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This page was generated on 2024-03-04 11:39:28 -0500 (Mon, 04 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4676
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" 4414
merida1macOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4441
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" 4417
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1191/2251HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
metagene2 1.19.0  (landing page)
Eric Fournier
Snapshot Date: 2024-03-01 14:00:22 -0500 (Fri, 01 Mar 2024)
git_url: https://git.bioconductor.org/packages/metagene2
git_branch: devel
git_last_commit: 7dd1bd1
git_last_commit_date: 2023-10-24 11:13:42 -0500 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  

CHECK results for metagene2 on merida1


To the developers/maintainers of the metagene2 package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/metagene2.git to reflect on this report. See Troubleshooting Build Report for more information.
- 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: 1.19.0
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_1.19.0.tar.gz
StartedAt: 2024-03-02 06:27:58 -0500 (Sat, 02 Mar 2024)
EndedAt: 2024-03-02 06:40:18 -0500 (Sat, 02 Mar 2024)
EllapsedTime: 739.6 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_1.19.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/metagene2.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* 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 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘metagene2/DESCRIPTION’ ... OK
* this is package ‘metagene2’ version ‘1.19.0’
* 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      8.813  0.694  12.018
as_is_region_order 5.965  0.572   7.869
metagene2_heatmap  5.986  0.508   7.955
coverage_order     4.043  0.425   5.376
* 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-3.19-bioc/meat/metagene2.Rcheck/00check.log’
for details.



Installation output

metagene2.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-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)

Tests output

metagene2.Rcheck/tests/runTests.Rout


R Under development (unstable) (2024-01-16 r85808) -- "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: '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, 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 -- Sat Mar  2 06:40:02 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 
171.166  13.233 219.008 

Example timings

metagene2.Rcheck/metagene2-Ex.timings

nameusersystemelapsed
Bam_Handler0.1440.0060.184
as_is_region_order5.9650.5727.869
coverage_order4.0430.4255.376
get_demo_bam_files0.0020.0010.004
get_demo_design0.0030.0010.004
get_demo_metagene3.4230.4134.618
get_demo_region_filenames0.1890.0030.234
get_demo_regions0.1890.0030.231
get_demo_rna_bam_files0.0010.0010.004
get_demo_rna_regions0.1890.0020.233
metagene23.4040.4074.840
metagene2_heatmap5.9860.5087.955
plot_metagene 8.813 0.69412.018