##############################################################################
##############################################################################
###
### 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_2.45.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/easyRNASeq.Rcheck’
* using R version 4.5.0 (2025-04-11)
* 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 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘easyRNASeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘easyRNASeq’ version ‘2.45.0’
* 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          73.628  0.685  76.408
easyRNASeq-package               47.760  2.497  50.957
easyRNASeq-synthetic-transcripts 35.499  0.163  35.860
BiocFileCache-methods             7.630  0.748  18.177
* 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 ... OK
* checking PDF version of manual ... OK
* DONE

Status: 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 ‘2.45.0’
** 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 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
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: GenomeInfoDb
No validation performed at that stage
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 -- Wed Jun 18 22:58:20 2025 
*********************************************** 
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: 9ad5a15aeaf53_ACTAGC.bam is considered unstranded.
2: In FUN(X[[i]], ...) :
  Bam file: 9ad5a15aeaf53_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.
3: In FUN(X[[i]], ...) :
  Bam file: 9ad5a4087b494_ATGGCT.bam is considered unstranded.
4: In FUN(X[[i]], ...) :
  Bam file: 9ad5a4087b494_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.
5: In FUN(X[[i]], ...) :
  Bam file: 9ad5a476ac6d4_ACACTG.bam is considered unstranded.
6: In FUN(X[[i]], ...) :
  Bam file: 9ad5a476ac6d4_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: 9ad5acaa5262_TTGCGA.bam is considered unstranded.
8: In FUN(X[[i]], ...) :
  Bam file: 9ad5acaa5262_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.
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 
 59.297   4.208  70.402