##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:easyRNASeq.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings easyRNASeq_2.46.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/easyRNASeq.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘easyRNASeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘easyRNASeq’ version ‘2.46.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Files named as vignettes but with no recognized vignette engine:
   ‘inst/doc/01-Introduction.Rmd’
   ‘inst/doc/02-AnnotParam.Rmd’
   ‘inst/doc/03-SyntheticTranscripts.Rmd’
   ‘inst/doc/04-BamParam.Rmd’
   ‘inst/doc/05-RnaSeqParam.Rmd’
   ‘inst/doc/06-simpleRNASeq.Rmd’
   ‘inst/doc/07-cleanUp.Rmd’
   ‘inst/doc/08-Session-Info.Rmd’
   ‘inst/doc/09-Acknowledgments.Rmd’
   ‘inst/doc/10-Foonotes.Rmd’
   ‘inst/doc/11-Images.Rmd’
   ‘inst/doc/12-Appendix.Rmd’
(Is a VignetteBuilder field missing?)
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘easyRNASeq’ 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 whether startup messages can be suppressed ... 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) easyRNASeq-AnnotParam.Rd:40-43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) easyRNASeq-AnnotParam.Rd:44-51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) easyRNASeq-RnaSeqParam-class.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) easyRNASeq-RnaSeqParam-class.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) easyRNASeq-annotation-methods.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) easyRNASeq-annotation-methods.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) easyRNASeq-correction-methods.Rd:48-50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) easyRNASeq-correction-methods.Rd:51-54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) easyRNASeq-datasets.Rd:11-21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) easyRNASeq-internal-AnnotParam-methods.Rd:25: Lost braces
    25 | These are \code{\linkS4class{AnnotParam}}{AnnotParam} class internal methods:
       |                                          ^
checkRd: (-1) easyRNASeq-package.Rd:109-112: Lost braces in \itemize; meant \describe ?
checkRd: (-1) easyRNASeq-package.Rd:113-121: Lost braces in \itemize; meant \describe ?
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Non-topic package-anchored link(s) in Rd file 'GenomicRanges-methods.Rd':
  ‘[BiocGenerics]{row_colnames}’

Non-topic package-anchored link(s) in Rd file 'easyRNASeq-AnnotParam-accessors.Rd':
  ‘[easyRNASeq:easyRNASeq-AnnotParam-class]{AnnotParam}’

Non-topic package-anchored link(s) in Rd file 'easyRNASeq-AnnotParam-class.Rd':
  ‘[easyRNASeq:easyRNASeq-AnnotParam]{AnnotParam}’
  ‘[easyRNASeq:easyRNASeq-RnaSeqParam]{RnaSeqParam constructor}’
  ‘[easyRNASeq:easyRNASeq-RnaSeqParam-accessors]{RnaSeqParam
  accessors}’ ‘[easyRNASeq:easyRNASeq-simpleRNASeq]{simpleRNASeq
  function}’ ‘[easyRNASeq:easyRNASeq-AnnotParam]{AnnotParam
  constructor}’

Non-topic package-anchored link(s) in Rd file 'easyRNASeq-AnnotParam.Rd':
  ‘[easyRNASeq:easyRNASeq-annotation-methods]{getAnnotation}’

Non-topic package-anchored link(s) in Rd file 'easyRNASeq-BamParam-accessors.Rd':
  ‘[easyRNASeq:easyRNASeq-BamParam-class]{BamParam}’
  ‘[easyRNASeq:easyRNASeq-RnaSeqParam-accessors]{RnaSeqParam
  yieldSize}’

Non-topic package-anchored link(s) in Rd file 'easyRNASeq-BamParam-class.Rd':
  ‘[easyRNASeq:easyRNASeq-BamParam-accessors]{BamParam accessors}’
  ‘[easyRNASeq:easyRNASeq-RnaSeqParam]{RnaSeqParam constructor}’
  ‘[easyRNASeq:easyRNASeq-RnaSeqParam-accessors]{RnaSeqParam
  accessors}’ ‘[easyRNASeq:easyRNASeq-simpleRNASeq]{simpleRNASeq
  function}’ ‘[easyRNASeq:easyRNASeq-AnnotParam]{AnnotParam
  constructor}’

Non-topic package-anchored link(s) in Rd file 'easyRNASeq-RnaSeqParam-accessors.Rd':
  ‘[easyRNASeq:easyRNASeq-AnnotParam-class]{AnnotParam}’
  ‘[easyRNASeq:easyRNASeq-BamParam-class]{BamParam}’
  ‘[easyRNASeq:easyRNASeq-RnaSeqParam-class]{RnaSeqParam}’
  ‘[easyRNASeq:easyRNASeq-BamParam-accessors]{BamParam yieldSize}’

Non-topic package-anchored link(s) in Rd file 'easyRNASeq-RnaSeqParam-class.Rd':
  ‘[easyRNASeq:easyRNASeq-simpleRNASeq]{simpleRNASeq function}’
  ‘[easyRNASeq:easyRNASeq-summarization-methods]{easyRNASeq
  summarization functions}’
  ‘[easyRNASeq:easyRNASeq-RnaSeqParam]{RnaSeqParam constructor}’
  ‘[easyRNASeq:easyRNASeq-RnaSeqParam-accessors]{RnaSeqParam
  accessors}’ ‘[easyRNASeq:easyRNASeq-AnnotParam]{AnnotParam
  constructor}’ ‘[easyRNASeq:easyRNASeq-BamParam]{BamParam
  constructor}’

Non-topic package-anchored link(s) in Rd file 'easyRNASeq-annotation-methods.Rd':
  ‘[genomeIntervals]{genomeIntervals-readGff3}’
  ‘[easyRNASeq:easyRNASeq-annotation-internal-methods]{readGffGtf}’

Non-topic package-anchored link(s) in Rd file 'easyRNASeq-class.Rd':
  ‘[easyRNASeq:easyRNASeq-easyRNASeq]{easyRNASeq}’
  ‘[easyRNASeq:easyRNASeq-accessors]{easyRNASeq accessors}’
  ‘[easyRNASeq:easyRNASeq-annotation-methods]{easyRNASeq annotation}’
  ‘[easyRNASeq:easyRNASeq-correction-methods]{easyRNASeq correction
  (FPKM)}’ ‘[easyRNASeq:easyRNASeq-coverage-methods]{easyRNASeq
  coverage}’ ‘[easyRNASeq:easyRNASeq-summarization-methods]{easyRNASeq
  summarization}’ ‘[easyRNASeq:print-methods]{easyRNASeq print
  methods}’

Non-topic package-anchored link(s) in Rd file 'easyRNASeq-correction-methods.Rd':
  ‘[easyRNASeq:easyRNASeq-accessors]{readCounts}’

Non-topic package-anchored link(s) in Rd file 'easyRNASeq-defunct-annotation-methods.Rd':
  ‘[easyRNASeq:easyRNASeq-annotation-methods]{getAnnotation}’

Non-topic package-anchored link(s) in Rd file 'easyRNASeq-defunct.Rd':
  ‘[easyRNASeq:easyRNASeq-easyRNASeq]{easyRNASeq}’
  ‘[easyRNASeq:easyRNASeq-coverage-methods]{fetchCoverage}’
  ‘[easyRNASeq:easyRNASeq-simpleRNASeq]{simpleRNASeq}’

Non-topic package-anchored link(s) in Rd file 'easyRNASeq-easyRNASeq.Rd':
  ‘[easyRNASeq:ShortRead-methods]{use ShortRead/Rsamtools methods}’
  ‘[easyRNASeq:easyRNASeq-annotation-methods]{fetch the annotations}’
  ‘[easyRNASeq:easyRNASeq-coverage-methods]{get the reads coverage}’
  ‘[easyRNASeq:easyRNASeq-summarization-methods]{summarize the reads}’
  ‘[easyRNASeq:easyRNASeq-correction-methods]{optionally apply}’
  ‘[easyRNASeq:edgeR-methods]{use edgeR methods}’
  ‘[easyRNASeq:easyRNASeq-annotation-internal-methods]{readGffGtf}’

Non-topic package-anchored link(s) in Rd file 'easyRNASeq-global-variables.Rd':
  ‘[base:ns-hooks]{.onAttach}’

Non-topic package-anchored link(s) in Rd file 'easyRNASeq-package.Rd':
  ‘[easyRNASeq:easyRNASeq-easyRNASeq]{easyRNASeq}’
  ‘[easyRNASeq:ShortRead-methods]{ShortRead methods}’
  ‘[easyRNASeq:easyRNASeq-annotation-methods]{easyRNASeq annotation
  methods}’ ‘[easyRNASeq:easyRNASeq-coverage-methods]{easyRNASeq
  coverage methods}’
  ‘[easyRNASeq:easyRNASeq-summarization-methods]{easyRNASeq
  summarization methods}’
  ‘[easyRNASeq:easyRNASeq-correction-methods]{easyRNASeq correction
  methods}’ ‘[easyRNASeq:edgeR-methods]{edgeR methods}’

Non-topic package-anchored link(s) in Rd file 'easyRNASeq-simpleRNASeq.Rd':
  ‘[easyRNASeq:easyRNASeq-easyRNASeq]{easyRNASeq}’
  ‘[easyRNASeq:easyRNASeq-annotation-methods]{annotations}’
  ‘[easyRNASeq:easyRNASeq-summarization-methods]{summarizes}’
  ‘[easyRNASeq:easyRNASeq-BamFileList]{getBamFileList}’

Non-topic package-anchored link(s) in Rd file 'easyRNASeq-summarization-internal-methods.Rd':
  ‘[easyRNASeq:easyRNASeq-easyRNASeq]{easyRNASeq}’

Non-topic package-anchored link(s) in Rd file 'easyRNASeq-summarization-methods.Rd':
  ‘[easyRNASeq:easyRNASeq-annotation-methods]{easyRNASeq annotation
  methods}’
  ‘[easyRNASeq:easyRNASeq-summarization-internal-methods]{.geneModelSummarization}’
  ‘[easyRNASeq:easyRNASeq-island-methods]{findIslands}’

Non-topic package-anchored link(s) in Rd file 'genomeIntervals-methods.Rd':
  ‘[genomeIntervals]{genomeIntervals-readGff3}’

See section 'Cross-references' in the 'Writing R Extensions' manual.

Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  BiocFileCache-methods.Rd: BiocFileCache-class
  GenomicRanges-methods.Rd: GRangesList-class, GAlignments-class,
    DataFrame-class
  IRanges-methods.Rd: IRangesList-class
  Rsamtools-methods.Rd: BamFile-class
  ShortRead-methods.Rd: AlignedRead-class, SRFilter-class
  basename-methods.Rd: BamFile-class
  easyRNASeq-annotation-internal-methods.Rd:
    Genome_intervals_stranded-class
  easyRNASeq-class.Rd: GRangesList-class, RleList-class
  easyRNASeq-coverage-methods.Rd: Rle-class
  easyRNASeq-easyRNASeq.Rd: GRangesList-class
  easyRNASeq-simpleRNASeq.Rd: BamFile-class
  edgeR-methods.Rd: DGEList-class
  file.exists-methods.Rd: BamFile-class
  genomeIntervals-methods.Rd: Genome_intervals-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Documented arguments not in \usage in Rd file 'easyRNASeq-annotation-internal-methods.Rd':
  ‘annotation.type’ ‘fields’ ‘filename’ ‘format’ ‘gAnnot’ ‘nbCore’

Objects in \usage without \alias in Rd file 'easyRNASeq-coverage-methods.Rd':
  ‘\S4method{fetchCoverage}{RNAseq}’

Documented arguments not in \usage in Rd file 'easyRNASeq-internal-AnnotParam-methods.Rd':
  ‘...’

Documented arguments not in \usage in Rd file 'easyRNASeq-internal-methods.Rd':
  ‘arg’ ‘chr.names’ ‘fun’ ‘organism’ ‘type’ ‘value’ ‘x’ ‘...’

Documented arguments not in \usage in Rd file 'easyRNASeq-summarization-internal-methods.Rd':
  ‘chr.map’ ‘chr.sel’ ‘cList’ ‘count’ ‘filename’ ‘filter’ ‘format’
  ‘gapped’ ‘min.cov’ ‘min.length’ ‘max.gap’ ‘plot’ ‘rnaSeq’
  ‘summarization’ ‘silent’ ‘subType’ ‘type’ ‘validity.check’ ‘values’
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                   user system elapsed
easyRNASeq-simpleRNASeq          73.105  0.650  75.733
easyRNASeq-package               46.147  1.561  48.543
easyRNASeq-synthetic-transcripts 33.920  0.056  34.032
BiocFileCache-methods             7.854  1.374  19.723
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.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 ‘simpleRNASeq.Rmd’ using rmarkdown
# Introduction

This vignette provides the implementation of the procedure described in point 
7 of our __Guidelines for RNA-Seq data analysis__[^1] protocol available from
the __Epigenesys__ [website](http://www.epigenesys.eu).

Briefly, it details the step necessary to:
1. create a non-redundant annotation

2. count reads per feature

3. pre-analyse the data, i.e. assess the pertinence of the samples' 
charateristics in the light of their biological provenance; _i.e._ in other words
perform a so called _"biological QA"_ using assessment methods such as _Principal
Component Analysis_, _Multi-dimensional Scaling_, _Hierarcical Clustering_, _etc._

The aim of this vignette is to go through these steps using the __easyRNASeq__
package, hence the rationale of the implementation will not be discussed, albeit
relevant litterature will be pointed at when necessarry.

Throughout this vignette we are going to replicate the analysis conducted in
Robinson, Delhomme et al.[@Robinson:2014p6362], a study looking at _sexual
dimorphism_ in _Eurasian aspen_.

To perform the listed steps, we need to instantiate a number 
of objects to store the minimal set of parameters describing the conducted 
__RNA-Seq__ experiment, _e.g._ the BAM files location, the annotation location 
and type, the sequencing parameters, _etc._

To get started with this process, we load the package into our R session:


``` r
library(easyRNASeq)
```

before instantiating an __AnnotParam__ object informing on the location and type
of the annotation to be used.




Quitting from ./Chapters/01-Introduction.Rmd:39-41 [vignetteData]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! download failed; see warnings()
---
Backtrace:
     ▆
  1. └─easyRNASeq::vignetteData()
  2.   ├─easyRNASeq (local) standardGeneric("vignetteData")
  3.   │ ├─BiocGenerics::eval(mc, env)
  4.   │ └─base::eval(mc, env)
  5.   │   └─base::eval(mc, env)
  6.   └─easyRNASeq::vignetteData()
  7.     ├─BiocGenerics::sapply(VIGNETTE.DATA, fetchData)
  8.     └─base::sapply(VIGNETTE.DATA, fetchData)
  9.       └─base::lapply(X = X, FUN = FUN, ...)
 10.         ├─easyRNASeq (local) FUN(X[[i]], ...)
 11.         └─easyRNASeq (local) FUN(X[[i]], ...)
 12.           ├─BiocFileCache::bfcdownload(bfc, rid, ask = FALSE)
 13.           └─BiocFileCache::bfcdownload(bfc, rid, ask = FALSE)
 14.             └─BiocFileCache:::.util_download_and_rename(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~


Quitting from simpleRNASeq.Rmd:29-30 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! download failed; see warnings()
---
Backtrace:
     ▆
  1. └─easyRNASeq::vignetteData()
  2.   ├─easyRNASeq (local) standardGeneric("vignetteData")
  3.   │ ├─BiocGenerics::eval(mc, env)
  4.   │ └─base::eval(mc, env)
  5.   │   └─base::eval(mc, env)
  6.   └─easyRNASeq::vignetteData()
  7.     ├─BiocGenerics::sapply(VIGNETTE.DATA, fetchData)
  8.     └─base::sapply(VIGNETTE.DATA, fetchData)
  9.       └─base::lapply(X = X, FUN = FUN, ...)
 10.         ├─easyRNASeq (local) FUN(X[[i]], ...)
 11.         └─easyRNASeq (local) FUN(X[[i]], ...)
 12.           ├─BiocFileCache::bfcdownload(bfc, rid, ask = FALSE)
 13.           └─BiocFileCache::bfcdownload(bfc, rid, ask = FALSE)
 14.             └─BiocFileCache:::.util_download_and_rename(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'simpleRNASeq.Rmd' failed with diagnostics:
download failed; see warnings()
--- failed re-building ‘simpleRNASeq.Rmd’

--- re-building ‘easyRNASeq.Rnw’ using Sweave
--- finished re-building ‘easyRNASeq.Rnw’

/home/biocbuild/bbs-3.22-bioc/R/bin/R CMD Sweave easyRNASeq.Rnw
Output file:  easyRNASeq.tex
/home/biocbuild/bbs-3.22-bioc/R/bin/Rscript -e "tools::texi2pdf('easyRNASeq.tex')"
/home/biocbuild/bbs-3.22-bioc/R/bin/Rscript -e "rmarkdown::render('simpleRNASeq.Rmd')"


processing file: simpleRNASeq.Rmd


processing file: ./Chapters/01-Introduction.Rmd
Error:
! download failed; see warnings()
Backtrace:
     ▆
  1. └─easyRNASeq::vignetteData()
  2.   ├─easyRNASeq (local) standardGeneric("vignetteData")
  3.   │ ├─BiocGenerics::eval(mc, env)
  4.   │ └─base::eval(mc, env)
  5.   │   └─base::eval(mc, env)
  6.   └─easyRNASeq::vignetteData()
  7.     ├─BiocGenerics::sapply(VIGNETTE.DATA, fetchData)
  8.     └─base::sapply(VIGNETTE.DATA, fetchData)
  9.       └─base::lapply(X = X, FUN = FUN, ...)
 10.         ├─easyRNASeq (local) FUN(X[[i]], ...)
 11.         └─easyRNASeq (local) FUN(X[[i]], ...)
 12.           ├─BiocFileCache::bfcdownload(bfc, rid, ask = FALSE)
 13.           └─BiocFileCache::bfcdownload(bfc, rid, ask = FALSE)
 14.             └─BiocFileCache:::.util_download_and_rename(...)
# Introduction

This vignette provides the implementation of the procedure described in point 
7 of our __Guidelines for RNA-Seq data analysis__[^1] protocol available from
the __Epigenesys__ [website](http://www.epigenesys.eu).

Briefly, it details the step necessary to:
1. create a non-redundant annotation

2. count reads per feature

3. pre-analyse the data, i.e. assess the pertinence of the samples' 
charateristics in the light of their biological provenance; _i.e._ in other words
perform a so called _"biological QA"_ using assessment methods such as _Principal
Component Analysis_, _Multi-dimensional Scaling_, _Hierarcical Clustering_, _etc._

The aim of this vignette is to go through these steps using the __easyRNASeq__
package, hence the rationale of the implementation will not be discussed, albeit
relevant litterature will be pointed at when necessarry.

Throughout this vignette we are going to replicate the analysis conducted in
Robinson, Delhomme et al.[@Robinson:2014p6362], a study looking at _sexual
dimorphism_ in _Eurasian aspen_.

To perform the listed steps, we need to instantiate a number 
of objects to store the minimal set of parameters describing the conducted 
__RNA-Seq__ experiment, _e.g._ the BAM files location, the annotation location 
and type, the sequencing parameters, _etc._

To get started with this process, we load the package into our R session:


``` r
library(easyRNASeq)
```

before instantiating an __AnnotParam__ object informing on the location and type
of the annotation to be used.




Quitting from ./Chapters/01-Introduction.Rmd:39-41 [vignetteData]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! download failed; see warnings()
---
Backtrace:
     ▆
  1. └─easyRNASeq::vignetteData()
  2.   ├─easyRNASeq (local) standardGeneric("vignetteData")
  3.   │ ├─BiocGenerics::eval(mc, env)
  4.   │ └─base::eval(mc, env)
  5.   │   └─base::eval(mc, env)
  6.   └─easyRNASeq::vignetteData()
  7.     ├─BiocGenerics::sapply(VIGNETTE.DATA, fetchData)
  8.     └─base::sapply(VIGNETTE.DATA, fetchData)
  9.       └─base::lapply(X = X, FUN = FUN, ...)
 10.         ├─easyRNASeq (local) FUN(X[[i]], ...)
 11.         └─easyRNASeq (local) FUN(X[[i]], ...)
 12.           ├─BiocFileCache::bfcdownload(bfc, rid, ask = FALSE)
 13.           └─BiocFileCache::bfcdownload(bfc, rid, ask = FALSE)
 14.             └─BiocFileCache:::.util_download_and_rename(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~


Quitting from simpleRNASeq.Rmd:29-30 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! download failed; see warnings()
---
Backtrace:
     ▆
  1. └─easyRNASeq::vignetteData()
  2.   ├─easyRNASeq (local) standardGeneric("vignetteData")
  3.   │ ├─BiocGenerics::eval(mc, env)
  4.   │ └─base::eval(mc, env)
  5.   │   └─base::eval(mc, env)
  6.   └─easyRNASeq::vignetteData()
  7.     ├─BiocGenerics::sapply(VIGNETTE.DATA, fetchData)
  8.     └─base::sapply(VIGNETTE.DATA, fetchData)
  9.       └─base::lapply(X = X, FUN = FUN, ...)
 10.         ├─easyRNASeq (local) FUN(X[[i]], ...)
 11.         └─easyRNASeq (local) FUN(X[[i]], ...)
 12.           ├─BiocFileCache::bfcdownload(bfc, rid, ask = FALSE)
 13.           └─BiocFileCache::bfcdownload(bfc, rid, ask = FALSE)
 14.             └─BiocFileCache:::.util_download_and_rename(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Execution halted
make: *** [Makefile:14: html] Error 1
Error in tools::buildVignettes(dir = "/home/biocbuild/bbs-3.22-bioc/meat/easyRNASeq.Rcheck/vign_test/easyRNASeq",  : 
  running 'make' failed
Execution halted

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

Status: 1 ERROR, 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/easyRNASeq.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL easyRNASeq
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘easyRNASeq’ ...
** this is package ‘easyRNASeq’ version ‘2.46.0’
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for ‘basename’ from package ‘base’ in package ‘easyRNASeq’
Creating a generic function for ‘file.exists’ from package ‘base’ in package ‘easyRNASeq’
** 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 (easyRNASeq)

R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 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.

> # get the example data
> library(easyRNASeq)
> tutorialData()
[1] "/home/biocbuild/.cache/easyRNASeq"
> 
> # set the env.var
> #TUTORIAL.DATA <- get("TUTORIAL.DATA",envir=as.environment("package:easyRNASeq"))
> 
> # run the tests
> BiocGenerics:::testPackage("easyRNASeq")
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

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

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

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

    basename

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

    IQR, mad, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    findMatches

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

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: Seqinfo
No validation performed at that stage
Ensembl site unresponsive, trying asia mirror
Ensembl site unresponsive, trying useast mirror
Validated a datasource of type biomaRt
No validation performed at that stage
Validated a datasource of type rda
Read 1000 records
Validated a datasource of type gtf
Read 999 records
Validated a datasource of type gff3


RUNIT TEST PROTOCOL -- Thu Mar  5 23:37:10 2026 
*********************************************** 
Number of test functions: 20 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
easyRNASeq RUnit Tests - 20 test functions, 0 errors, 0 failures
Number of test functions: 20 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: In FUN(X[[i]], ...) :
  Bam file: 3fd9dc25d47590_ATGGCT.bam is considered unstranded.
2: In FUN(X[[i]], ...) :
  Bam file: 3fd9dc25d47590_ATGGCT.bam Strandedness could not be determined using 18462 regions spanning 1280337 bp on either strand at a 90% cutoff; 74.26 percent appear to be stranded.
3: In FUN(X[[i]], ...) :
  Bam file: 3fd9dc3fd79a6a_TTGCGA.bam is considered unstranded.
4: In FUN(X[[i]], ...) :
  Bam file: 3fd9dc3fd79a6a_TTGCGA.bam Strandedness could not be determined using 19659 regions spanning 1381886 bp on either strand at a 90% cutoff; 73.37 percent appear to be stranded.
5: In FUN(X[[i]], ...) :
  Bam file: 3fd9dc60178153_ACACTG.bam is considered unstranded.
6: In FUN(X[[i]], ...) :
  Bam file: 3fd9dc60178153_ACACTG.bam Strandedness could not be determined using 18615 regions spanning 1300192 bp on either strand at a 90% cutoff; 73.67 percent appear to be stranded.
7: In FUN(X[[i]], ...) :
  Bam file: 3fd9dc7d4807e_ACTAGC.bam is considered unstranded.
8: In FUN(X[[i]], ...) :
  Bam file: 3fd9dc7d4807e_ACTAGC.bam Strandedness could not be determined using 14772 regions spanning 1023473 bp on either strand at a 90% cutoff; 76.6 percent appear to be stranded.
9: In simpleRNASeq(bamFiles = bamFiles, param = param, verbose = FALSE) :
  As of version 2.15.5, easyRNASeq assumes that, if the data is strand specific, the sequencing was done using a protocol such as the Illumina TruSeq, where the reverse strand is quantified - i.e. the strandProtocol argument of the BamParam class defaults to 'reverse'.
> 
> # cleanup
> # removebfc(easyRNASeq:::.get_cache(),ask=FALSE)
> 
> proc.time()
   user  system elapsed 
 60.777   4.262 100.686