R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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(): 2021-10-20
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 C:/Users/biocbuild/bbs-3.14-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-3.14-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-3.14-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
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 C:/Users/biocbuild/bbs-3.14-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-3.14-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-3.14-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-3.14-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-3.14-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-3.14-bioc/meat/ENCODExplorer.Rcheck/tests_i386"


RUNIT TEST PROTOCOL -- Tue Apr 12 19:24:24 2022 
*********************************************** 
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

R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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(): 2021-10-20
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 C:/Users/biocbuild/bbs-3.14-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-3.14-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-3.14-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
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 C:/Users/biocbuild/bbs-3.14-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-3.14-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-3.14-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-3.14-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-3.14-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-3.14-bioc/meat/ENCODExplorer.Rcheck/tests_x64"


RUNIT TEST PROTOCOL -- Tue Apr 12 19:26:25 2022 
*********************************************** 
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