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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:autonomics.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings autonomics_1.15.36.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/autonomics.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 ‘autonomics/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘autonomics’ version ‘1.15.36’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 29 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘autonomics’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 ... NOTE
Warning: program compiled against libxml 212 using older 211
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘autonomics-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: .read_rnaseq_bams
> ### Title: Read rnaseq counts/bams
> ### Aliases: .read_rnaseq_bams .read_rnaseq_counts read_rnaseq_bams
> ###   read_rnaseq_counts
> 
> ### ** Examples
> 
> # read_rnaseq_bams
>   if (requireNamespace('Rsubread')){
+       dir <- download_data('billing16.bam.zip')
+       object <- read_rnaseq_bams(dir, paired = TRUE, genome = 'hg38')  
+       object <- read_rnaseq_bams(dir, paired = TRUE, genome = 'hg38', plot = TRUE)  
+   }
Loading required namespace: Rsubread
unzip
Warning in unzip(filepath, exdir = substr(filepath, 1, nchar(filepath) -  :
  error 1 in extracting from zip file
NCBI RefSeq annotation for hg38 (build 38.2) is used.
Error in (function (files, annot.inbuilt = "mm39", annot.ext = NULL, isGTFAnnotationFile = FALSE,  : 
  No read files provided!
Calls: read_rnaseq_bams ... .read_rnaseq_bams -> count_reads -> do.call -> <Anonymous>
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                            user system elapsed
read_diann_proteingroups 150.020  1.361 148.698
fit                       29.659  1.365  31.061
plot_exprs_per_coef       28.323  0.207  28.602
plot_exprs                27.765  0.112  27.949
default_formula           24.399  0.606  24.918
plot_volcano              21.899  0.072  22.025
analyze                   18.246  0.191  18.475
plot_summary              17.458  0.148  17.666
read_metabolon            17.180  0.040  17.252
plot_densities            12.968  0.112  13.109
ftype                     10.658  0.176  10.857
read_fragpipe              9.655  0.132   9.661
plot_sample_nas            8.699  0.044   8.765
fcluster                   8.258  0.076   8.350
extract_coef_features      8.024  0.096   8.137
code                       7.359  0.008   7.380
biplot_covariates          7.249  0.011   7.275
plot_subgroup_points       6.204  0.012   6.231
dot-plot_survival          5.696  0.136   5.844
plot_violins               5.522  0.067   5.603
log2transform              5.203  0.044   5.260
biplot                     5.039  0.047   5.098
* 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 ERROR, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/autonomics.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL autonomics
###
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* installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’
* installing *source* package ‘autonomics’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** 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 (autonomics)

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(autonomics)

Attaching package: 'autonomics'

The following objects are masked from 'package:stats':

    biplot, loadings

The following object is masked from 'package:base':

    beta

> 
> test_check("autonomics")
[ FAIL 0 | WARN 0 | SKIP 2 | PASS 156 ]

══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• empty test (2): 'test-8_fit.R:89:5', 'test-8_fit.R:99:5'

[ FAIL 0 | WARN 0 | SKIP 2 | PASS 156 ]
> 
> proc.time()
   user  system elapsed 
203.804   2.698 205.935