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CHECK report for ENCODExplorer on merida1

This page was generated on 2020-04-15 12:41:54 -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: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ENCODExplorer.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ENCODExplorer_2.12.1.tar.gz
StartedAt: 2020-04-15 02:05:01 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 02:14:41 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 580.3 seconds
RetCode: 0
Status:  OK 
CheckDir: ENCODExplorer.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ENCODExplorer.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ENCODExplorer_2.12.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/ENCODExplorer.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ENCODExplorer/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ENCODExplorer’ version ‘2.12.1’
* 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 for sufficient/correct file permissions ... 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
* 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 ... OK
Examples with CPU or elapsed time > 5s
                                user system elapsed
get_encode_df_full            61.802  2.478  65.022
ENCODEBindingConsensus-class  46.800  4.225  57.015
ENCODEExpressionSummary-class 10.527  2.771  14.776
queryTranscriptExpression      9.146  2.243  15.460
buildExpressionSummary         8.817  2.448  16.645
queryGeneExpression            7.136  1.207   6.606
queryExpressionGeneric         5.370  1.862   4.634
buildConsensusPeaks            4.682  1.615  12.271
ENCODESummary-class            5.057  0.992   3.318
queryConsensusPeaks            3.710  1.978   3.041
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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
  ‘/Users/biocbuild/bbs-3.10-bioc/meat/ENCODExplorer.Rcheck/00check.log’
for details.



Installation output

ENCODExplorer.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘ENCODExplorer’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ENCODExplorer)

Tests output

ENCODExplorer.Rcheck/tests/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-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> #Run all tests in the ENCODExplorer package
> BiocGenerics:::testPackage("ENCODExplorer")
Using temporary cache /tmp/Rtmp6pnweF/BiocFileCache
snapshotDate(): 2019-10-29
Using temporary cache /tmp/Rtmp6pnweF/BiocFileCache
Using temporary cache /tmp/Rtmp6pnweF/BiocFileCache
Using temporary cache /tmp/Rtmp6pnweF/BiocFileCache
Using temporary cache /tmp/Rtmp6pnweF/BiocFileCache
downloading 1 resources
retrieving 1 resource
Using temporary cache /tmp/Rtmp6pnweF/BiocFileCache
loading from cache
Using temporary cache /tmp/Rtmp6pnweF/BiocFileCache
Using temporary cache /tmp/Rtmp6pnweF/BiocFileCache
Using temporary cache /tmp/Rtmp6pnweF/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 /Users/biocbuild/bbs-3.10-bioc/meat/ENCODExplorer.Rcheck/tests"
[1] "Success downloading file : ./ENCFF002COC.bed.gz"
[1] "Success downloading file : ./ENCFF001VDM.bed.gz"
[1] "Files can be found at /Users/biocbuild/bbs-3.10-bioc/meat/ENCODExplorer.Rcheck/tests"
[1] "Success downloading file : Test_dir/ENCFF002COC.bed.gz"
[1] "Success downloading file : Test_dir/ENCFF001VDM.bed.gz"
[1] "Files can be found at /Users/biocbuild/bbs-3.10-bioc/meat/ENCODExplorer.Rcheck/tests"
Results: 9 files, 1 datasets
Results: 9 files, 1 datasets
Results: 16 files, 5 datasets
Results: 16 files, 5 datasets
Results: 16 files, 5 datasets
Results: 9 files, 1 datasets
No result found in encode_df. You can try the <searchEncode> function or set the fuzzy option to TRUE.
Results : 318 files, 11 datasets
Results : 81 files, 23 datasets
Results : 3 files, 1 datasets
Results : 318 files, 11 datasets
Results : 338 files, 53 datasets
Results : 228 files, 8 datasets
results : 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 /Users/biocbuild/bbs-3.10-bioc/meat/ENCODExplorer.Rcheck/tests"
An object of class ENCODEBindingConsensus.
Summarizing 3 ENCODE files into 1 categories.

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

Consensus regions:
GRangesList object of length 1:
$a
GRanges object with 31922 ranges and 0 metadata columns:
                         seqnames        ranges strand
                            <Rle>     <IRanges>  <Rle>
      [1]                    chr3 354378-354727      *
      [2]                    chr3 468197-468546      *
      [3]                    chr3 481714-482063      *
      [4]                    chr3 632583-632932      *
      [5]                    chr3 902188-902537      *
      ...                     ...           ...    ...
  [31918]        chrUn_GL000219v1   40145-40494      *
  [31919]        chrUn_GL000219v1  99577-100139      *
  [31920]        chrUn_GL000219v1 125366-125738      *
  [31921] chr17_GL000205v2_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 /Users/biocbuild/bbs-3.10-bioc/meat/ENCODExplorer.Rcheck/tests"
Results : 58 files, 3 datasets
Found the following output_type: peaks and background as input for IDR, conservative IDR thresholded peaks, optimal IDR thresholded peaks
Selecting optimal idr thresholded peaks. To choose another output_type, specify it in the 'output_type', argument or set use_interactive to TRUE.
[1] "Success downloading file : ./ENCFF356LIU.bed.gz"
[1] "Success downloading file : ./ENCFF023RJC.bed.gz"
[1] "Success downloading file : ./ENCFF960ZGP.bed.gz"
[1] "Files can be found at /Users/biocbuild/bbs-3.10-bioc/meat/ENCODExplorer.Rcheck/tests"
Results : 126 files, 36 datasets
Found the following assembly: GRCh38, hg19
Selecting GRCh38. To choose another assembly, specify it in the 'assembly', argument or set use_interactive to TRUE.
Found the following assay: total RNA-seq, polyA plus RNA-seq, RAMPAGE, small RNA-seq, scRNA-seq, CAGE, polyA minus RNA-seq, icSHAPE, microRNA-seq
Selecting total RNA-seq. To choose another assay, specify it in the 'assay', argument or set use_interactive to TRUE.
[1] "Success downloading file : ./ENCFF783VBA.tsv"
[1] "Success downloading file : ./ENCFF906LSJ.tsv"
[1] "Success downloading file : ./ENCFF418FIT.tsv"
[1] "Success downloading file : ./ENCFF306TLL.tsv"
[1] "Success downloading file : ./ENCFF781YWT.tsv"
[1] "Success downloading file : ./ENCFF680ZFZ.tsv"
[1] "Files can be found at /Users/biocbuild/bbs-3.10-bioc/meat/ENCODExplorer.Rcheck/tests"
An object of class ENCODEExpressionSummary.
Summarizing 6 ENCODE files into 3 categories.

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

Sumarizing 61471 gene expression levels.
Results : 126 files, 36 datasets
Found the following assembly: GRCh38, hg19
Selecting GRCh38. To choose another assembly, specify it in the 'assembly', argument or set use_interactive to TRUE.
Found the following assay: total RNA-seq, polyA plus RNA-seq, RAMPAGE, small RNA-seq, scRNA-seq, CAGE, polyA minus RNA-seq, icSHAPE, microRNA-seq
Selecting total RNA-seq. To choose another assay, specify it in the 'assay', argument or set use_interactive to TRUE.
[1] "Success downloading file : ./ENCFF783VBA.tsv"
[1] "Success downloading file : ./ENCFF906LSJ.tsv"
[1] "Success downloading file : ./ENCFF418FIT.tsv"
[1] "Success downloading file : ./ENCFF306TLL.tsv"
[1] "Success downloading file : ./ENCFF781YWT.tsv"
[1] "Success downloading file : ./ENCFF680ZFZ.tsv"
[1] "Files can be found at /Users/biocbuild/bbs-3.10-bioc/meat/ENCODExplorer.Rcheck/tests"
Results : 126 files, 36 datasets
Found the following assembly: GRCh38, hg19
Selecting GRCh38. To choose another assembly, specify it in the 'assembly', argument or set use_interactive to TRUE.
Found the following assay: total RNA-seq, polyA plus RNA-seq, RAMPAGE, small RNA-seq, scRNA-seq, CAGE, polyA minus RNA-seq, icSHAPE, microRNA-seq
Selecting total RNA-seq. To choose another assay, specify it in the 'assay', argument or set use_interactive to TRUE.
[1] "Success downloading file : ./ENCFF783VBA.tsv"
[1] "Success downloading file : ./ENCFF906LSJ.tsv"
[1] "Success downloading file : ./ENCFF418FIT.tsv"
[1] "Success downloading file : ./ENCFF306TLL.tsv"
[1] "Success downloading file : ./ENCFF781YWT.tsv"
[1] "Success downloading file : ./ENCFF680ZFZ.tsv"
[1] "Files can be found at /Users/biocbuild/bbs-3.10-bioc/meat/ENCODExplorer.Rcheck/tests"


RUNIT TEST PROTOCOL -- Wed Apr 15 02:14:35 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 
111.667  37.461 132.906 

Example timings

ENCODExplorer.Rcheck/ENCODExplorer-Ex.timings

nameusersystemelapsed
ENCODEBindingConsensus-class46.800 4.22557.015
ENCODEExpressionSummary-class10.527 2.77114.776
ENCODESummary-class5.0570.9923.318
buildConsensusPeaks 4.682 1.61512.271
buildExpressionSummary 8.817 2.44816.645
createDesign1.1581.1200.491
downloadEncode0.1690.1970.052
fuzzySearch0.1760.2150.056
get_encode_df0.0010.0010.000
get_encode_df_demo0.1530.1730.048
get_encode_df_full61.802 2.47865.022
queryConsensusPeaks3.7101.9783.041
queryEncode0.1560.1400.087
queryEncodeGeneric0.9581.2780.307
queryExpressionGeneric5.3701.8624.634
queryGeneExpression7.1361.2076.606
queryTranscriptExpression 9.146 2.24315.460
searchEncode0.0950.0051.163
searchToquery0.0810.0161.013
shinyEncode0.0010.0010.000