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### Running command:
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###   /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 153.868  3.915 163.850
fit                       30.858  0.275  31.772
plot_exprs                28.110  0.240  28.413
plot_exprs_per_coef       27.122  0.075  27.398
default_formula           24.722  0.747  25.414
plot_volcano              21.460  0.076  21.576
analyze                   19.059  0.232  19.385
read_metabolon            18.311  0.035  19.072
plot_summary              17.089  0.147  17.268
plot_densities            12.885  0.143  13.055
ftype                     10.563  0.064  10.630
read_fragpipe              9.873  0.168  10.439
fcluster                   8.631  0.159   8.809
plot_sample_nas            8.628  0.076   8.722
extract_coef_features      8.240  0.180   8.441
code                       7.391  0.100   7.506
biplot_covariates          7.212  0.188   7.414
plot_subgroup_points       6.097  0.028   6.136
dot-plot_survival          5.632  0.172   5.819
plot_violins               5.371  0.012   5.393
log2transform              5.251  0.016   5.278
biplot                     4.890  0.240   5.138
* 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.