Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-07-24 11:39 -0400 (Wed, 24 Jul 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4688 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4284 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4455 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4404 |
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 2246/2248 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
zitools 0.99.3 (landing page) Carlotta Meyring
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | ERROR | ERROR | skipped | skipped | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | 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: 0.99.3 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:zitools.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings zitools_0.99.3.tar.gz |
StartedAt: 2024-07-24 05:27:53 -0400 (Wed, 24 Jul 2024) |
EndedAt: 2024-07-24 05:36:38 -0400 (Wed, 24 Jul 2024) |
EllapsedTime: 524.7 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: zitools.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:zitools.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings zitools_0.99.3.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/zitools.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘zitools/DESCRIPTION’ ... OK * this is package ‘zitools’ version ‘0.99.3’ * 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 loading without being on the library search path ... 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 ... OK * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed plus 5.556 0.040 5.613 assays 5.260 0.168 5.428 * 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 re-building of vignette outputs ... ERROR Error(s) in re-building vignettes: ... --- re-building ‘zitools_tutorial.Rmd’ using rmarkdown Quitting from lines 47-51 [unnamed-chunk-4] (zitools_tutorial.Rmd) Error: processing vignette 'zitools_tutorial.Rmd' failed with diagnostics: there is no package called 'microbiome' --- failed re-building ‘zitools_tutorial.Rmd’ SUMMARY: processing the following file failed: ‘zitools_tutorial.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 2 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/zitools.Rcheck/00check.log’ for details.
zitools.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL zitools ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-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 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu 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 38.519 2.844 41.378
zitools.Rcheck/zitools-Ex.timings
name | user | system | elapsed | |
MissingValueHeatmap | 0.000 | 0.003 | 0.004 | |
assays | 5.260 | 0.168 | 5.428 | |
boxplot | 4.011 | 0.120 | 4.157 | |
colData | 2.915 | 0.048 | 2.964 | |
colMeans2 | 2.861 | 0.064 | 2.924 | |
colMedians | 2.851 | 0.016 | 2.867 | |
cor | 3.851 | 0.088 | 3.939 | |
cov | 2.688 | 0.032 | 2.719 | |
deinflatedcounts | 2.668 | 0.044 | 2.713 | |
heatmap | 2.678 | 0.015 | 2.694 | |
inputcounts | 3.719 | 0.136 | 3.855 | |
inputdata | 2.597 | 0.008 | 2.621 | |
log1p | 2.758 | 0.024 | 2.798 | |
log2p | 2.743 | 0.008 | 2.752 | |
mean | 3.509 | 0.080 | 3.589 | |
median | 2.539 | 0.004 | 2.557 | |
model | 2.474 | 0.008 | 2.482 | |
otu_table | 2.531 | 0.012 | 2.544 | |
plot | 3.291 | 0.004 | 3.298 | |
plus | 5.556 | 0.040 | 5.613 | |
quantile | 2.882 | 0.004 | 2.885 | |
resample_deinflatedcounts | 3.710 | 0.104 | 3.813 | |
rowData | 2.768 | 0.012 | 2.781 | |
rowQuantiles | 2.780 | 0.016 | 2.795 | |
rowSds | 2.876 | 0.016 | 2.892 | |
rowVars | 4.061 | 0.012 | 4.073 | |
rowWeightedMeans | 2.885 | 0.016 | 2.901 | |
rowWeightedSds | 2.691 | 0.016 | 2.724 | |
sample_data | 2.738 | 0.000 | 2.737 | |
sd | 3.738 | 0.079 | 3.820 | |
show | 2.704 | 0.024 | 2.750 | |
slash | 2.694 | 0.000 | 2.695 | |
subset_feature | 2.799 | 0.032 | 2.834 | |
subset_sample | 3.776 | 0.072 | 3.858 | |
t | 2.684 | 0.024 | 2.707 | |
tax_table | 2.764 | 0.036 | 2.816 | |
times | 2.759 | 0.008 | 2.767 | |
var | 3.621 | 0.036 | 3.658 | |
weighted.mean | 2.655 | 0.024 | 2.679 | |
weightedVar | 2.707 | 0.028 | 2.735 | |
weights | 2.752 | 0.020 | 2.772 | |
zi2deseq2 | 4.176 | 0.020 | 4.196 | |
zi2phyloseq | 2.708 | 0.076 | 2.783 | |
ziMain | 2.798 | 0.004 | 2.802 | |