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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:autonomics.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings autonomics_1.12.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/autonomics.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘autonomics/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘autonomics’ version ‘1.12.1’
* 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 ... 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 ... OK
* 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 ... NOTE
checkRd: (-1) dequantify.Rd:24: Lost braces; missing escapes or markup?
    24 | Encode {channel} as suffix.
       |        ^
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
read_diann_proteingroups 87.786  4.303  87.549
read_rnaseq_counts       25.975  1.127  26.922
plot_exprs               18.473  0.196  18.548
plot_exprs_per_coef      17.408  0.160  17.489
rm_diann_contaminants    17.051  0.296  17.354
default_formula          13.681  0.492  13.782
fit                      12.233  0.453  11.665
analyze                  11.322  0.128  11.350
read_metabolon           11.138  0.232  11.253
read_somascan            11.179  0.060  11.131
plot_summary             10.844  0.116  10.857
plot_volcano              9.046  0.092   9.079
plot_densities            8.547  0.216   8.683
plot_sample_nas           5.543  0.024   5.499
reset_fit                 5.057  0.112   5.046
read_fragpipe             5.071  0.096   4.904
* 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 re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘autonomics_platformaware_analysis.Rmd’ using rmarkdown
The magick package is required to crop "/home/biocbuild/bbs-3.19-bioc/meat/autonomics.Rcheck/vign_test/autonomics/vignettes/autonomics_platformaware_analysis_files/figure-html/unnamed-chunk-2-1.png" but not available.
trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE161nnn/GSE161731/suppl//GSE161731_counts.csv.gz?tool=geoquery'
Content type 'application/x-gzip' length 8347405 bytes (8.0 MB)
==================================================
downloaded 8.0 MB

trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE161nnn/GSE161731/suppl//GSE161731_counts_key.csv.gz?tool=geoquery'
Content type 'application/x-gzip' length 2443 bytes
==================================================
downloaded 2443 bytes

trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE161nnn/GSE161731/suppl//GSE161731_key.csv.gz?tool=geoquery'
Content type 'application/x-gzip' length 2398 bytes
==================================================
downloaded 2398 bytes

trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE161nnn/GSE161731/suppl//GSE161731_xpr_nlcpm.csv.gz?tool=geoquery'
Content type 'application/x-gzip' length 16839511 bytes (16.1 MB)

downloaded 16 KB


Quitting from lines 62-73 [unnamed-chunk-3] (autonomics_platformaware_analysis.Rmd)
Error: processing vignette 'autonomics_platformaware_analysis.Rmd' failed with diagnostics:
Failed to download /tmp/Rtmpw5KiR7/datasets/GSE161731/GSE161731_xpr_nlcpm.csv.gz!
--- failed re-building ‘autonomics_platformaware_analysis.Rmd’

SUMMARY: processing the following file failed:
  ‘autonomics_platformaware_analysis.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/autonomics.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL autonomics
###
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* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/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 version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-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

> 
> test_check("autonomics")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 159 ]
> 
> proc.time()
   user  system elapsed 
126.299   3.951 127.667