BioC 3.2: CHECK report for metagene on oaxaca

Package: metagene

Version: 2.1.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings metagene_2.1.1.tar.gz

StartedAt: 2015-08-24 01:33:31 -0700 (Mon, 24 Aug 2015)

EndedAt: 2015-08-24 01:39:45 -0700 (Mon, 24 Aug 2015)

EllapsedTime: 374.3 seconds

RetCode: 1

Status:  ERROR

CheckDir: metagene.Rcheck

Warnings: NA

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings metagene_2.1.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/metagene.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘metagene/DESCRIPTION’ ... OK
* this is package ‘metagene’ version ‘2.1.1’
* 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 ... [20s/21s] 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 loading without being on the library search path ... 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
intoNbins: no visible global function definition for ‘IRanges’
* 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 line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [12s/13s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [175s/161s]
 ERROR
Running the tests in ‘tests/runTests.R’ failed.
Last 13 lines of output:
  FAILURE in test.metagene_initialize_invalid_extra_seqnames: Error in checkIdentical(obs, exp, msg) : 
    FALSE metagene heatmap -  Invalid regions seqnames did not give the expected error message.
  
  Test files with failing tests
  
     test_metagene.R 
       test.metagene_initialize_all_extra_seqnames_force_seqlevels 
       test.metagene_initialize_invalid_extra_seqnames 
  
  
  Error in BiocGenerics:::testPackage("metagene") : 
    unit tests failed for package metagene
  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: 1 ERROR, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/metagene.Rcheck/00check.log’
for details.

R version 3.2.2 (2015-08-14) -- "Fire Safety"
Copyright (C) 2015 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin13.4.0 (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, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, as.vector, cbind, colnames, 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, rep.int, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unlist, unsplit

Timing stopped at: 0.483 0.006 0.495 
Error in checkIdentical(obs, exp, msg) : 
  FALSE metagene heatmap -  Invalid all extra seqnames did not generate the expected error with force_seqlevels = TRUE.
Timing stopped at: 0.417 0.005 0.423 
Error in checkIdentical(obs, exp, msg) : 
  FALSE metagene heatmap -  Invalid regions seqnames did not give the expected error message.


RUNIT TEST PROTOCOL -- Mon Aug 24 01:39:38 2015 
*********************************************** 
Number of test functions: 105 
Number of errors: 0 
Number of failures: 2 

 
1 Test Suite : 
metagene RUnit Tests - 105 test functions, 0 errors, 2 failures
FAILURE in test.metagene_initialize_all_extra_seqnames_force_seqlevels: Error in checkIdentical(obs, exp, msg) : 
  FALSE metagene heatmap -  Invalid all extra seqnames did not generate the expected error with force_seqlevels = TRUE.
FAILURE in test.metagene_initialize_invalid_extra_seqnames: Error in checkIdentical(obs, exp, msg) : 
  FALSE metagene heatmap -  Invalid regions seqnames did not give the expected error message.

Test files with failing tests

   test_metagene.R 
     test.metagene_initialize_all_extra_seqnames_force_seqlevels 
     test.metagene_initialize_invalid_extra_seqnames 


Error in BiocGenerics:::testPackage("metagene") : 
  unit tests failed for package metagene
Execution halted

* installing *source* package ‘metagene’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (metagene)

name	user	system	elapsed
Bam_Handler	0.444	0.007	0.457
getGenes	0.000	0.000	0.001
getGenesBiomart	0.000	0.000	0.001
get_demo_bam_files	0.002	0.001	0.003
get_demo_regions	0.002	0.000	0.002
metagene	1.963	0.029	2.003