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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:metagene2.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings metagene2_1.23.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/metagene2.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* using platform: x86_64-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 Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘metagene2/DESCRIPTION’ ... OK
* this is package ‘metagene2’ version ‘1.23.0’
* 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'
 OK
* 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 ‘metagene2’ 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 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 ... WARNING
checkRd: (5) Bam_Handler.Rd:20: \item in \describe must have non-empty label
checkRd: (5) Bam_Handler.Rd:40: \item in \describe must have non-empty label
checkRd: (5) Bam_Handler.Rd:44: \item in \describe must have non-empty label
checkRd: (5) Bam_Handler.Rd:48: \item in \describe must have non-empty label
checkRd: (5) Bam_Handler.Rd:52: \item in \describe must have non-empty label
checkRd: (5) Bam_Handler.Rd:56: \item in \describe must have non-empty label
checkRd: (5) Bam_Handler.Rd:59-60: \item in \describe must have non-empty label
checkRd: (5) Bam_Handler.Rd:69-70: \item in \describe must have non-empty label
checkRd: (5) metagene2.Rd:451: \item in \describe must have non-empty label
checkRd: (5) metagene2.Rd:456: \item in \describe must have non-empty label
checkRd: (5) metagene2.Rd:461: \item in \describe must have non-empty label
checkRd: (5) metagene2.Rd:466: \item in \describe must have non-empty label
checkRd: (5) metagene2.Rd:475: \item in \describe must have non-empty label
checkRd: (5) metagene2.Rd:480: \item in \describe must have non-empty label
checkRd: (5) metagene2.Rd:485: \item in \describe must have non-empty label
* 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 ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... 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
* 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
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/metagene2.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL metagene2
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘metagene2’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** 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 (metagene2)

R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-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.

> ## Run all tests in the metagene package
> BiocGenerics:::testPackage("metagene2")

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 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


Attaching package: 'S4Vectors'

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

    findMatches

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

    I, expand.grid, unname

region_name is missing from the new metadata. Recreating it.
region_name is missing from the new metadata. Recreating it.
region_name is missing from the new metadata. Recreating it.
Replace region_metadata with metadata which would result in a different region split. All caches at the 'split_regions' step will be invalidated, and split_by will be reset to its default value.


RUNIT TEST PROTOCOL -- Wed Nov 27 23:45:12 2024 
*********************************************** 
Number of test functions: 128 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
metagene2 RUnit Tests - 128 test functions, 0 errors, 0 failures
Number of test functions: 128 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: In checkIdentical(obs, warning(exp)) : 

Some bam files have discrepancies in their seqnames.

This could be caused by chromosome names present only in a subset of the bam files (i.e.: chrY in some bam files, but absent in others.

This could also be caused by discrepancies in the seqlevels style (i.e.: UCSC:chr1 versus NCBI:1)


2: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
  GRanges object contains 100 out-of-bound ranges located on sequence chr1.
  Note that ranges located on a sequence whose length is unknown (NA) or on a
  circular sequence are not considered out-of-bound (use seqlengths() and
  isCircular() to get the lengths and circularity flags of the underlying
  sequences). You can use trim() to trim these ranges. See
  ?`trim,GenomicRanges-method` for more information.
3: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
  GRanges object contains 200 out-of-bound ranges located on sequence chr1.
  Note that ranges located on a sequence whose length is unknown (NA) or on a
  circular sequence are not considered out-of-bound (use seqlengths() and
  isCircular() to get the lengths and circularity flags of the underlying
  sequences). You can use trim() to trim these ranges. See
  ?`trim,GenomicRanges-method` for more information.
4: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
  GRanges object contains 600 out-of-bound ranges located on sequence chr1.
  Note that ranges located on a sequence whose length is unknown (NA) or on a
  circular sequence are not considered out-of-bound (use seqlengths() and
  isCircular() to get the lengths and circularity flags of the underlying
  sequences). You can use trim() to trim these ranges. See
  ?`trim,GenomicRanges-method` for more information.
> #BiocGenerics:::testPackage("metagene2", pattern="^test_demo.*\\.R$")
> 
> proc.time()
   user  system elapsed 
 68.308   8.760  77.637