##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:easyRNASeq.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings easyRNASeq_2.46.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/easyRNASeq.Rcheck’
* using R version 4.5.2 Patched (2025-11-04 r88984)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘easyRNASeq-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: easyRNASeq package
> ### Title: Count summarization and normalization pipeline for Next
> ###   Generation Sequencing data.
> ### Aliases: 'easyRNASeq package' easyRNASeq-package assay type BamFileList
> ###   BamFileList-class IRanges GRanges-class GRanges SRFilterResult
> ###   SummarizedExperiment RangedSummarizedExperiment-class
> ###   chromosomeFilter compose nFilter
> ### Keywords: "_PACKAGE" internal package
> 
> ### ** Examples
> 
>  # the data
>  tdir <- tutorialData()











> 
>   # get the example annotation file - we retrieve a gtf file from GitHub
>   annot <- fetchData("Drosophila_melanogaster.BDGP5.77.with-chr.gtf.gz")

> 
>   # create the AnnotParam
>   annotParam <- AnnotParam(
+     datasource=annot,
+     type="gtf")
> 
>   # create the synthetic transcripts
>   annotParam <- createSyntheticTranscripts(annotParam,verbose=FALSE)
> 
>  # create the RnaSeqParam
>  rnaSeqParam <- RnaSeqParam(annotParam=annotParam,countBy="gene")
> 
>   # get the bamfiles (from the Bioc cache in this example)
>  filenames <- dir(tdir,pattern="[A,T].*\\.bam$",full.names=TRUE)
>  indexnames <- sapply(paste0(sub(".*_","",basename(filenames)),".bai"),fetchData)
Error while performing HEAD request.
   Proceeding without cache information.
Warning: download failed
  web resource path: ‘https://github.com/UPSCb/UPSCb/raw/master/tutorial/easyRNASeq/TTGCGA.bam.bai’
  local file path: ‘~/Library/Caches/easyRNASeq/file851f7127f327’
  reason: HTTP 504 Gateway Timeout.
Warning: bfcdownload() failed
  rid: BFC22
  file: ‘https://github.com/UPSCb/UPSCb/raw/master/tutorial/easyRNASeq/TTGCGA.bam.bai’
  reason: download failed
Error: download failed; see warnings()
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
BiocFileCache-methods  12.512  1.342  34.586
easyRNASeq-BamFileList  9.619  0.868  18.455
Rsamtools-methods       6.329  0.663  12.871
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 ERROR
Running the tests in ‘tests/runTests.R’ failed.
Last 13 lines of output:
  > library(easyRNASeq)
  > tutorialData()
  Error while performing HEAD request.
     Proceeding without cache information.
  Error: download failed; see warnings()
  In addition: Warning messages:
  1: download failed
    web resource path: 'https://github.com/UPSCb/UPSCb/raw/master/tutorial/easyRNASeq/ACACTG.bam'
    local file path: '~/Library/Caches/easyRNASeq/filededf107225f1'
    reason: HTTP 504 Gateway Timeout. 
  2: bfcdownload() failed
    rid: BFC15
    file: 'https://github.com/UPSCb/UPSCb/raw/master/tutorial/easyRNASeq/ACACTG.bam'
    reason: download failed 
  Execution halted
* 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: 2 ERRORs, 1 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/easyRNASeq.Rcheck/00check.log’
for details.

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL easyRNASeq
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/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 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-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.

> # get the example data
> library(easyRNASeq)
> tutorialData()
Error while performing HEAD request.
   Proceeding without cache information.
Error: download failed; see warnings()
In addition: Warning messages:
1: download failed
  web resource path: 'https://github.com/UPSCb/UPSCb/raw/master/tutorial/easyRNASeq/ACACTG.bam'
  local file path: '~/Library/Caches/easyRNASeq/filededf107225f1'
  reason: HTTP 504 Gateway Timeout. 
2: bfcdownload() failed
  rid: BFC15
  file: 'https://github.com/UPSCb/UPSCb/raw/master/tutorial/easyRNASeq/ACACTG.bam'
  reason: download failed 
Execution halted