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This page was generated on 2024-07-18 11:39 -0400 (Thu, 18 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4683
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4379
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4450
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4399
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 2246/2248HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
zitools 0.99.3  (landing page)
Carlotta Meyring
Snapshot Date: 2024-07-17 14:00 -0400 (Wed, 17 Jul 2024)
git_url: https://git.bioconductor.org/packages/zitools
git_branch: devel
git_last_commit: 5f45d49
git_last_commit_date: 2024-04-24 10:21:43 -0400 (Wed, 24 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    ERROR  
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for zitools on nebbiolo2

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: 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: 2024-07-18 05:25:31 -0400 (Thu, 18 Jul 2024)
EndedAt: 2024-07-18 05:31:03 -0400 (Thu, 18 Jul 2024)
EllapsedTime: 332.1 seconds
RetCode: 1
Status:   ERROR  
CheckDir: zitools.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### 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
* 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.


Installation output

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)

Tests output

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 
 26.827   2.229  29.045 

Example timings

zitools.Rcheck/zitools-Ex.timings

nameusersystemelapsed
MissingValueHeatmap0.0000.0030.002
assays3.3340.1723.506
boxplot2.5440.1642.707
colData1.7950.0321.827
colMeans21.7310.0521.783
colMedians1.7350.0171.751
cor2.3500.1352.486
cov1.7350.0081.743
deinflatedcounts1.7030.0121.715
heatmap1.8250.0201.845
inputcounts2.6070.1152.724
inputdata1.7760.0281.804
log1p1.7770.0151.793
log2p1.9220.0121.934
mean2.4140.0722.486
median1.7190.0041.723
model1.7650.0241.789
otu_table1.8650.0111.877
plot2.3430.0482.391
plus3.5320.0363.568
quantile1.7860.0171.802
resample_deinflatedcounts2.3480.1162.464
rowData1.7190.0071.727
rowQuantiles1.7350.0151.752
rowSds1.7650.0041.769
rowVars2.4110.0232.435
rowWeightedMeans1.7550.0121.767
rowWeightedSds1.7430.0121.754
sample_data1.8130.0241.838
sd2.2750.0482.323
show1.7260.0001.726
slash1.7300.0031.734
subset_feature1.8070.0011.806
subset_sample2.3900.0272.417
t1.6940.0281.722
tax_table1.7770.0081.785
times1.8160.0001.815
var2.3970.0282.424
weighted.mean1.7030.0011.703
weightedVar1.7590.0191.778
weights1.7830.0121.794
zi2deseq22.5570.0402.596
zi2phyloseq1.7690.0231.793
ziMain1.7570.0121.768