Back to Multiple platform build/check report for BioC 3.13
ABCDEFGHIJKL[M]NOPQRSTUVWXYZ

This page was generated on 2021-10-15 15:06:11 -0400 (Fri, 15 Oct 2021).

CHECK results for metagene on tokay2

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? here 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 1084/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
metagene 2.24.0  (landing page)
Charles Joly Beauparlant
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/metagene
git_branch: RELEASE_3_13
git_last_commit: f85b3d4
git_last_commit_date: 2021-05-19 12:06:34 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    ERROR  
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    ERROR    OK  
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    ERROR    OK  

Summary

Package: metagene
Version: 2.24.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:metagene.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings metagene_2.24.0.tar.gz
StartedAt: 2021-10-15 01:36:34 -0400 (Fri, 15 Oct 2021)
EndedAt: 2021-10-15 01:45:37 -0400 (Fri, 15 Oct 2021)
EllapsedTime: 543.1 seconds
RetCode: 1
Status:   ERROR  
CheckDir: metagene.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:metagene.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings metagene_2.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/metagene.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'metagene/DESCRIPTION' ... OK
* this is package 'metagene' version '2.24.0'
* 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  7.2Mb
  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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... 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 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 ERROR
Running the tests in 'tests/runTests.R' failed.
Last 13 lines of output:
  FAILURE in test.metagene_initialize_valid_regions_supplementary_seqlevels: Error in checkIdentical(obs, exp) : FALSE 
   
  
  Test files with failing tests
  
     test_metagene.R 
       test.metagene_initialize_all_extra_seqnames_force_seqlevels 
       test.metagene_initialize_invalid_extra_seqnames 
       test.metagene_initialize_valid_regions_supplementary_seqlevels 
  
  
  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
** running tests for arch 'x64' ...
  Running 'runTests.R'
 ERROR
Running the tests in 'tests/runTests.R' failed.
Last 13 lines of output:
  FAILURE in test.metagene_initialize_valid_regions_supplementary_seqlevels: Error in checkIdentical(obs, exp) : FALSE 
   
  
  Test files with failing tests
  
     test_metagene.R 
       test.metagene_initialize_all_extra_seqnames_force_seqlevels 
       test.metagene_initialize_invalid_extra_seqnames 
       test.metagene_initialize_valid_regions_supplementary_seqlevels 
  
  
  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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/metagene.Rcheck/00check.log'
for details.

Installation output

metagene.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/metagene_2.24.0.tar.gz && rm -rf metagene.buildbin-libdir && mkdir metagene.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=metagene.buildbin-libdir metagene_2.24.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL metagene_2.24.0.zip && rm metagene_2.24.0.tar.gz metagene_2.24.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 66 4876k   66 3251k    0     0  3204k      0  0:00:01  0:00:01 --:--:-- 3206k
100 4876k  100 4876k    0     0  3696k      0  0:00:01  0:00:01 --:--:-- 3699k

install for i386

* 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
  converting help for package 'metagene'
    finding HTML links ... done
    Bam_Handler                             html  
    avoid_gaps_update                       html  
    bed_file_filter                         html  
    exon_by_gene_with_observed_transcripts
                                            html  
    get_demo_bam_files                      html  
    get_demo_design                         html  
    get_demo_metagene                       html  
    get_demo_regions                        html  
    get_promoters_txdb                      html  
    metagene                                html  
    permutation_test                        html  
    plot_metagene                           html  
    promoters_hg18                          html  
    promoters_hg19                          html  
    promoters_mm10                          html  
    promoters_mm9                           html  
    write_bed_file_filter_result            html  
** 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

install for x64

* installing *source* package 'metagene' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'metagene' as metagene_2.24.0.zip
* DONE (metagene)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'metagene' successfully unpacked and MD5 sums checked

Tests output

metagene.Rcheck/tests_i386/runTests.Rout.fail


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 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
Timing stopped at: 0.28 0 0.29
Error in checkIdentical(obs, exp) : FALSE 
 
In addition: There were 50 or more warnings (use warnings() to see the first 50)
Timing stopped at: 0.25 0 0.25
Error in checkIdentical(obs, exp) : FALSE 
 
Timing stopped at: 0.27 0 0.27
Error in checkIdentical(obs, exp) : FALSE 
 
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 Oct 15 01:43:45 2021 
*********************************************** 
Number of test functions: 204 
Number of errors: 0 
Number of failures: 3 

 
1 Test Suite : 
metagene RUnit Tests - 204 test functions, 0 errors, 3 failures
FAILURE in test.metagene_initialize_all_extra_seqnames_force_seqlevels: Error in checkIdentical(obs, exp) : FALSE 
 
FAILURE in test.metagene_initialize_invalid_extra_seqnames: Error in checkIdentical(obs, exp) : FALSE 
 
FAILURE in test.metagene_initialize_valid_regions_supplementary_seqlevels: Error in checkIdentical(obs, exp) : FALSE 
 

Test files with failing tests

   test_metagene.R 
     test.metagene_initialize_all_extra_seqnames_force_seqlevels 
     test.metagene_initialize_invalid_extra_seqnames 
     test.metagene_initialize_valid_regions_supplementary_seqlevels 


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

metagene.Rcheck/tests_x64/runTests.Rout.fail


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 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
Timing stopped at: 0.17 0 0.17
Error in checkIdentical(obs, exp) : FALSE 
 
In addition: There were 50 or more warnings (use warnings() to see the first 50)
Timing stopped at: 0.17 0 0.17
Error in checkIdentical(obs, exp) : FALSE 
 
Timing stopped at: 0.16 0 0.15
Error in checkIdentical(obs, exp) : FALSE 
 
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 Oct 15 01:45:14 2021 
*********************************************** 
Number of test functions: 204 
Number of errors: 0 
Number of failures: 3 

 
1 Test Suite : 
metagene RUnit Tests - 204 test functions, 0 errors, 3 failures
FAILURE in test.metagene_initialize_all_extra_seqnames_force_seqlevels: Error in checkIdentical(obs, exp) : FALSE 
 
FAILURE in test.metagene_initialize_invalid_extra_seqnames: Error in checkIdentical(obs, exp) : FALSE 
 
FAILURE in test.metagene_initialize_valid_regions_supplementary_seqlevels: Error in checkIdentical(obs, exp) : FALSE 
 

Test files with failing tests

   test_metagene.R 
     test.metagene_initialize_all_extra_seqnames_force_seqlevels 
     test.metagene_initialize_invalid_extra_seqnames 
     test.metagene_initialize_valid_regions_supplementary_seqlevels 


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/examples_i386/metagene-Ex.timings

nameusersystemelapsed
Bam_Handler0.840.010.85
avoid_gaps_update000
bed_file_filter000
exon_by_gene_with_observed_transcripts000
get_demo_bam_files000
get_demo_design000
get_demo_metagene2.160.222.63
get_demo_regions000
get_promoters_txdb000
metagene0.310.010.32
permutation_test000
plot_metagene1.080.141.22
promoters_hg18000
promoters_hg19000
promoters_mm100.000.020.02
promoters_mm9000
write_bed_file_filter_result000

metagene.Rcheck/examples_x64/metagene-Ex.timings

nameusersystemelapsed
Bam_Handler0.150.000.14
avoid_gaps_update000
bed_file_filter000
exon_by_gene_with_observed_transcripts000
get_demo_bam_files000
get_demo_design000
get_demo_metagene1.780.041.82
get_demo_regions000
get_promoters_txdb000
metagene0.300.010.31
permutation_test000
plot_metagene0.910.000.91
promoters_hg18000
promoters_hg190.000.020.01
promoters_mm10000
promoters_mm9000
write_bed_file_filter_result000