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This page was generated on 2025-01-16 12:10 -0500 (Thu, 16 Jan 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4746
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4489
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4517
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4469
taishanLinux (openEuler 24.03 LTS)aarch644.4.2 (2024-10-31) -- "Pile of Leaves" 4387
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 2287/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
zitools 1.0.0  (landing page)
Carlotta Meyring
Snapshot Date: 2025-01-13 13:00 -0500 (Mon, 13 Jan 2025)
git_url: https://git.bioconductor.org/packages/zitools
git_branch: RELEASE_3_20
git_last_commit: 64fc513
git_last_commit_date: 2024-10-29 11:31:47 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    ERROR  skipped


CHECK results for zitools on kjohnson1

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: 1.0.0
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: 2025-01-15 13:33:19 -0500 (Wed, 15 Jan 2025)
EndedAt: 2025-01-15 13:40:22 -0500 (Wed, 15 Jan 2025)
EllapsedTime: 423.2 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_1.0.0.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   5.108  1.059   6.199
assays 4.583  0.612   5.227
* 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.


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/4.4-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)

Tests output

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 
 35.681   4.687  40.365 

Example timings

zitools.Rcheck/zitools-Ex.timings

nameusersystemelapsed
MissingValueHeatmap0.0030.0020.005
assays4.5830.6125.227
boxplot2.7650.6753.455
colData3.5930.6234.234
colMeans23.5550.6314.240
colMedians3.6500.6744.346
cor2.5750.5083.094
cov2.5960.5943.201
deinflatedcounts2.6300.4993.153
heatmap3.4840.5074.009
inputcounts2.5890.4883.088
inputdata2.6050.5773.201
log1p2.6370.6423.395
log2p3.4910.5664.079
mean2.5410.5073.063
median2.5720.5873.175
model2.5570.5633.140
otu_table3.4920.5824.074
plot2.5060.5533.060
plus5.1081.0596.199
quantile3.3700.2913.661
resample_deinflatedcounts2.5070.2972.804
rowData2.5740.5503.124
rowQuantiles2.5440.2872.831
rowSds3.4380.2903.759
rowVars2.4900.4142.905
rowWeightedMeans2.5410.4342.974
rowWeightedSds2.5620.3012.863
sample_data2.6240.4843.108
sd3.3060.4663.791
show2.5090.6183.128
slash2.5260.4152.941
subset_feature2.5550.3002.854
subset_sample3.4860.6074.092
t2.5430.3902.934
tax_table2.5630.4192.982
times2.5800.3182.898
var3.3610.4863.847
weighted.mean2.5020.4242.926
weightedVar2.5310.3412.882
weights2.5460.2672.813
zi2deseq23.7210.2984.018
zi2phyloseq2.5480.5753.123
ziMain2.5120.4532.996