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This page was generated on 2025-10-01 12:07 -0400 (Wed, 01 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4843
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4631
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4575
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4576
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 2336/2337HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
zitools 1.3.0  (landing page)
Carlotta Meyring
Snapshot Date: 2025-09-30 13:45 -0400 (Tue, 30 Sep 2025)
git_url: https://git.bioconductor.org/packages/zitools
git_branch: devel
git_last_commit: 9d83d53
git_last_commit_date: 2025-04-15 13:36:49 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    WARNINGS  


CHECK results for zitools on kjohnson3

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.

raw results


Summary

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: 2025-09-30 22:24:33 -0400 (Tue, 30 Sep 2025)
EndedAt: 2025-09-30 22:26:48 -0400 (Tue, 30 Sep 2025)
EllapsedTime: 134.6 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: zitools.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### 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.


Installation output

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)

Tests output

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 
 10.067   1.408  11.473 

Example timings

zitools.Rcheck/zitools-Ex.timings

nameusersystemelapsed
MissingValueHeatmap0.0010.0010.001
assays1.1460.1551.301
boxplot1.1080.1661.273
colData0.8410.2271.067
colMeans20.8450.2241.070
colMedians1.1180.1821.300
cor0.8000.1460.946
cov0.8010.1280.930
deinflatedcounts0.8030.1250.928
heatmap1.0790.1711.251
inputcounts0.8100.1450.959
inputdata0.8170.1420.960
log1p0.8330.1981.036
log2p1.1210.1981.319
mean0.8140.2431.058
median0.8070.1430.950
model0.8130.1280.942
otu_table1.1120.1701.288
plot0.8010.1660.970
plus1.7610.2932.057
quantile0.6880.0980.786
resample_deinflatedcounts0.7000.0850.785
rowData0.6980.0510.749
rowQuantiles0.9530.1091.061
rowSds0.6990.1280.828
rowVars0.6940.0960.790
rowWeightedMeans0.6950.0750.770
rowWeightedSds0.9480.1021.050
sample_data0.6950.0930.788
sd0.6920.0750.768
show0.9530.0841.037
slash0.6880.0830.771
subset_feature0.7070.1120.818
subset_sample0.7060.0630.769
t0.9580.0741.032
tax_table0.7000.0990.799
times0.6980.0880.789
var0.9540.0881.041
weighted.mean0.6870.0840.772
weightedVar0.6950.1170.812
weights0.6960.1100.805
zi2deseq21.0220.0961.118
zi2phyloseq0.7070.0880.795
ziMain0.6970.0790.776