R version 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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.

> require(testthat)
Loading required package: testthat
> if (requireNamespace('Rsubread', quietly = TRUE)){
+     context('read_rnaseq_bams')
+     file <- download_data('billing16.bam.zip')
+     test_that('read_rnaseq_bams(file, cpm = FALSE)', {
+         object <- read_rnaseq_bams(file, paired = TRUE, genome = 'hg38', cpm = FALSE)
+         expect_s4_class(object, 'SummarizedExperiment')
+         expect_true('log2counts' %in% SummarizedExperiment::assayNames(object))
+     })
+ 
+     test_that('read_rnaseq_bams(file)', {
+         object <- read_rnaseq_bams(file, paired = TRUE, genome = 'hg38')
+         expect_s4_class(object, 'SummarizedExperiment')
+         expect_true('log2cpm' %in% SummarizedExperiment::assayNames(object))
+     })
+ 
+     test_that('read_rnaseq_bams(file, pca = TRUE)', {
+         object <- read_rnaseq_bams(file, paired = TRUE, genome = 'hg38', pca = TRUE)
+         expect_s4_class(object, 'SummarizedExperiment')
+         expect_true('log2cpm' %in% SummarizedExperiment::assayNames(object))
+         expect_true(any(stri_detect_fixed(         svars(object),  'pca1')))
+         expect_true(any(stri_detect_fixed(         fvars(object),  'pca1')))
+         expect_true(any(stri_detect_fixed(names(metadata(object)), 'pca' )))
+     })
+ 
+     test_that("read_rnaseq_counts(file, fit = 'limma')", {
+         object <- read_rnaseq_bams(file, paired = TRUE, genome = 'hg38', fit = 'limma')
+         expect_s4_class(object, 'SummarizedExperiment')
+         expect_true(any(stri_detect_fixed(fvars(object), 'limma')))
+     })
+ }
Error in download_data("billing16.bam.zip") : 
  could not find function "download_data"
Execution halted

R version 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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.

> #============================================================================
> #
> #                     read_fastahdrs
> #                    parse_fastahdrs
> #
> #============================================================================
> 
> context('`read_fastahdrs/parse_fastahdrs`')
Error in context("`read_fastahdrs/parse_fastahdrs`") : 
  could not find function "context"
Execution halted

R version 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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.

> require(testthat)
Loading required package: testthat
> 
> sumexp_contains_fit <- function(object, fit = 'limma'){
+     is(object, 'SummarizedExperiment') &
+     is.array(S4Vectors::metadata(object)[[fit]]) &
+     (nrow(S4Vectors::metadata(object)[[fit]])==nrow(object)) 
+ }
> 
> #==============================================================================
> 
> context('fit: GSE161731')
> 
>     # Prepare minimal full-feature datset: subgroup, block, weights
>         require(magrittr)
Loading required package: magrittr

Attaching package: 'magrittr'

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

    equals, is_less_than, not

>         object <- .read_rnaseq_counts(file, sfile = sfile, by.y = 'rna_id')
Error in .read_rnaseq_counts(file, sfile = sfile, by.y = "rna_id") : 
  could not find function ".read_rnaseq_counts"
Execution halted

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no autonomics_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc-longtests/meat/autonomics.Rcheck’
* using R version 4.5.0 RC (2025-04-04 r88126)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘autonomics/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘autonomics’ version ‘1.16.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 30 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 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 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 ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Non-topic package-anchored link(s) in Rd file 'reexports.Rd':
  ‘[magrittr:compound]{%<>%}’ ‘[magrittr:pipe]{%>%}’
  ‘[magrittr:aliases]{extract}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... SKIPPED
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
  Running ‘LT3.1_rnaseq_bams.R’
  Running ‘LT3.2_proteingroups_1fasta.R’
  Running ‘LT8_fit.R’
 ERROR
Running the tests in ‘longtests/LT3.1_rnaseq_bams.R’ failed.
Last 13 lines of output:
  +         expect_true('log2cpm' %in% SummarizedExperiment::assayNames(object))
  +         expect_true(any(stri_detect_fixed(         svars(object),  'pca1')))
  +         expect_true(any(stri_detect_fixed(         fvars(object),  'pca1')))
  +         expect_true(any(stri_detect_fixed(names(metadata(object)), 'pca' )))
  +     })
  + 
  +     test_that("read_rnaseq_counts(file, fit = 'limma')", {
  +         object <- read_rnaseq_bams(file, paired = TRUE, genome = 'hg38', fit = 'limma')
  +         expect_s4_class(object, 'SummarizedExperiment')
  +         expect_true(any(stri_detect_fixed(fvars(object), 'limma')))
  +     })
  + }
  Error in download_data("billing16.bam.zip") : 
    could not find function "download_data"
  Execution halted
Running the tests in ‘longtests/LT3.2_proteingroups_1fasta.R’ failed.
Complete output:
  > #============================================================================
  > #
  > #                     read_fastahdrs
  > #                    parse_fastahdrs
  > #
  > #============================================================================
  > 
  > context('`read_fastahdrs/parse_fastahdrs`')
  Error in context("`read_fastahdrs/parse_fastahdrs`") : 
    could not find function "context"
  Execution halted
Running the tests in ‘longtests/LT8_fit.R’ failed.
Last 13 lines of output:
  > 
  >     # Prepare minimal full-feature datset: subgroup, block, weights
  >         require(magrittr)
  Loading required package: magrittr
  
  Attaching package: 'magrittr'
  
  The following objects are masked from 'package:testthat':
  
      equals, is_less_than, not
  
  >         object <- .read_rnaseq_counts(file, sfile = sfile, by.y = 'rna_id')
  Error in .read_rnaseq_counts(file, sfile = sfile, by.y = "rna_id") : 
    could not find function ".read_rnaseq_counts"
  Execution halted
* DONE

Status: 1 ERROR, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc-longtests/meat/autonomics.Rcheck/00check.log’
for details.

* installing *source* package ‘autonomics’ ...
** this is package ‘autonomics’ version ‘1.16.0’
** 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)