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 12:08 -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: 2024-12-21 13:36:43 -0500 (Sat, 21 Dec 2024) |
EndedAt: 2024-12-21 13:43:51 -0500 (Sat, 21 Dec 2024) |
EllapsedTime: 427.5 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 5.140 0.842 5.982 assays 4.585 0.640 5.256 * 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 35.443 4.952 40.403
zitools.Rcheck/zitools-Ex.timings
name | user | system | elapsed | |
MissingValueHeatmap | 0.002 | 0.002 | 0.005 | |
assays | 4.585 | 0.640 | 5.256 | |
boxplot | 2.741 | 0.555 | 3.314 | |
colData | 3.518 | 0.547 | 4.079 | |
colMeans2 | 3.458 | 0.516 | 3.980 | |
colMedians | 3.487 | 0.510 | 3.997 | |
cor | 2.507 | 0.578 | 3.085 | |
cov | 2.530 | 0.411 | 2.941 | |
deinflatedcounts | 2.536 | 0.210 | 2.746 | |
heatmap | 3.416 | 0.451 | 3.878 | |
inputcounts | 2.564 | 0.508 | 3.079 | |
inputdata | 2.564 | 0.610 | 3.174 | |
log1p | 2.547 | 0.434 | 2.981 | |
log2p | 3.426 | 0.425 | 3.856 | |
mean | 2.541 | 0.508 | 3.049 | |
median | 2.521 | 0.508 | 3.030 | |
model | 2.534 | 0.303 | 2.837 | |
otu_table | 3.323 | 0.243 | 3.565 | |
plot | 2.499 | 0.480 | 2.997 | |
plus | 5.140 | 0.842 | 5.982 | |
quantile | 3.427 | 0.314 | 3.742 | |
resample_deinflatedcounts | 2.538 | 0.377 | 2.915 | |
rowData | 2.563 | 0.216 | 2.779 | |
rowQuantiles | 2.545 | 0.205 | 2.750 | |
rowSds | 2.565 | 0.137 | 2.702 | |
rowVars | 3.363 | 0.650 | 4.013 | |
rowWeightedMeans | 2.512 | 0.571 | 3.083 | |
rowWeightedSds | 2.559 | 0.309 | 2.869 | |
sample_data | 2.606 | 0.522 | 3.128 | |
sd | 3.384 | 0.485 | 3.869 | |
show | 2.545 | 0.570 | 3.115 | |
slash | 2.560 | 0.603 | 3.190 | |
subset_feature | 2.584 | 0.284 | 2.870 | |
subset_sample | 3.391 | 0.400 | 3.790 | |
t | 2.528 | 0.412 | 2.939 | |
tax_table | 2.523 | 0.330 | 2.853 | |
times | 2.584 | 0.330 | 2.923 | |
var | 3.366 | 0.384 | 3.751 | |
weighted.mean | 2.491 | 0.367 | 2.859 | |
weightedVar | 2.480 | 0.286 | 2.765 | |
weights | 2.544 | 0.275 | 2.819 | |
zi2deseq2 | 3.689 | 0.535 | 4.224 | |
zi2phyloseq | 2.588 | 0.432 | 3.020 | |
ziMain | 2.545 | 0.444 | 2.991 | |