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### Running command:
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###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:easyRNASeq.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings easyRNASeq_2.42.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/easyRNASeq.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* 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 ‘2.42.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
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 ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... NOTE
Documented arguments not in \usage in Rd file 'easyRNASeq-annotation-internal-methods.Rd':
  ‘annotation.type’ ‘fields’ ‘filename’ ‘format’ ‘gAnnot’ ‘nbCore’

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          72.152  1.532  75.913
easyRNASeq-package               51.045  2.022  53.735
easyRNASeq-synthetic-transcripts 38.725  0.243  39.279
BiocFileCache-methods             9.783  1.673  19.608
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/easyRNASeq.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL easyRNASeq
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* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘easyRNASeq’ ...
** 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 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 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

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, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table,
    tapply, union, 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
Ensembl site unresponsive, trying asia mirror
Ensembl site unresponsive, trying useast mirror
Ensembl site unresponsive, trying asia mirror
Ensembl site unresponsive, trying useast mirror
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 -- Thu Feb 27 22:22:09 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: 18f5d313143639_TTGCGA.bam is considered unstranded.
2: In FUN(X[[i]], ...) :
  Bam file: 18f5d313143639_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.
3: In FUN(X[[i]], ...) :
  Bam file: 18f5d325a4333c_ACACTG.bam is considered unstranded.
4: In FUN(X[[i]], ...) :
  Bam file: 18f5d325a4333c_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.
5: In FUN(X[[i]], ...) :
  Bam file: 18f5d33157cb04_ATGGCT.bam is considered unstranded.
6: In FUN(X[[i]], ...) :
  Bam file: 18f5d33157cb04_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.
7: In FUN(X[[i]], ...) :
  Bam file: 18f5d36d668a1a_ACTAGC.bam is considered unstranded.
8: In FUN(X[[i]], ...) :
  Bam file: 18f5d36d668a1a_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 
 67.017   3.582  82.314