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### Running command:
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###   /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_2.43.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/easyRNASeq.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* using platform: aarch64-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 Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘easyRNASeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘easyRNASeq’ version ‘2.43.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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
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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                   user system elapsed
easyRNASeq-simpleRNASeq          35.184  0.407  35.940
easyRNASeq-package               22.604  0.312  23.283
easyRNASeq-synthetic-transcripts 16.941  0.141  17.312
BiocFileCache-methods             1.960  0.290  14.585
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/easyRNASeq.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL easyRNASeq
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/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 Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"
Copyright (C) 2024 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()
[1] "/Users/biocbuild/Library/Caches/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 -- Tue Nov 26 21:41:04 2024 
*********************************************** 
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: 178b815783bc9_TTGCGA.bam is considered unstranded.
2: In FUN(X[[i]], ...) :
  Bam file: 178b815783bc9_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: 178b85f760f3b_ATGGCT.bam is considered unstranded.
4: In FUN(X[[i]], ...) :
  Bam file: 178b85f760f3b_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: 178b8633c44db_ACTAGC.bam is considered unstranded.
6: In FUN(X[[i]], ...) :
  Bam file: 178b8633c44db_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.
7: In FUN(X[[i]], ...) :
  Bam file: 178b86ed40b9c_ACACTG.bam is considered unstranded.
8: In FUN(X[[i]], ...) :
  Bam file: 178b86ed40b9c_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.
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 
 24.675   0.514  30.006