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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_1.2.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/zitools.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* 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-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘zitools/DESCRIPTION’ ... OK
* this is package ‘zitools’ version ‘1.2.0’
* 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 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                      11.962  0.079  12.066
rowWeightedSds             7.402  0.104   7.521
tax_table                  7.194  0.088   7.293
otu_table                  7.133  0.020   7.168
weightedVar                7.060  0.079   7.152
assays                     6.982  0.084   7.080
slash                      6.886  0.088   6.984
rowQuantiles               6.826  0.124   6.962
boxplot                    6.800  0.063   6.877
log2p                      6.797  0.040   6.848
ziMain                     6.701  0.100   6.811
cor                        6.677  0.028   6.717
quantile                   6.596  0.108   6.720
inputcounts                6.664  0.024   6.699
var                        6.536  0.024   6.572
zi2deseq2                  6.464  0.000   6.474
sample_data                6.413  0.016   6.441
subset_feature             6.408  0.016   6.433
t                          6.374  0.036   6.420
times                      6.361  0.024   6.395
colMeans2                  6.367  0.008   6.388
weights                    6.302  0.012   6.325
sd                         6.285  0.016   6.311
rowVars                    6.239  0.036   6.286
rowWeightedMeans           6.220  0.024   6.257
rowSds                     6.150  0.059   6.220
colMedians                 6.180  0.004   6.196
subset_sample              6.166  0.012   6.187
colData                    6.149  0.020   6.181
mean                       6.136  0.000   6.146
plot                       5.992  0.124   6.130
resample_deinflatedcounts  6.058  0.040   6.115
zi2phyloseq                6.050  0.036   6.095
median                     6.056  0.020   6.086
heatmap                    6.057  0.000   6.067
weighted.mean              6.050  0.004   6.063
rowData                    6.004  0.028   6.046
model                      5.990  0.004   6.007
show                       5.932  0.016   5.958
cov                        5.910  0.012   5.931
deinflatedcounts           5.892  0.000   5.903
log1p                      5.862  0.005   5.877
inputdata                  5.725  0.006   5.742
* 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-devel_2025-02-19/site-library’
* installing *source* package ‘zitools’ ...
** this is package ‘zitools’ version ‘1.2.0’
** 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)

R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
Copyright (C) 2025 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 
 64.482   0.930  65.486