Multiple platform build/check report for BioC 3.10 - CHECK report for ENCODExplorer on malbec1

Package: ENCODExplorer

Version: 2.12.1

Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:ENCODExplorer.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings ENCODExplorer_2.12.1.tar.gz

StartedAt: 2020-04-15 03:01:24 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 03:11:41 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 617.2 seconds

RetCode: 0

Status: OK

CheckDir: ENCODExplorer.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:ENCODExplorer.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings ENCODExplorer_2.12.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/ENCODExplorer.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (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            60.220  0.692  61.334
ENCODEBindingConsensus-class  35.064  0.768  43.124
queryTranscriptExpression      9.928  1.020  27.172
queryConsensusPeaks            8.056  0.080   7.396
ENCODEExpressionSummary-class  6.472  1.168  34.020
buildExpressionSummary         6.700  0.620  40.288
buildConsensusPeaks            3.976  0.612  17.194
* 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
  ‘/home/biocbuild/bbs-3.10-bioc/meat/ENCODExplorer.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL ENCODExplorer
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/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)


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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(): 2019-10-29
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 /home/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 /home/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 /home/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 /home/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 /home/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 /home/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 /home/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 /home/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 /home/biocbuild/bbs-3.10-bioc/meat/ENCODExplorer.Rcheck/tests"


RUNIT TEST PROTOCOL -- Wed Apr 15 03:11:37 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 
 96.140   3.236 148.423

name	user	system	elapsed
ENCODEBindingConsensus-class	35.064	0.768	43.124
ENCODEExpressionSummary-class	6.472	1.168	34.020
ENCODESummary-class	3.068	0.024	2.407
buildConsensusPeaks	3.976	0.612	17.194
buildExpressionSummary	6.700	0.620	40.288
createDesign	3.144	0.016	1.162
downloadEncode	0.296	0.000	0.104
fuzzySearch	0.280	0.000	0.086
get_encode_df	0.004	0.000	0.000
get_encode_df_demo	0.028	0.000	0.028
get_encode_df_full	60.220	0.692	61.334
queryConsensusPeaks	8.056	0.080	7.396
queryEncode	0.916	0.016	0.260
queryEncodeGeneric	0.660	0.016	0.243
queryExpressionGeneric	4.284	0.068	4.112
queryGeneExpression	4.216	0.100	4.050
queryTranscriptExpression	9.928	1.020	27.172
searchEncode	1.168	0.016	2.182
searchToquery	0.424	0.020	1.311
shinyEncode	0	0	0

CHECK report for ENCODExplorer on malbec1

Summary

Command output

Installation output

Tests output

Example timings