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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_0.99.3.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/zitools.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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
Examples with CPU (user + system) or elapsed time > 5s
                            user system elapsed
plus                      12.169  0.040  12.232
assays                     7.373  0.104   7.493
zi2deseq2                  7.300  0.057   7.372
subset_sample              6.797  0.076   6.888
colMedians                 6.787  0.084   6.883
colData                    6.725  0.096   6.833
otu_table                  6.762  0.059   6.834
colMeans2                  6.778  0.028   6.817
quantile                   6.757  0.040   6.810
sample_data                6.770  0.012   6.793
heatmap                    6.602  0.124   6.737
sd                         6.689  0.012   6.714
var                        6.647  0.012   6.671
log2p                      6.336  0.080   6.430
rowSds                     6.316  0.056   6.385
resample_deinflatedcounts  6.085  0.008   6.104
t                          6.056  0.016   6.083
times                      6.065  0.004   6.080
weights                    6.035  0.002   6.048
weightedVar                5.983  0.016   6.011
show                       5.978  0.016   6.004
tax_table                  5.954  0.016   5.980
zi2phyloseq                5.942  0.015   5.970
subset_feature             5.919  0.012   5.944
rowWeightedSds             5.910  0.008   5.924
rowData                    5.804  0.008   5.823
weighted.mean              5.783  0.008   5.804
model                      5.762  0.012   5.785
slash                      5.724  0.008   5.743
rowWeightedMeans           5.695  0.022   5.723
ziMain                     5.678  0.032   5.722
boxplot                    5.632  0.071   5.716
cor                        5.670  0.020   5.700
deinflatedcounts           5.678  0.004   5.693
plot                       5.631  0.016   5.658
median                     5.614  0.000   5.625
rowVars                    5.579  0.022   5.609
rowQuantiles               5.490  0.000   5.500
mean                       5.464  0.000   5.476
log1p                      5.445  0.004   5.460
cov                        5.389  0.024   5.423
inputdata                  5.379  0.014   5.405
inputcounts                5.353  0.002   5.367
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-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-4.4.1/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 version 4.4.1 (2024-06-14) -- "Race for Your Life"
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 
 63.537   1.541  65.180