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This page was generated on 2023-10-20 09:38:06 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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Package 1175/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
metagene2 1.16.0  (landing page)
Eric Fournier
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/metagene2
git_branch: RELEASE_3_17
git_last_commit: f0a5b2c
git_last_commit_date: 2023-04-25 11:10:10 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

CHECK results for metagene2 on kjohnson2


To the developers/maintainers of the metagene2 package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: metagene2
Version: 1.16.0
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_1.16.0.tar.gz
StartedAt: 2023-10-18 05:55:20 -0400 (Wed, 18 Oct 2023)
EndedAt: 2023-10-18 06:04:11 -0400 (Wed, 18 Oct 2023)
EllapsedTime: 531.6 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: metagene2.Rcheck
Warnings: 1

Command output

##############################################################################
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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_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/metagene2.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* 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 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘metagene2/DESCRIPTION’ ... OK
* this is package ‘metagene2’ version ‘1.16.0’
* checking package namespace information ... OK
* checking package dependencies ... 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 R 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
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
plot_metagene     5.934  0.244   9.535
metagene2_heatmap 3.903  0.162   6.099
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... 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-3.17-bioc-mac-arm64/meat/metagene2.Rcheck/00check.log’
for details.



Installation output

metagene2.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL metagene2
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/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)

Tests output

metagene2.Rcheck/tests/runTests.Rout


R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (64-bit)

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: '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, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, 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 Oct 18 06:03:56 2023 
*********************************************** 
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 
 98.791   5.685 152.134 

Example timings

metagene2.Rcheck/metagene2-Ex.timings

nameusersystemelapsed
Bam_Handler0.0920.0070.130
as_is_region_order2.6690.2233.732
coverage_order2.1940.1413.185
get_demo_bam_files0.0010.0010.006
get_demo_design0.0010.0010.002
get_demo_metagene1.8180.1372.965
get_demo_region_filenames0.1240.0020.195
get_demo_regions0.1130.0020.177
get_demo_rna_bam_files0.0010.0010.005
get_demo_rna_regions0.1100.0030.179
metagene21.7920.1242.981
metagene2_heatmap3.9030.1626.099
plot_metagene5.9340.2449.535