| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-24 12:07 -0400 (Fri, 24 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4898 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4688 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4634 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4658 |
| 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 2358/2359 | 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 12.7.6 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 | 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: 1.3.0 |
| 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: 2025-10-23 22:53:19 -0400 (Thu, 23 Oct 2025) |
| EndedAt: 2025-10-23 22:55:32 -0400 (Thu, 23 Oct 2025) |
| EllapsedTime: 132.4 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_1.3.0.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: aarch64-apple-darwin20
* R was compiled by
Apple clang version 16.0.0 (clang-1600.0.26.6)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.7
* 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-arm64/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: 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
9.430 0.716 10.145
zitools.Rcheck/zitools-Ex.timings
| name | user | system | elapsed | |
| MissingValueHeatmap | 0.001 | 0.001 | 0.002 | |
| assays | 1.435 | 0.092 | 1.527 | |
| boxplot | 0.788 | 0.198 | 0.987 | |
| colData | 0.772 | 0.203 | 0.975 | |
| colMeans2 | 0.787 | 0.160 | 0.946 | |
| colMedians | 1.137 | 0.180 | 1.317 | |
| cor | 0.795 | 0.184 | 0.979 | |
| cov | 0.815 | 0.133 | 0.948 | |
| deinflatedcounts | 1.058 | 0.168 | 1.227 | |
| heatmap | 0.778 | 0.122 | 0.900 | |
| inputcounts | 0.770 | 0.128 | 0.898 | |
| inputdata | 0.772 | 0.097 | 0.871 | |
| log1p | 1.068 | 0.087 | 1.156 | |
| log2p | 0.786 | 0.121 | 0.907 | |
| mean | 0.767 | 0.069 | 0.836 | |
| median | 0.752 | 0.070 | 0.822 | |
| model | 1.018 | 0.096 | 1.115 | |
| otu_table | 0.764 | 0.081 | 0.846 | |
| plot | 0.755 | 0.072 | 0.828 | |
| plus | 1.956 | 0.331 | 2.287 | |
| quantile | 0.800 | 0.163 | 0.963 | |
| resample_deinflatedcounts | 0.788 | 0.217 | 1.005 | |
| rowData | 1.051 | 0.146 | 1.197 | |
| rowQuantiles | 0.774 | 0.086 | 0.860 | |
| rowSds | 0.750 | 0.074 | 0.824 | |
| rowVars | 0.747 | 0.121 | 0.869 | |
| rowWeightedMeans | 0.965 | 0.128 | 1.094 | |
| rowWeightedSds | 0.701 | 0.083 | 0.784 | |
| sample_data | 0.705 | 0.084 | 0.789 | |
| sd | 0.953 | 0.094 | 1.047 | |
| show | 0.699 | 0.087 | 0.785 | |
| slash | 0.691 | 0.060 | 0.752 | |
| subset_feature | 0.696 | 0.028 | 0.725 | |
| subset_sample | 0.961 | 0.062 | 1.022 | |
| t | 0.694 | 0.071 | 0.765 | |
| tax_table | 0.698 | 0.055 | 0.754 | |
| times | 0.703 | 0.066 | 0.769 | |
| var | 0.953 | 0.087 | 1.039 | |
| weighted.mean | 0.691 | 0.064 | 0.756 | |
| weightedVar | 0.687 | 0.063 | 0.751 | |
| weights | 0.947 | 0.044 | 0.992 | |
| zi2deseq2 | 0.763 | 0.068 | 0.830 | |
| zi2phyloseq | 0.708 | 0.061 | 0.769 | |
| ziMain | 0.702 | 0.066 | 0.768 | |