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This page was generated on 2021-12-01 17:18:16 -0500 (Wed, 01 Dec 2021).

CHECK results for ENCODExplorer on machv2

To the developers/maintainers of the ENCODExplorer package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ENCODExplorer.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 575/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ENCODExplorer 2.20.0  (landing page)
Charles Joly Beauparlant
Snapshot Date: 2021-11-30 04:15:05 -0500 (Tue, 30 Nov 2021)
git_url: https://git.bioconductor.org/packages/ENCODExplorer
git_branch: RELEASE_3_14
git_last_commit: 5a12d2d
git_last_commit_date: 2021-10-26 12:20:28 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 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: ENCODExplorer
Version: 2.20.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ENCODExplorer.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ENCODExplorer_2.20.0.tar.gz
StartedAt: 2021-11-30 16:10:53 -0500 (Tue, 30 Nov 2021)
EndedAt: 2021-11-30 16:21:28 -0500 (Tue, 30 Nov 2021)
EllapsedTime: 634.6 seconds
RetCode: 1
Status:   ERROR  
CheckDir: ENCODExplorer.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ENCODExplorer.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ENCODExplorer_2.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/ENCODExplorer.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ENCODExplorer/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ENCODExplorer’ version ‘2.20.0’
* 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 ‘ENCODExplorer’ can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'ENCODExplorer' is deprecated and will be removed from
See ‘/Users/biocbuild/bbs-3.14-bioc/meat/ENCODExplorer.Rcheck/00install.out’ for details.
* 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 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
createDesign: no visible binding for global variable ‘file_format’
createDesign: no visible binding for global variable ‘status’
createDesign: no visible binding for global variable ‘accession’
createDesign: no visible binding for global variable ‘controls’
createDesign : get_ctrl_design: no visible binding for global variable
  ‘accession’
createDesign : get_ctrl_design: no visible binding for global variable
  ‘href’
createDesign: no visible global function definition for ‘.’
createDesign: no visible binding for global variable ‘href’
createDesign: no visible binding for global variable ‘Experiment’
createDesign: no visible binding for global variable ‘Value’
downloadEncode: no visible binding for global variable ‘file_accession’
downloadEncode: no visible binding for global variable ‘file_format’
downloadEncode: no visible binding for global variable ‘accession’
shinyEncode: no visible binding for global variable ‘ui’
shinyEncode: no visible binding for global variable ‘server’
Undefined global functions or variables:
  . Experiment Value accession controls file_accession file_format href
  server status ui
* 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 include directives in Makefiles ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                user system elapsed
get_encode_df_full            63.771  1.002  65.518
ENCODEBindingConsensus-class  40.125  1.028  46.672
ENCODEExpressionSummary-class  6.036  3.079  15.036
buildExpressionSummary         8.069  0.562  29.366
queryTranscriptExpression      7.515  0.505  16.209
queryConsensusPeaks            7.017  0.075   7.094
buildConsensusPeaks            3.577  0.248  13.817
* 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:
  1 Test Suite : 
  ENCODExplorer RUnit Tests - 28 test functions, 0 errors, 1 failure
  FAILURE in test.ret_content: Error in checkTrue(expr = !is.null(res$accession), msg = "res should be get an accession entry") : 
    Test not TRUE
  res should be get an accession entry
  
  Test files with failing tests
  
     test_search.R 
       test.ret_content 
  
  
  Error in BiocGenerics:::testPackage("ENCODExplorer") : 
    unit tests failed for package ENCODExplorer
  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 WARNING, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/ENCODExplorer.Rcheck/00check.log’
for details.


Installation output

ENCODExplorer.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ENCODExplorer
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘ENCODExplorer’ ...
** using staged installation
** R
** 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: Package 'ENCODExplorer' is deprecated and will be removed from
  Bioconductor version 3.15
** testing if installed package can be loaded from final location
Warning: Package 'ENCODExplorer' is deprecated and will be removed from
  Bioconductor version 3.15
** testing if installed package keeps a record of temporary installation path
* DONE (ENCODExplorer)

Tests output

ENCODExplorer.Rcheck/tests/runTests.Rout.fail


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
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 ENCODExplorer package
> BiocGenerics:::testPackage("ENCODExplorer")
snapshotDate(): 2021-10-20
loading from cache
Results : 2 files, 1 datasets
[1] "Success downloading file : ./ENCFF002COC.bed.gz"
[1] "Success downloading file : ./ENCFF001VDM.bed.gz"
[1] "Files can be found at /Users/biocbuild/bbs-3.14-bioc/meat/ENCODExplorer.Rcheck/tests"
[1] "Success downloading file : ./ENCFF002COC.bed.gz"
[1] "Success downloading file : ./ENCFF001VDM.bed.gz"
[1] "Files can be found at /Users/biocbuild/bbs-3.14-bioc/meat/ENCODExplorer.Rcheck/tests"
[1] "Success downloading file : Test_dir/ENCFF002COC.bed.gz"
[1] "Success downloading file : Test_dir/ENCFF001VDM.bed.gz"
[1] "Files can be found at /Users/biocbuild/bbs-3.14-bioc/meat/ENCODExplorer.Rcheck/tests"
Results: 9 files, 1 datasets
Results: 9 files, 1 datasets
Results: 16 files, 5 datasets
Results: 16 files, 5 datasets
Results: 16 files, 5 datasets
Results: 9 files, 1 datasets
No result found in encode_df. You can try the <searchEncode> function or set the fuzzy option to TRUE.
Results : 318 files, 11 datasets
Results : 81 files, 23 datasets
Results : 3 files, 1 datasets
Results : 318 files, 11 datasets
Results : 338 files, 53 datasets
Results : 228 files, 8 datasets
results : 0
Timing stopped at: 0 0 0
Error in checkTrue(expr = !is.null(res$accession), msg = "res should be get an accession entry") : 
  Test not TRUE
res should be get an accession entry
In addition: Warning message:
Package 'ENCODExplorer' is deprecated and will be removed from
  Bioconductor version 3.15 
Results : 58 files, 3 datasets
Found the following output_type: peaks and background as input for IDR, conservative IDR thresholded peaks, optimal IDR thresholded peaks
Selecting optimal idr thresholded peaks. To choose another output_type, specify it in the 'output_type', argument or set use_interactive to TRUE.
[1] "Success downloading file : ./ENCFF356LIU.bed.gz"
[1] "Success downloading file : ./ENCFF023RJC.bed.gz"
[1] "Success downloading file : ./ENCFF960ZGP.bed.gz"
[1] "Files can be found at /Users/biocbuild/bbs-3.14-bioc/meat/ENCODExplorer.Rcheck/tests"
An object of class ENCODEBindingConsensus.
Summarizing 3 ENCODE files into 1 categories.

Metadata:
  treatment treatment_amount treatment_amount_unit treatment_duration
a      <NA>               NA                  <NA>                 NA
  treatment_duration_unit    split_group
a                    <NA> NA;NA;NA;NA;NA

Consensus regions:
GRangesList object of length 1:
$a
GRanges object with 31922 ranges and 0 metadata columns:
                        seqnames        ranges strand
                           <Rle>     <IRanges>  <Rle>
      [1]                   chr3 354378-354727      *
      [2]                   chr3 468197-468546      *
      [3]                   chr3 481714-482063      *
      [4]                   chr3 632583-632932      *
      [5]                   chr3 902188-902537      *
      ...                    ...           ...    ...
  [31918]       chrUn_GL000219v1   40145-40494      *
  [31919]       chrUn_GL000219v1  99577-100139      *
  [31920]       chrUn_GL000219v1 125366-125738      *
  [31921] chr17_GL000205v2_ran..   56276-56625      *
  [31922] chr1_KI270714v1_random   35674-36023      *
  -------
  seqinfo: 30 sequences from an unspecified genome; no seqlengths

Results : 58 files, 3 datasets
Found the following output_type: peaks and background as input for IDR, conservative IDR thresholded peaks, optimal IDR thresholded peaks
Selecting optimal idr thresholded peaks. To choose another output_type, specify it in the 'output_type', argument or set use_interactive to TRUE.
[1] "Success downloading file : ./ENCFF356LIU.bed.gz"
[1] "Success downloading file : ./ENCFF023RJC.bed.gz"
[1] "Success downloading file : ./ENCFF960ZGP.bed.gz"
[1] "Files can be found at /Users/biocbuild/bbs-3.14-bioc/meat/ENCODExplorer.Rcheck/tests"
Results : 58 files, 3 datasets
Found the following output_type: peaks and background as input for IDR, conservative IDR thresholded peaks, optimal IDR thresholded peaks
Selecting optimal idr thresholded peaks. To choose another output_type, specify it in the 'output_type', argument or set use_interactive to TRUE.
[1] "Success downloading file : ./ENCFF356LIU.bed.gz"
[1] "Success downloading file : ./ENCFF023RJC.bed.gz"
[1] "Success downloading file : ./ENCFF960ZGP.bed.gz"
[1] "Files can be found at /Users/biocbuild/bbs-3.14-bioc/meat/ENCODExplorer.Rcheck/tests"
Results : 126 files, 36 datasets
Found the following assembly: GRCh38, hg19
Selecting GRCh38. To choose another assembly, specify it in the 'assembly', argument or set use_interactive to TRUE.
Found the following assay: total RNA-seq, polyA plus RNA-seq, RAMPAGE, small RNA-seq, scRNA-seq, CAGE, polyA minus RNA-seq, icSHAPE, microRNA-seq
Selecting total RNA-seq. To choose another assay, specify it in the 'assay', argument or set use_interactive to TRUE.
[1] "Success downloading file : ./ENCFF783VBA.tsv"
[1] "Success downloading file : ./ENCFF906LSJ.tsv"
[1] "Success downloading file : ./ENCFF418FIT.tsv"
[1] "Success downloading file : ./ENCFF306TLL.tsv"
[1] "Success downloading file : ./ENCFF781YWT.tsv"
[1] "Success downloading file : ./ENCFF680ZFZ.tsv"
[1] "Files can be found at /Users/biocbuild/bbs-3.14-bioc/meat/ENCODExplorer.Rcheck/tests"
An object of class ENCODEExpressionSummary.
Summarizing 6 ENCODE files into 3 categories.

Metadata:
                                                                                                                                                                                                                                                                dataset_description
a The libraries contained in this experiment come from independent growths of cell line GM12878.  They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.  These data were collected as part of the RNA Evaluation Study.
b                                                                                                                                                                                                                                   RNA Evaluation Gm12878 Long Total from Graveley
c                                        The libraries contained in this experiment come from the nucleolar fraction of independent growths of cell line GM12878. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
  treatment treatment_amount treatment_amount_unit treatment_duration
a      <NA>               NA                  <NA>                 NA
b      <NA>               NA                  <NA>                 NA
c      <NA>               NA                  <NA>                 NA
  treatment_duration_unit
a                    <NA>
b                    <NA>
c                    <NA>
                                                                                                                                                                                                                                                                                       split_group
a The libraries contained in this experiment come from independent growths of cell line GM12878.  They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.  These data were collected as part of the RNA Evaluation Study.;NA;NA;NA;NA;NA
b                                                                                                                                                                                                                                   RNA Evaluation Gm12878 Long Total from Graveley;NA;NA;NA;NA;NA
c                                        The libraries contained in this experiment come from the nucleolar fraction of independent growths of cell line GM12878. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.;NA;NA;NA;NA;NA

Sumarizing 61471 gene expression levels.
Results : 126 files, 36 datasets
Found the following assembly: GRCh38, hg19
Selecting GRCh38. To choose another assembly, specify it in the 'assembly', argument or set use_interactive to TRUE.
Found the following assay: total RNA-seq, polyA plus RNA-seq, RAMPAGE, small RNA-seq, scRNA-seq, CAGE, polyA minus RNA-seq, icSHAPE, microRNA-seq
Selecting total RNA-seq. To choose another assay, specify it in the 'assay', argument or set use_interactive to TRUE.
[1] "Success downloading file : ./ENCFF783VBA.tsv"
[1] "Success downloading file : ./ENCFF906LSJ.tsv"
[1] "Success downloading file : ./ENCFF418FIT.tsv"
[1] "Success downloading file : ./ENCFF306TLL.tsv"
[1] "Success downloading file : ./ENCFF781YWT.tsv"
[1] "Success downloading file : ./ENCFF680ZFZ.tsv"
[1] "Files can be found at /Users/biocbuild/bbs-3.14-bioc/meat/ENCODExplorer.Rcheck/tests"
Results : 126 files, 36 datasets
Found the following assembly: GRCh38, hg19
Selecting GRCh38. To choose another assembly, specify it in the 'assembly', argument or set use_interactive to TRUE.
Found the following assay: total RNA-seq, polyA plus RNA-seq, RAMPAGE, small RNA-seq, scRNA-seq, CAGE, polyA minus RNA-seq, icSHAPE, microRNA-seq
Selecting total RNA-seq. To choose another assay, specify it in the 'assay', argument or set use_interactive to TRUE.
[1] "Success downloading file : ./ENCFF783VBA.tsv"
[1] "Success downloading file : ./ENCFF906LSJ.tsv"
[1] "Success downloading file : ./ENCFF418FIT.tsv"
[1] "Success downloading file : ./ENCFF306TLL.tsv"
[1] "Success downloading file : ./ENCFF781YWT.tsv"
[1] "Success downloading file : ./ENCFF680ZFZ.tsv"
[1] "Files can be found at /Users/biocbuild/bbs-3.14-bioc/meat/ENCODExplorer.Rcheck/tests"


RUNIT TEST PROTOCOL -- Tue Nov 30 16:21:19 2021 
*********************************************** 
Number of test functions: 28 
Number of errors: 0 
Number of failures: 1 

 
1 Test Suite : 
ENCODExplorer RUnit Tests - 28 test functions, 0 errors, 1 failure
FAILURE in test.ret_content: Error in checkTrue(expr = !is.null(res$accession), msg = "res should be get an accession entry") : 
  Test not TRUE
res should be get an accession entry

Test files with failing tests

   test_search.R 
     test.ret_content 


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

Example timings

ENCODExplorer.Rcheck/ENCODExplorer-Ex.timings

nameusersystemelapsed
ENCODEBindingConsensus-class40.125 1.02846.672
ENCODEExpressionSummary-class 6.036 3.07915.036
ENCODESummary-class2.7760.0902.867
buildConsensusPeaks 3.577 0.24813.817
buildExpressionSummary 8.069 0.56229.366
createDesign0.1130.0110.128
downloadEncode0.0400.0070.046
fuzzySearch0.0430.0060.048
get_encode_df0.0010.0000.000
get_encode_df_demo0.0390.0050.044
get_encode_df_full63.771 1.00265.518
queryConsensusPeaks7.0170.0757.094
queryEncode0.0580.0150.073
queryEncodeGeneric0.2450.0120.257
queryExpressionGeneric3.1990.0963.297
queryGeneExpression4.2170.1094.328
queryTranscriptExpression 7.515 0.50516.209
searchEncode0.1020.0171.466
searchToquery0.0830.0091.296
shinyEncode0.0010.0000.000