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This page was generated on 2024-05-17 11:37:06 -0400 (Fri, 17 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4751
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4485
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4515
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 1215/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
metagene 2.36.0  (landing page)
Charles Joly Beauparlant
Snapshot Date: 2024-05-16 14:00:15 -0400 (Thu, 16 May 2024)
git_url: https://git.bioconductor.org/packages/metagene
git_branch: RELEASE_3_19
git_last_commit: 9ead778
git_last_commit_date: 2024-04-30 10:37:46 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    ERROR  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    ERROR    OK  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for metagene on palomino3


To the developers/maintainers of the metagene package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/metagene.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: metagene
Version: 2.36.0
Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:metagene.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings metagene_2.36.0.tar.gz
StartedAt: 2024-05-17 03:41:53 -0400 (Fri, 17 May 2024)
EndedAt: 2024-05-17 03:48:37 -0400 (Fri, 17 May 2024)
EllapsedTime: 404.2 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: metagene.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:metagene.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings metagene_2.36.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/metagene.Rcheck'
* using R version 4.4.0 (2024-04-24 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'metagene/DESCRIPTION' ... OK
* this is package 'metagene' version '2.36.0'
* 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 whether package 'metagene' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  7.1Mb
  sub-directories of 1Mb or more:
    extdata   5.4Mb
* 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 ... NOTE
NCIS.internal: no visible global function definition for
  'est.norm.med.search'
avoid_gaps_update: no visible binding for global variable 'value'
avoid_gaps_update: no visible binding for global variable 'bam'
avoid_gaps_update: no visible binding for global variable 'tab'
avoid_gaps_update: no visible binding for global variable 'nuc'
bin.data: no visible global function definition for 'hist'
permutation_test: no visible global function definition for '.'
permutation_test: no visible binding for global variable 'value'
plot_metagene: no visible binding for global variable 'bin'
plot_metagene: no visible binding for global variable 'value'
plot_metagene: no visible binding for global variable 'qinf'
plot_metagene: no visible binding for global variable 'qsup'
plot_metagene: no visible binding for global variable 'group'
plot_metagene: no visible binding for global variable 'nuc'
plot_metagene: no visible binding for global variable 'design'
plot_metagene: no visible binding for global variable 'nuctot'
Undefined global functions or variables:
  . bam bin design est.norm.med.search group hist nuc nuctot qinf qsup
  tab value
Consider adding
  importFrom("graphics", "hist")
to your NAMESPACE file.
* checking Rd files ... WARNING
checkRd: (5) Bam_Handler.Rd:22: \item in \describe must have non-empty label
checkRd: (5) Bam_Handler.Rd:42: \item in \describe must have non-empty label
checkRd: (5) Bam_Handler.Rd:46: \item in \describe must have non-empty label
checkRd: (5) Bam_Handler.Rd:50: \item in \describe must have non-empty label
checkRd: (5) Bam_Handler.Rd:54: \item in \describe must have non-empty label
checkRd: (5) Bam_Handler.Rd:58: \item in \describe must have non-empty label
checkRd: (5) Bam_Handler.Rd:61-62: \item in \describe must have non-empty label
checkRd: (5) Bam_Handler.Rd:71-72: \item in \describe must have non-empty label
checkRd: (5) Bam_Handler.Rd:81: \item in \describe must have non-empty label
checkRd: (5) metagene.Rd:23-26: \item in \describe must have non-empty label
checkRd: (5) metagene.Rd:61-62: \item in \describe must have non-empty label
checkRd: (5) metagene.Rd:77-78: \item in \describe must have non-empty label
checkRd: (5) metagene.Rd:102-103: \item in \describe must have non-empty label
checkRd: (5) metagene.Rd:116: \item in \describe must have non-empty label
checkRd: (5) metagene.Rd:119: \item in \describe must have non-empty label
checkRd: (5) metagene.Rd:122: \item in \describe must have non-empty label
checkRd: (5) metagene.Rd:127: \item in \describe must have non-empty label
checkRd: (5) metagene.Rd:130: \item in \describe must have non-empty label
checkRd: (5) metagene.Rd:133: \item in \describe must have non-empty label
checkRd: (5) metagene.Rd:144: \item in \describe must have non-empty label
checkRd: (5) metagene.Rd:147: \item in \describe must have non-empty label
checkRd: (5) metagene.Rd:155: \item in \describe must have non-empty label
checkRd: (5) metagene.Rd:164: \item in \describe must have non-empty label
checkRd: (5) metagene.Rd:170: \item in \describe must have non-empty label
checkRd: (5) metagene.Rd:179: \item in \describe must have non-empty label
checkRd: (5) metagene.Rd:183: \item in \describe must have non-empty label
checkRd: (5) metagene.Rd:186: \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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... 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, 2 NOTEs
See
  'F:/biocbuild/bbs-3.19-bioc/meat/metagene.Rcheck/00check.log'
for details.


Installation output

metagene.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL metagene
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.19-bioc/R/library'
* installing *source* package 'metagene' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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
Warning in fun(libname, pkgname) :
  Package 'metagene' is deprecated and will be removed from Bioconductor
  version 3.20
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'metagene' is deprecated and will be removed from Bioconductor
  version 3.20
** testing if installed package keeps a record of temporary installation path
* DONE (metagene)

Tests output

metagene.Rcheck/tests/runTests.Rout


R version 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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("metagene")

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


Attaching package: 'IRanges'

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

    windows

produce data table : ChIP-Seq
produce data frame : ChIP-Seq
produce data table : ChIP-Seq
produce data frame : ChIP-Seq
produce data table : ChIP-Seq
produce data frame : ChIP-Seq
produce data table : ChIP-Seq
produce data frame : ChIP-Seq
produce data table : ChIP-Seq
produce data frame : ChIP-Seq
produce data table : ChIP-Seq
produce data frame : ChIP-Seq
produce data table : ChIP-Seq
produce data frame : ChIP-Seq
produce data table : ChIP-Seq
produce data frame : ChIP-Seq
produce data table : ChIP-Seq
produce data frame : ChIP-Seq
produce data table : ChIP-Seq
produce data frame : ChIP-Seq
produce data table : ChIP-Seq
produce data frame : ChIP-Seq
produce data table : ChIP-Seq
produce data frame : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data frame : ChIP-Seq
[1] TRUE
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
ChIP-Seq flip/unflip
Normalization done
produce data table : ChIP-Seq
[1] TRUE
produce data table : ChIP-Seq
[1] TRUE
produce data table : ChIP-Seq
[1] TRUE
produce data table : ChIP-Seq
[1] TRUE
produce data table : ChIP-Seq
[1] TRUE
produce data table : ChIP-Seq
produce data table : ChIP-Seq
ChIP-Seq flip/unflip
ChIP-Seq flip/unflip
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
[1] TRUE


RUNIT TEST PROTOCOL -- Fri May 17 03:48:27 2024 
*********************************************** 
Number of test functions: 204 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
metagene RUnit Tests - 204 test functions, 0 errors, 0 failures
Number of test functions: 204 
Number of errors: 0 
Number of failures: 0 
There were 50 or more warnings (use warnings() to see the first 50)
> 
> proc.time()
   user  system elapsed 
  77.84    4.70   82.53 

Example timings

metagene.Rcheck/metagene-Ex.timings

nameusersystemelapsed
Bam_Handler0.090.010.11
avoid_gaps_update000
bed_file_filter000
exon_by_gene_with_observed_transcripts000
get_demo_bam_files000
get_demo_design0.010.000.02
get_demo_metagene2.160.162.36
get_demo_regions000
get_promoters_txdb000
metagene0.330.040.37
permutation_test000
plot_metagene0.830.040.86
promoters_hg180.000.010.02
promoters_hg19000
promoters_mm100.000.020.02
promoters_mm90.000.010.01
write_bed_file_filter_result000