Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-07-23 15:06:02 -0400 (Fri, 23 Jul 2021).

CHECK results for ENCODExplorer on tokay2

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 568/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ENCODExplorer 2.18.0  (landing page)
Charles Joly Beauparlant
Snapshot Date: 2021-07-22 04:50:13 -0400 (Thu, 22 Jul 2021)
URL: https://git.bioconductor.org/packages/ENCODExplorer
Branch: RELEASE_3_13
Last Commit: 618ef8e
Last Changed Date: 2021-05-19 12:13:26 -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: ENCODExplorer
Version: 2.18.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ENCODExplorer.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings ENCODExplorer_2.18.0.tar.gz
StartedAt: 2021-07-22 22:55:17 -0400 (Thu, 22 Jul 2021)
EndedAt: 2021-07-22 23:10:05 -0400 (Thu, 22 Jul 2021)
EllapsedTime: 888.4 seconds
RetCode: 1
Status:   ERROR  
CheckDir: ENCODExplorer.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ENCODExplorer.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings ENCODExplorer_2.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/ENCODExplorer.Rcheck'
* using R version 4.1.0 (2021-05-18)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ENCODExplorer/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ENCODExplorer' version '2.18.0'
* 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 'ENCODExplorer' can be installed ... 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
* 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
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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                               user system elapsed
get_encode_df_full            61.66   6.89   73.02
ENCODEBindingConsensus-class  36.05   2.36   44.42
ENCODEExpressionSummary-class  4.85   0.86   11.03
queryTranscriptExpression      4.66   1.05   14.96
buildExpressionSummary         5.09   0.16   17.06
queryExpressionGeneric         4.58   0.50    5.08
buildConsensusPeaks            2.62   0.15   15.33
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                               user system elapsed
get_encode_df_full            50.41   0.69   51.52
ENCODEBindingConsensus-class  31.06   0.70   36.54
queryTranscriptExpression      5.22   0.17   12.99
queryConsensusPeaks            5.27   0.11    5.37
buildExpressionSummary         5.10   0.19   17.26
ENCODEExpressionSummary-class  4.20   0.72   11.30
buildConsensusPeaks            2.25   0.12   12.39
* 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:
  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
** running tests for arch 'x64' ...
  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: 2 ERRORs, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/ENCODExplorer.Rcheck/00check.log'
for details.


Installation output

ENCODExplorer.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/ENCODExplorer_2.18.0.tar.gz && rm -rf ENCODExplorer.buildbin-libdir && mkdir ENCODExplorer.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ENCODExplorer.buildbin-libdir ENCODExplorer_2.18.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL ENCODExplorer_2.18.0.zip && rm ENCODExplorer_2.18.0.tar.gz ENCODExplorer_2.18.0.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
100  763k  100  763k    0     0  2521k      0 --:--:-- --:--:-- --:--:-- 2527k

install for i386

* installing *source* package 'ENCODExplorer' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'ENCODExplorer'
    finding HTML links ... done
    ENCODEBindingConsensus-class            html  
REDIRECT:topic	 names<-,ENCODEBindingConsensus,character-method -> ENCODEBindingConsensus-class.html [ FAIL ]
    finding level-2 HTML links ... done

    ENCODEExpressionSummary-class           html  
REDIRECT:topic	 names<-,ENCODEExpressionSummary,character-method -> ENCODEExpressionSummary-class.html [ FAIL ]
    ENCODESummary-class                     html  
REDIRECT:topic	 names<-,ENCODESummary,character-method -> ENCODESummary-class.html [ FAIL ]
    ENCODExplorer                           html  
    GenomicOverlaps-class                   html  
    GenomicOverlaps                         html  
    buildConsensusPeaks                     html  
    buildExpressionSummary                  html  
    choose_interactive_value                html  
    combined_regions-GenomicOverlaps-method
                                            html  
    combined_regions-set-GenomicOverlaps-GRanges-method
                                            html  
REDIRECT:topic	 combined_regions<-,GenomicOverlaps,GRanges-method -> combined_regions-set-GenomicOverlaps-GRanges-method.html [ FAIL ]
    consensus_indices                       html  
    consensus_regions                       html  
    createDesign                            html  
    downloadEncode                          html  
    download_dt_file                        html  
    download_single_file                    html  
    fuzzySearch                             html  
    get_encode_df                           html  
    get_encode_df_demo                      html  
    get_encode_df_full                      html  
    initial_regions-GenomicOverlaps-method
                                            html  
    intersect_indices                       html  
    intersect_matrix                        html  
    intersect_regions                       html  
    length-GenomicOverlaps-method           html  
    names-GenomicOverlaps-method            html  
    names-set-GenomicOverlaps-character-method
                                            html  
REDIRECT:topic	 names<-,GenomicOverlaps,character-method -> names-set-GenomicOverlaps-character-method.html [ FAIL ]
    pairwise_overlap                        html  
    queryConsensusPeaks                     html  
    queryEncode                             html  
    queryEncodeGeneric                      html  
    queryExpressionGeneric                  html  
    queryGeneExpression                     html  
    queryTranscriptExpression               html  
    searchEncode                            html  
    searchToquery                           html  
    shinyEncode                             html  
    split_by_metadata                       html  
    union_indices                           html  
    union_regions                           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 'ENCODExplorer' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ENCODExplorer' as ENCODExplorer_2.18.0.zip
* DONE (ENCODExplorer)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'ENCODExplorer' successfully unpacked and MD5 sums checked

Tests output

ENCODExplorer.Rcheck/tests_i386/runTests.Rout.fail


R version 4.1.0 (2021-05-18) -- "Camp Pontanezen"
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 ENCODExplorer package
> BiocGenerics:::testPackage("ENCODExplorer")
snapshotDate(): 2021-05-18
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 C:/Users/biocbuild/bbs-3.13-bioc/meat/ENCODExplorer.Rcheck/tests_i386"
[1] "Success downloading file : ./ENCFF002COC.bed.gz"
[1] "Success downloading file : ./ENCFF001VDM.bed.gz"
[1] "Files can be found at C:/Users/biocbuild/bbs-3.13-bioc/meat/ENCODExplorer.Rcheck/tests_i386"
[1] "Success downloading file : Test_dir/ENCFF002COC.bed.gz"
[1] "Success downloading file : Test_dir/ENCFF001VDM.bed.gz"
[1] "Files can be found at C:/Users/biocbuild/bbs-3.13-bioc/meat/ENCODExplorer.Rcheck/tests_i386"
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
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 C:/Users/biocbuild/bbs-3.13-bioc/meat/ENCODExplorer.Rcheck/tests_i386"
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 C:/Users/biocbuild/bbs-3.13-bioc/meat/ENCODExplorer.Rcheck/tests_i386"
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 C:/Users/biocbuild/bbs-3.13-bioc/meat/ENCODExplorer.Rcheck/tests_i386"
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 C:/Users/biocbuild/bbs-3.13-bioc/meat/ENCODExplorer.Rcheck/tests_i386"
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 C:/Users/biocbuild/bbs-3.13-bioc/meat/ENCODExplorer.Rcheck/tests_i386"
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 C:/Users/biocbuild/bbs-3.13-bioc/meat/ENCODExplorer.Rcheck/tests_i386"


RUNIT TEST PROTOCOL -- Thu Jul 22 23:08:09 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

ENCODExplorer.Rcheck/tests_x64/runTests.Rout.fail


R version 4.1.0 (2021-05-18) -- "Camp Pontanezen"
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 ENCODExplorer package
> BiocGenerics:::testPackage("ENCODExplorer")
snapshotDate(): 2021-05-18
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 C:/Users/biocbuild/bbs-3.13-bioc/meat/ENCODExplorer.Rcheck/tests_x64"
[1] "Success downloading file : ./ENCFF002COC.bed.gz"
[1] "Success downloading file : ./ENCFF001VDM.bed.gz"
[1] "Files can be found at C:/Users/biocbuild/bbs-3.13-bioc/meat/ENCODExplorer.Rcheck/tests_x64"
[1] "Success downloading file : Test_dir/ENCFF002COC.bed.gz"
[1] "Success downloading file : Test_dir/ENCFF001VDM.bed.gz"
[1] "Files can be found at C:/Users/biocbuild/bbs-3.13-bioc/meat/ENCODExplorer.Rcheck/tests_x64"
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
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 C:/Users/biocbuild/bbs-3.13-bioc/meat/ENCODExplorer.Rcheck/tests_x64"
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 C:/Users/biocbuild/bbs-3.13-bioc/meat/ENCODExplorer.Rcheck/tests_x64"
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 C:/Users/biocbuild/bbs-3.13-bioc/meat/ENCODExplorer.Rcheck/tests_x64"
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 C:/Users/biocbuild/bbs-3.13-bioc/meat/ENCODExplorer.Rcheck/tests_x64"
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 C:/Users/biocbuild/bbs-3.13-bioc/meat/ENCODExplorer.Rcheck/tests_x64"
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 C:/Users/biocbuild/bbs-3.13-bioc/meat/ENCODExplorer.Rcheck/tests_x64"


RUNIT TEST PROTOCOL -- Thu Jul 22 23:09:55 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/examples_i386/ENCODExplorer-Ex.timings

nameusersystemelapsed
ENCODEBindingConsensus-class36.05 2.3644.42
ENCODEExpressionSummary-class 4.85 0.8611.03
ENCODESummary-class2.070.202.26
buildConsensusPeaks 2.62 0.1515.33
buildExpressionSummary 5.09 0.1617.06
createDesign0.180.000.72
downloadEncode0.040.020.06
fuzzySearch0.070.000.07
get_encode_df000
get_encode_df_demo0.040.000.04
get_encode_df_full61.66 6.8973.02
queryConsensusPeaks2.550.152.70
queryEncode0.030.030.06
queryEncodeGeneric0.230.040.27
queryExpressionGeneric4.580.505.08
queryGeneExpression1.861.433.29
queryTranscriptExpression 4.66 1.0514.96
searchEncode0.620.593.14
searchToquery0.060.021.36
shinyEncode000

ENCODExplorer.Rcheck/examples_x64/ENCODExplorer-Ex.timings

nameusersystemelapsed
ENCODEBindingConsensus-class31.06 0.7036.54
ENCODEExpressionSummary-class 4.20 0.7211.30
ENCODESummary-class2.170.112.28
buildConsensusPeaks 2.25 0.1212.39
buildExpressionSummary 5.10 0.1917.26
createDesign0.110.000.11
downloadEncode0.030.000.03
fuzzySearch0.030.000.04
get_encode_df000
get_encode_df_demo0.030.000.03
get_encode_df_full50.41 0.6951.52
queryConsensusPeaks5.270.115.37
queryEncode0.030.000.05
queryEncodeGeneric0.260.030.30
queryExpressionGeneric2.830.092.92
queryGeneExpression1.530.051.58
queryTranscriptExpression 5.22 0.1712.99
searchEncode3.120.164.70
searchToquery0.060.011.53
shinyEncode000