0.001 | 0.003 | |
assays | 3.203 | 0.450 | 3.653 | |
boxplot | 2.012 | 0.386 | 2.402 | |
colData | 2.483 | 0.414 | 2.900 | |
colMeans2 | 2.473 | 0.308 | 2.781 | |
colMedians | 2.457 | 0.322 | 2.781 | |
cor | 1.849 | 0.414 | 2.263 | |
cov | 1.893 | 0.344 | 2.239 | |
deinflatedcounts | 1.902 | 0.361 | 2.267 | |
heatmap | 2.422 | 0.487 | 2.909 | |
inputcounts | 1.843 | 0.231 | 2.073 | |
inputdata | 1.870 | 0.446 | 2.317 | |
log1p | 1.878 | 0.318 | 2.198 | |
log2p | 2.400 | 0.369 | 2.769 | |
mean | 1.864 | 0.420 | 2.285 | |
median | 1.864 | 0.428 | 2.291 | |
model | 1.848 | 0.193 | 2.041 | |
otu_table | 2.470 | 0.278 | 2.752 | |
plot | 1.847 | 0.465 | 2.315 | |
plus | 3.795 | 0.761 | 4.558 | |
quantile | 1.904 | 0.309 | 2.214 | |
resample_deinflatedcounts | 2.392 | 0.387 | 2.781 | |
rowData | 1.901 | 0.509 | 2.411 | |
rowQuantiles | 1.884 | 0.411 | 2.297 | |
rowSds | 1.882 | 0.406 | 2.290 | |
rowVars | 2.365 | 0.373 | 2.738 | |
rowWeightedMeans | 1.824 | 0.263 | 2.088 | |
rowWeightedSds | 1.871 | 0.503 | 2.374 | |
sample_data | 2.416 | 0.213 | 2.629 | |
sd | 1.840 | 0.385 | 2.225 | |
show | 1.867 | 0.354 | 2.223 | |
slash | 1.876 | 0.324 | 2.200 | |
subset_feature | 1.929 | 0.236 | 2.166 | |
subset_sample | 2.409 | 0.473 | 2.884 | |
t | 1.838 | 0.446 | 2.285 | |
tax_table | 1.897 | 0.310 | 2.207 | |
times | 1.832 | 0.154 | 1.985 | |
var | 2.291 | 0.220 | 2.511 | |
weighted.mean | 1.810 | 0.438 | 2.248 | |
weightedVar | 1.804 | 0.170 | 1.975 | |
weights | 1.860 | 0.334 | 2.195 | |
zi2deseq2 | 2.635 | 0.249 | 2.885 | |
zi2phyloseq | 1.918 | 0.302 | 2.220 | |
ziMain | 1.825 | 0.399 | 2.223 | |