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CHECK report for metagene on merida1

This page was generated on 2021-05-06 12:35:39 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the metagene package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1051/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
metagene 2.22.0  (landing page)
Charles Joly Beauparlant
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/metagene
Branch: RELEASE_3_12
Last Commit: cdf1dbb
Last Changed Date: 2020-10-27 10:58:00 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: metagene
Version: 2.22.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:metagene.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings metagene_2.22.0.tar.gz
StartedAt: 2021-05-06 03:27:53 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 03:36:21 -0400 (Thu, 06 May 2021)
EllapsedTime: 508.5 seconds
RetCode: 0
Status:   OK  
CheckDir: metagene.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:metagene.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings metagene_2.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/metagene.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘metagene/DESCRIPTION’ ... OK
* this is package ‘metagene’ version ‘2.22.0’
* 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 ‘metagene’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  7.2Mb
  sub-directories of 1Mb or more:
    extdata   5.4Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘similaRpeak’
A package should be listed in only one of these fields.
* 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 ... NOTE
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'
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 group nuc nuctot qinf qsup tab value
* checking Rd files ... OK
* 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 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 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.12-bioc/meat/metagene.Rcheck/00check.log’
for details.



Installation output

metagene.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL metagene
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (metagene)

Tests output

metagene.Rcheck/tests/runTests.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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("metagene")

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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, 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:base':

    expand.grid

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
produce data table : ChIP-Seq
[1] TRUE
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 -- Thu May  6 03:36:08 2021 
*********************************************** 
Number of test functions: 219 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
metagene RUnit Tests - 219 test functions, 0 errors, 0 failures
Number of test functions: 219 
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 
127.511  15.720 143.952 

Example timings

metagene.Rcheck/metagene-Ex.timings

nameusersystemelapsed
Bam_Handler0.8820.0080.893
avoid_gaps_update0.0010.0010.001
bed_file_filter0.0000.0010.000
exon_by_gene_with_observed_transcripts0.0010.0000.000
get_demo_bam_files0.0030.0010.003
get_demo_design0.0030.0010.003
get_demo_metagene2.5420.3382.891
get_demo_regions0.0020.0000.001
get_promoters_txdb000
metagene0.4160.0340.450
permutation_test000
plot_metagene1.0450.0771.124
promoters_hg180.0030.0020.005
promoters_hg190.0020.0020.004
promoters_mm100.0010.0010.003
promoters_mm90.0010.0010.003
write_bed_file_filter_result000