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This page was generated on 2023-02-06 11:05:15 -0500 (Mon, 06 Feb 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" 4483
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2023-01-10 r83596 ucrt) -- "Unsuffered Consequences" 4249
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" 4272
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

CHECK results for metagene on nebbiolo1


To the developers/maintainers of the metagene package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1134/2164HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
metagene 2.31.0  (landing page)
Charles Joly Beauparlant
Snapshot Date: 2023-02-05 14:00:11 -0500 (Sun, 05 Feb 2023)
git_url: https://git.bioconductor.org/packages/metagene
git_branch: master
git_last_commit: 7597c31
git_last_commit_date: 2022-11-01 11:10:04 -0500 (Tue, 01 Nov 2022)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    OK    ERROR  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    ERROR    OK  

Summary

Package: metagene
Version: 2.31.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:metagene.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings metagene_2.31.0.tar.gz
StartedAt: 2023-02-05 21:43:32 -0500 (Sun, 05 Feb 2023)
EndedAt: 2023-02-05 21:51:20 -0500 (Sun, 05 Feb 2023)
EllapsedTime: 468.7 seconds
RetCode: 1
Status:   ERROR  
CheckDir: metagene.Rcheck
Warnings: NA

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:metagene.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings metagene_2.31.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/metagene.Rcheck’
* using R Under development (unstable) (2023-01-10 r83596)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘metagene/DESCRIPTION’ ... OK
* this is package ‘metagene’ version ‘2.31.0’
* 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  6.2Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
* 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 ... 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’
 ERROR
Running the tests in ‘tests/runTests.R’ failed.
Last 13 lines of output:
   
  FAILURE in test.parallel_job_set_core_count_valid_multiple_core_biocparallelparam: Error in checkIdentical(obs, exp) : FALSE 
   
  
  Test files with failing tests
  
     test_parallel_job.R 
       test.parallel_job_get_core_count_valid_multiple_core_biocparallelparam 
       test.parallel_job_set_core_count_valid_multiple_core_biocparallelparam 
  
  
  Error in BiocGenerics:::testPackage("metagene") : 
    unit tests failed for package metagene
  In addition: There were 50 or more warnings (use warnings() to see the first 50)
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘metagene.Rmd’ using ‘UTF-8’... OK
  ‘metagene_rnaseq.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/metagene.Rcheck/00check.log’
for details.


Installation output

metagene.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL metagene
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-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
** 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.fail


R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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: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 objects are masked from 'package:base':

    I, expand.grid, unname

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
Timing stopped at: 0.927 0 0.927
Error in checkIdentical(obs, exp) : FALSE 
 
In addition: There were 50 or more warnings (use warnings() to see the first 50)
Timing stopped at: 0.957 0 0.958
Error in checkIdentical(obs, exp) : FALSE 
 
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 -- Sun Feb  5 21:49:27 2023 
*********************************************** 
Number of test functions: 218 
Number of errors: 0 
Number of failures: 2 

 
1 Test Suite : 
metagene RUnit Tests - 218 test functions, 0 errors, 2 failures
FAILURE in test.parallel_job_get_core_count_valid_multiple_core_biocparallelparam: Error in checkIdentical(obs, exp) : FALSE 
 
FAILURE in test.parallel_job_set_core_count_valid_multiple_core_biocparallelparam: Error in checkIdentical(obs, exp) : FALSE 
 

Test files with failing tests

   test_parallel_job.R 
     test.parallel_job_get_core_count_valid_multiple_core_biocparallelparam 
     test.parallel_job_set_core_count_valid_multiple_core_biocparallelparam 


Error in BiocGenerics:::testPackage("metagene") : 
  unit tests failed for package metagene
In addition: There were 50 or more warnings (use warnings() to see the first 50)
Execution halted

Example timings

metagene.Rcheck/metagene-Ex.timings

nameusersystemelapsed
Bam_Handler0.0880.0090.098
avoid_gaps_update0.0000.0010.001
bed_file_filter000
exon_by_gene_with_observed_transcripts000
get_demo_bam_files0.0020.0000.003
get_demo_design0.0020.0000.001
get_demo_metagene1.7550.1801.938
get_demo_regions0.0010.0000.001
get_promoters_txdb000
metagene0.3220.0280.350
permutation_test0.0010.0000.000
plot_metagene0.9830.0721.036
promoters_hg180.0030.0040.007
promoters_hg190.0010.0000.001
promoters_mm100.0000.0010.001
promoters_mm90.0000.0010.001
write_bed_file_filter_result000