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### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:zitools.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings zitools_1.1.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/zitools.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘zitools/DESCRIPTION’ ... OK
* this is package ‘zitools’ version ‘1.1.0’
* 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 ...Warning: program compiled against libxml 212 using older 211
 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 ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                            user system elapsed
plus                      12.339  0.024  12.391
assays                     7.362  0.072   7.448
rowQuantiles               6.614  0.008   6.633
deinflatedcounts           6.535  0.001   6.549
rowWeightedSds             6.401  0.016   6.427
log1p                      6.268  0.052   6.332
colMeans2                  6.291  0.024   6.328
cov                        6.287  0.012   6.311
colData                    6.271  0.024   6.308
weights                    6.210  0.004   6.223
cor                        6.160  0.020   6.192
zi2deseq2                  6.056  0.004   6.071
quantile                   5.888  0.020   5.920
zi2phyloseq                5.876  0.012   5.899
resample_deinflatedcounts  5.856  0.012   5.879
model                      5.852  0.008   5.869
times                      5.848  0.004   5.860
rowData                    5.808  0.020   5.838
subset_feature             5.809  0.016   5.833
boxplot                    5.739  0.012   5.763
inputcounts                5.726  0.016   5.755
heatmap                    5.704  0.022   5.738
plot                       5.703  0.008   5.723
rowSds                     5.666  0.008   5.684
colMedians                 5.649  0.012   5.673
rowWeightedMeans           5.650  0.008   5.668
weighted.mean              5.635  0.004   5.649
inputdata                  5.612  0.016   5.639
sample_data                5.584  0.008   5.601
sd                         5.533  0.004   5.545
show                       5.509  0.016   5.534
rowVars                    5.501  0.000   5.511
slash                      5.493  0.004   5.506
weightedVar                5.497  0.000   5.506
ziMain                     5.464  0.004   5.476
log2p                      5.410  0.019   5.440
otu_table                  5.378  0.004   5.391
subset_sample              5.250  0.020   5.277
mean                       5.257  0.004   5.270
t                          5.165  0.008   5.179
tax_table                  5.132  0.028   5.167
var                        5.144  0.004   5.156
median                     5.088  0.004   5.100
* 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
  ‘/home/biocbuild/bbs-3.21-bioc/meat/zitools.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL zitools
###
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* installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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)

R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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 
 62.429   1.171  63.715