Back to Long Tests report for BioC 3.19

This page was generated on 2024-05-11 23:55:02 -0400 (Sat, 11 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4751
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4485
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4515
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 2/33HostnameOS / ArchCHECK
autonomics 1.12.0  (landing page)
Aditya Bhagwat
Snapshot Date: 2024-05-11 09:55:01 -0400 (Sat, 11 May 2024)
git_url: https://git.bioconductor.org/packages/autonomics
git_branch: RELEASE_3_19
git_last_commit: a23e37e
git_last_commit_date: 2024-04-30 11:31:54 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  ERROR  
palomino3Windows Server 2022 Datacenter / x64  ERROR  
lconwaymacOS 12.7.1 Monterey / x86_64  ERROR  

CHECK results for autonomics on lconway


To the developers/maintainers of the autonomics package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: autonomics
Version: 1.12.0
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_1.12.0.tar.gz
StartedAt: 2024-05-11 16:00:54 -0400 (Sat, 11 May 2024)
EndedAt: 2024-05-11 16:03:41 -0400 (Sat, 11 May 2024)
EllapsedTime: 167.3 seconds
RetCode: 1
Status:   ERROR  
CheckDir: autonomics.Rcheck
Warnings: NA

Tests output

autonomics.Rcheck/tests/LT3.1_rnaseq_bams.Rout.fail


R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 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

autonomics.Rcheck/tests/LT3.2_proteingroups_1fasta.Rout.fail


R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 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

autonomics.Rcheck/tests/LT8_fit.Rout.fail


R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 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

'R CMD check' output

##############################################################################
##############################################################################
###
### 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_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc-longtests/meat/autonomics.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* 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 ‘1.12.0’
* 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 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 ... 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 ... 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-3.19-bioc-longtests/meat/autonomics.Rcheck/00check.log’
for details.


Installation output

autonomics.Rcheck/00install.out

* 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)