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CHECK report for ENCODExplorer on tokay1

This page was generated on 2020-04-15 12:24:55 -0400 (Wed, 15 Apr 2020).

Package 518/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ENCODExplorer 2.12.1
Charles Joly Beauparlant
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/ENCODExplorer
Branch: RELEASE_3_10
Last Commit: 303e786
Last Changed Date: 2019-12-12 10:14:57 -0400 (Thu, 12 Dec 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ENCODExplorer
Version: 2.12.1
Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ENCODExplorer.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings ENCODExplorer_2.12.1.tar.gz
StartedAt: 2020-04-15 02:54:41 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 03:19:27 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 1486.4 seconds
RetCode: 0
Status:  OK  
CheckDir: ENCODExplorer.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ENCODExplorer.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings ENCODExplorer_2.12.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/ENCODExplorer.Rcheck'
* using R version 3.6.3 (2020-02-29)
* 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 '2.12.1'
* 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 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
clean_column: no visible binding for global variable 'col_name'
clean_column: no visible binding for global variable 'value'
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 col_name controls file_accession
  file_format href server status ui value
* 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 or elapsed time > 5s
                               user system elapsed
get_encode_df_full            57.95   5.57   68.30
ENCODEBindingConsensus-class  39.49   3.20   52.83
ENCODEExpressionSummary-class  5.36   1.00   31.31
buildExpressionSummary         4.58   0.13  126.58
queryTranscriptExpression      4.19   0.32   63.80
buildConsensusPeaks            2.06   0.25   11.37
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                               user system elapsed
get_encode_df_full            68.12   1.60   73.23
ENCODEBindingConsensus-class  29.03   0.89  108.45
buildExpressionSummary         7.44   0.16   70.89
ENCODEExpressionSummary-class  4.39   0.64   35.94
queryTranscriptExpression      4.25   0.27   63.67
buildConsensusPeaks            1.68   0.11   13.12
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.R'
 OK
* 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 NOTE
See
  'C:/Users/biocbuild/bbs-3.10-bioc/meat/ENCODExplorer.Rcheck/00check.log'
for details.



Installation output

ENCODExplorer.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/ENCODExplorer_2.12.1.tar.gz && rm -rf ENCODExplorer.buildbin-libdir && mkdir ENCODExplorer.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ENCODExplorer.buildbin-libdir ENCODExplorer_2.12.1.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL ENCODExplorer_2.12.1.zip && rm ENCODExplorer_2.12.1.tar.gz ENCODExplorer_2.12.1.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  768k  100  768k    0     0  17.7M      0 --:--:-- --:--:-- --:--:-- 19.7M

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  
    finding level-2 HTML links ... done

    ENCODEExpressionSummary-class           html  
    ENCODESummary-class                     html  
    ENCODExplorer                           html  
    GenomicOverlaps-class                   html  
    GenomicOverlaps                         html  
    buildConsensusPeaks                     html  
    buildExpressionSummary                  html  
    choose_interactive_value                html  
    clean_column                            html  
    clean_table                             html  
    combined_regions-GenomicOverlaps-method
                                            html  
    combined_regions-set-GenomicOverlaps-GRanges-method
                                            html  
    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  
    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_2.12.1.zip
* DONE (ENCODExplorer)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'ENCODExplorer' successfully unpacked and MD5 sums checked

Tests output

ENCODExplorer.Rcheck/tests_i386/runTests.Rout


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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")
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\RtmpghvyLS/BiocFileCache
snapshotDate(): 2019-10-29
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\RtmpghvyLS/BiocFileCache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\RtmpghvyLS/BiocFileCache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\RtmpghvyLS/BiocFileCache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\RtmpghvyLS/BiocFileCache
downloading 1 resources
retrieving 1 resource
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\RtmpghvyLS/BiocFileCache
loading from cache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\RtmpghvyLS/BiocFileCache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\RtmpghvyLS/BiocFileCache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\RtmpghvyLS/BiocFileCache
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-3.10-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-3.10-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-3.10-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 : 4
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-3.10-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_random   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-3.10-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-3.10-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-3.10-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-3.10-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-3.10-bioc/meat/ENCODExplorer.Rcheck/tests_i386"


RUNIT TEST PROTOCOL -- Wed Apr 15 03:15:28 2020 
*********************************************** 
Number of test functions: 38 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
ENCODExplorer RUnit Tests - 38 test functions, 0 errors, 0 failures
Number of test functions: 38 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  69.35    5.00  207.39 

ENCODExplorer.Rcheck/tests_x64/runTests.Rout


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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")
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmpmix2az/BiocFileCache
snapshotDate(): 2019-10-29
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmpmix2az/BiocFileCache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmpmix2az/BiocFileCache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmpmix2az/BiocFileCache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmpmix2az/BiocFileCache
downloading 1 resources
retrieving 1 resource
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmpmix2az/BiocFileCache
loading from cache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmpmix2az/BiocFileCache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmpmix2az/BiocFileCache
Using temporary cache C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmpmix2az/BiocFileCache
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-3.10-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-3.10-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-3.10-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 : 4
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-3.10-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_random   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-3.10-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-3.10-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-3.10-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-3.10-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-3.10-bioc/meat/ENCODExplorer.Rcheck/tests_x64"


RUNIT TEST PROTOCOL -- Wed Apr 15 03:19:16 2020 
*********************************************** 
Number of test functions: 38 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
ENCODExplorer RUnit Tests - 38 test functions, 0 errors, 0 failures
Number of test functions: 38 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  97.07    3.48  227.81 

Example timings

ENCODExplorer.Rcheck/examples_i386/ENCODExplorer-Ex.timings

nameusersystemelapsed
ENCODEBindingConsensus-class39.49 3.2052.83
ENCODEExpressionSummary-class 5.36 1.0031.31
ENCODESummary-class2.850.142.98
buildConsensusPeaks 2.06 0.2511.37
buildExpressionSummary 4.58 0.13126.58
createDesign0.430.071.49
downloadEncode0.040.030.06
fuzzySearch0.060.000.06
get_encode_df000
get_encode_df_demo0.050.000.05
get_encode_df_full57.95 5.5768.30
queryConsensusPeaks2.340.142.49
queryEncode0.030.030.06
queryEncodeGeneric0.710.050.75
queryExpressionGeneric4.450.414.87
queryGeneExpression2.340.943.28
queryTranscriptExpression 4.19 0.3263.80
searchEncode0.310.782.17
searchToquery0.070.000.97
shinyEncode000

ENCODExplorer.Rcheck/examples_x64/ENCODExplorer-Ex.timings

nameusersystemelapsed
ENCODEBindingConsensus-class 29.03 0.89108.45
ENCODEExpressionSummary-class 4.39 0.6435.94
ENCODESummary-class2.520.192.67
buildConsensusPeaks 1.68 0.1113.12
buildExpressionSummary 7.44 0.1670.89
createDesign0.330.030.30
downloadEncode0.030.000.03
fuzzySearch0.030.000.03
get_encode_df000
get_encode_df_demo0.050.000.05
get_encode_df_full68.12 1.6073.23
queryConsensusPeaks3.020.093.11
queryEncode0.050.000.05
queryEncodeGeneric2.510.092.56
queryExpressionGeneric2.250.112.36
queryGeneExpression2.690.142.83
queryTranscriptExpression 4.25 0.2763.67
searchEncode1.730.283.09
searchToquery0.100.001.14
shinyEncode000