| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:04 -0400 (Fri, 15 Oct 2021).
|
To the developers/maintainers of the ENCODExplorer package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ENCODExplorer.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 568/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ENCODExplorer 2.18.0 (landing page) Charles Joly Beauparlant
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | ERROR | OK | |||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | ERROR | OK | |||||||||
| Package: ENCODExplorer |
| Version: 2.18.0 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ENCODExplorer.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings ENCODExplorer_2.18.0.tar.gz |
| StartedAt: 2021-10-14 22:42:34 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 22:57:31 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 897.6 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: ENCODExplorer.Rcheck |
| Warnings: NA |
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ENCODExplorer.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings ENCODExplorer_2.18.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/ENCODExplorer.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ENCODExplorer/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ENCODExplorer' version '2.18.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'ENCODExplorer' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
createDesign: no visible binding for global variable 'file_format'
createDesign: no visible binding for global variable 'status'
createDesign: no visible binding for global variable 'accession'
createDesign: no visible binding for global variable 'controls'
createDesign : get_ctrl_design: no visible binding for global variable
'accession'
createDesign : get_ctrl_design: no visible binding for global variable
'href'
createDesign: no visible global function definition for '.'
createDesign: no visible binding for global variable 'href'
createDesign: no visible binding for global variable 'Experiment'
createDesign: no visible binding for global variable 'Value'
downloadEncode: no visible binding for global variable 'file_accession'
downloadEncode: no visible binding for global variable 'file_format'
downloadEncode: no visible binding for global variable 'accession'
shinyEncode: no visible binding for global variable 'ui'
shinyEncode: no visible binding for global variable 'server'
Undefined global functions or variables:
. Experiment Value accession controls file_accession file_format href
server status ui
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
get_encode_df_full 58.46 8.48 68.24
ENCODEBindingConsensus-class 33.11 1.92 40.42
queryTranscriptExpression 5.32 1.81 15.72
buildExpressionSummary 6.12 0.14 19.06
ENCODEExpressionSummary-class 4.49 1.05 12.28
buildConsensusPeaks 2.28 0.25 17.84
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
get_encode_df_full 50.28 0.84 51.82
ENCODEBindingConsensus-class 29.64 0.66 37.38
queryTranscriptExpression 5.03 0.41 15.00
buildExpressionSummary 5.12 0.22 18.50
queryConsensusPeaks 5.16 0.01 5.18
ENCODEExpressionSummary-class 3.80 0.42 12.08
buildConsensusPeaks 2.43 0.08 14.58
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R'
ERROR
Running the tests in 'tests/runTests.R' failed.
Last 13 lines of output:
1 Test Suite :
ENCODExplorer RUnit Tests - 28 test functions, 0 errors, 1 failure
FAILURE in test.ret_content: Error in checkTrue(expr = !is.null(res$accession), msg = "res should be get an accession entry") :
Test not TRUE
res should be get an accession entry
Test files with failing tests
test_search.R
test.ret_content
Error in BiocGenerics:::testPackage("ENCODExplorer") :
unit tests failed for package ENCODExplorer
Execution halted
** running tests for arch 'x64' ...
Running 'runTests.R'
ERROR
Running the tests in 'tests/runTests.R' failed.
Last 13 lines of output:
1 Test Suite :
ENCODExplorer RUnit Tests - 28 test functions, 0 errors, 1 failure
FAILURE in test.ret_content: Error in checkTrue(expr = !is.null(res$accession), msg = "res should be get an accession entry") :
Test not TRUE
res should be get an accession entry
Test files with failing tests
test_search.R
test.ret_content
Error in BiocGenerics:::testPackage("ENCODExplorer") :
unit tests failed for package ENCODExplorer
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 ERRORs, 1 NOTE
See
'C:/Users/biocbuild/bbs-3.13-bioc/meat/ENCODExplorer.Rcheck/00check.log'
for details.
ENCODExplorer.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/ENCODExplorer_2.18.0.tar.gz && rm -rf ENCODExplorer.buildbin-libdir && mkdir ENCODExplorer.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ENCODExplorer.buildbin-libdir ENCODExplorer_2.18.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL ENCODExplorer_2.18.0.zip && rm ENCODExplorer_2.18.0.tar.gz ENCODExplorer_2.18.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 763k 100 763k 0 0 1554k 0 --:--:-- --:--:-- --:--:-- 1557k
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
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_2.18.0.zip
* DONE (ENCODExplorer)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'ENCODExplorer' successfully unpacked and MD5 sums checked
|
ENCODExplorer.Rcheck/tests_i386/runTests.Rout.fail
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> #Run all tests in the ENCODExplorer package
> BiocGenerics:::testPackage("ENCODExplorer")
snapshotDate(): 2021-05-18
loading from cache
Results : 2 files, 1 datasets
[1] "Success downloading file : ./ENCFF002COC.bed.gz"
[1] "Success downloading file : ./ENCFF001VDM.bed.gz"
[1] "Files can be found at C:/Users/biocbuild/bbs-3.13-bioc/meat/ENCODExplorer.Rcheck/tests_i386"
[1] "Success downloading file : ./ENCFF002COC.bed.gz"
[1] "Success downloading file : ./ENCFF001VDM.bed.gz"
[1] "Files can be found at C:/Users/biocbuild/bbs-3.13-bioc/meat/ENCODExplorer.Rcheck/tests_i386"
[1] "Success downloading file : Test_dir/ENCFF002COC.bed.gz"
[1] "Success downloading file : Test_dir/ENCFF001VDM.bed.gz"
[1] "Files can be found at C:/Users/biocbuild/bbs-3.13-bioc/meat/ENCODExplorer.Rcheck/tests_i386"
Results: 9 files, 1 datasets
Results: 9 files, 1 datasets
Results: 16 files, 5 datasets
Results: 16 files, 5 datasets
Results: 16 files, 5 datasets
Results: 9 files, 1 datasets
No result found in encode_df. You can try the <searchEncode> function or set the fuzzy option to TRUE.
Results : 318 files, 11 datasets
Results : 81 files, 23 datasets
Results : 3 files, 1 datasets
Results : 318 files, 11 datasets
Results : 338 files, 53 datasets
Results : 228 files, 8 datasets
results : 0
Timing stopped at: 0 0 0
Error in checkTrue(expr = !is.null(res$accession), msg = "res should be get an accession entry") :
Test not TRUE
res should be get an accession entry
Results : 58 files, 3 datasets
Found the following output_type: peaks and background as input for IDR, conservative IDR thresholded peaks, optimal IDR thresholded peaks
Selecting optimal idr thresholded peaks. To choose another output_type, specify it in the 'output_type', argument or set use_interactive to TRUE.
[1] "Success downloading file : ./ENCFF356LIU.bed.gz"
[1] "Success downloading file : ./ENCFF023RJC.bed.gz"
[1] "Success downloading file : ./ENCFF960ZGP.bed.gz"
[1] "Files can be found at C:/Users/biocbuild/bbs-3.13-bioc/meat/ENCODExplorer.Rcheck/tests_i386"
An object of class ENCODEBindingConsensus.
Summarizing 3 ENCODE files into 1 categories.
Metadata:
treatment treatment_amount treatment_amount_unit treatment_duration
a <NA> NA <NA> NA
treatment_duration_unit split_group
a <NA> NA;NA;NA;NA;NA
Consensus regions:
GRangesList object of length 1:
$a
GRanges object with 31922 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chr3 354378-354727 *
[2] chr3 468197-468546 *
[3] chr3 481714-482063 *
[4] chr3 632583-632932 *
[5] chr3 902188-902537 *
... ... ... ...
[31918] chrUn_GL000219v1 40145-40494 *
[31919] chrUn_GL000219v1 99577-100139 *
[31920] chrUn_GL000219v1 125366-125738 *
[31921] chr17_GL000205v2_ran.. 56276-56625 *
[31922] chr1_KI270714v1_random 35674-36023 *
-------
seqinfo: 30 sequences from an unspecified genome; no seqlengths
Results : 58 files, 3 datasets
Found the following output_type: peaks and background as input for IDR, conservative IDR thresholded peaks, optimal IDR thresholded peaks
Selecting optimal idr thresholded peaks. To choose another output_type, specify it in the 'output_type', argument or set use_interactive to TRUE.
[1] "Success downloading file : ./ENCFF356LIU.bed.gz"
[1] "Success downloading file : ./ENCFF023RJC.bed.gz"
[1] "Success downloading file : ./ENCFF960ZGP.bed.gz"
[1] "Files can be found at C:/Users/biocbuild/bbs-3.13-bioc/meat/ENCODExplorer.Rcheck/tests_i386"
Results : 58 files, 3 datasets
Found the following output_type: peaks and background as input for IDR, conservative IDR thresholded peaks, optimal IDR thresholded peaks
Selecting optimal idr thresholded peaks. To choose another output_type, specify it in the 'output_type', argument or set use_interactive to TRUE.
[1] "Success downloading file : ./ENCFF356LIU.bed.gz"
[1] "Success downloading file : ./ENCFF023RJC.bed.gz"
[1] "Success downloading file : ./ENCFF960ZGP.bed.gz"
[1] "Files can be found at C:/Users/biocbuild/bbs-3.13-bioc/meat/ENCODExplorer.Rcheck/tests_i386"
Results : 126 files, 36 datasets
Found the following assembly: GRCh38, hg19
Selecting GRCh38. To choose another assembly, specify it in the 'assembly', argument or set use_interactive to TRUE.
Found the following assay: total RNA-seq, polyA plus RNA-seq, RAMPAGE, small RNA-seq, scRNA-seq, CAGE, polyA minus RNA-seq, icSHAPE, microRNA-seq
Selecting total RNA-seq. To choose another assay, specify it in the 'assay', argument or set use_interactive to TRUE.
[1] "Success downloading file : ./ENCFF783VBA.tsv"
[1] "Success downloading file : ./ENCFF906LSJ.tsv"
[1] "Success downloading file : ./ENCFF418FIT.tsv"
[1] "Success downloading file : ./ENCFF306TLL.tsv"
[1] "Success downloading file : ./ENCFF781YWT.tsv"
[1] "Success downloading file : ./ENCFF680ZFZ.tsv"
[1] "Files can be found at C:/Users/biocbuild/bbs-3.13-bioc/meat/ENCODExplorer.Rcheck/tests_i386"
An object of class ENCODEExpressionSummary.
Summarizing 6 ENCODE files into 3 categories.
Metadata:
dataset_description
a The libraries contained in this experiment come from independent growths of cell line GM12878. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size. These data were collected as part of the RNA Evaluation Study.
b RNA Evaluation Gm12878 Long Total from Graveley
c The libraries contained in this experiment come from the nucleolar fraction of independent growths of cell line GM12878. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
treatment treatment_amount treatment_amount_unit treatment_duration
a <NA> NA <NA> NA
b <NA> NA <NA> NA
c <NA> NA <NA> NA
treatment_duration_unit
a <NA>
b <NA>
c <NA>
split_group
a The libraries contained in this experiment come from independent growths of cell line GM12878. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size. These data were collected as part of the RNA Evaluation Study.;NA;NA;NA;NA;NA
b RNA Evaluation Gm12878 Long Total from Graveley;NA;NA;NA;NA;NA
c The libraries contained in this experiment come from the nucleolar fraction of independent growths of cell line GM12878. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.;NA;NA;NA;NA;NA
Sumarizing 61471 gene expression levels.
Results : 126 files, 36 datasets
Found the following assembly: GRCh38, hg19
Selecting GRCh38. To choose another assembly, specify it in the 'assembly', argument or set use_interactive to TRUE.
Found the following assay: total RNA-seq, polyA plus RNA-seq, RAMPAGE, small RNA-seq, scRNA-seq, CAGE, polyA minus RNA-seq, icSHAPE, microRNA-seq
Selecting total RNA-seq. To choose another assay, specify it in the 'assay', argument or set use_interactive to TRUE.
[1] "Success downloading file : ./ENCFF783VBA.tsv"
[1] "Success downloading file : ./ENCFF906LSJ.tsv"
[1] "Success downloading file : ./ENCFF418FIT.tsv"
[1] "Success downloading file : ./ENCFF306TLL.tsv"
[1] "Success downloading file : ./ENCFF781YWT.tsv"
[1] "Success downloading file : ./ENCFF680ZFZ.tsv"
[1] "Files can be found at C:/Users/biocbuild/bbs-3.13-bioc/meat/ENCODExplorer.Rcheck/tests_i386"
Results : 126 files, 36 datasets
Found the following assembly: GRCh38, hg19
Selecting GRCh38. To choose another assembly, specify it in the 'assembly', argument or set use_interactive to TRUE.
Found the following assay: total RNA-seq, polyA plus RNA-seq, RAMPAGE, small RNA-seq, scRNA-seq, CAGE, polyA minus RNA-seq, icSHAPE, microRNA-seq
Selecting total RNA-seq. To choose another assay, specify it in the 'assay', argument or set use_interactive to TRUE.
[1] "Success downloading file : ./ENCFF783VBA.tsv"
[1] "Success downloading file : ./ENCFF906LSJ.tsv"
[1] "Success downloading file : ./ENCFF418FIT.tsv"
[1] "Success downloading file : ./ENCFF306TLL.tsv"
[1] "Success downloading file : ./ENCFF781YWT.tsv"
[1] "Success downloading file : ./ENCFF680ZFZ.tsv"
[1] "Files can be found at C:/Users/biocbuild/bbs-3.13-bioc/meat/ENCODExplorer.Rcheck/tests_i386"
RUNIT TEST PROTOCOL -- Thu Oct 14 22:55:28 2021
***********************************************
Number of test functions: 28
Number of errors: 0
Number of failures: 1
1 Test Suite :
ENCODExplorer RUnit Tests - 28 test functions, 0 errors, 1 failure
FAILURE in test.ret_content: Error in checkTrue(expr = !is.null(res$accession), msg = "res should be get an accession entry") :
Test not TRUE
res should be get an accession entry
Test files with failing tests
test_search.R
test.ret_content
Error in BiocGenerics:::testPackage("ENCODExplorer") :
unit tests failed for package ENCODExplorer
Execution halted
|
ENCODExplorer.Rcheck/tests_x64/runTests.Rout.fail
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> #Run all tests in the ENCODExplorer package
> BiocGenerics:::testPackage("ENCODExplorer")
snapshotDate(): 2021-05-18
loading from cache
Results : 2 files, 1 datasets
[1] "Success downloading file : ./ENCFF002COC.bed.gz"
[1] "Success downloading file : ./ENCFF001VDM.bed.gz"
[1] "Files can be found at C:/Users/biocbuild/bbs-3.13-bioc/meat/ENCODExplorer.Rcheck/tests_x64"
[1] "Success downloading file : ./ENCFF002COC.bed.gz"
[1] "Success downloading file : ./ENCFF001VDM.bed.gz"
[1] "Files can be found at C:/Users/biocbuild/bbs-3.13-bioc/meat/ENCODExplorer.Rcheck/tests_x64"
[1] "Success downloading file : Test_dir/ENCFF002COC.bed.gz"
[1] "Success downloading file : Test_dir/ENCFF001VDM.bed.gz"
[1] "Files can be found at C:/Users/biocbuild/bbs-3.13-bioc/meat/ENCODExplorer.Rcheck/tests_x64"
Results: 9 files, 1 datasets
Results: 9 files, 1 datasets
Results: 16 files, 5 datasets
Results: 16 files, 5 datasets
Results: 16 files, 5 datasets
Results: 9 files, 1 datasets
No result found in encode_df. You can try the <searchEncode> function or set the fuzzy option to TRUE.
Results : 318 files, 11 datasets
Results : 81 files, 23 datasets
Results : 3 files, 1 datasets
Results : 318 files, 11 datasets
Results : 338 files, 53 datasets
Results : 228 files, 8 datasets
results : 0
Timing stopped at: 0 0 0
Error in checkTrue(expr = !is.null(res$accession), msg = "res should be get an accession entry") :
Test not TRUE
res should be get an accession entry
Results : 58 files, 3 datasets
Found the following output_type: peaks and background as input for IDR, conservative IDR thresholded peaks, optimal IDR thresholded peaks
Selecting optimal idr thresholded peaks. To choose another output_type, specify it in the 'output_type', argument or set use_interactive to TRUE.
[1] "Success downloading file : ./ENCFF356LIU.bed.gz"
[1] "Success downloading file : ./ENCFF023RJC.bed.gz"
[1] "Success downloading file : ./ENCFF960ZGP.bed.gz"
[1] "Files can be found at C:/Users/biocbuild/bbs-3.13-bioc/meat/ENCODExplorer.Rcheck/tests_x64"
An object of class ENCODEBindingConsensus.
Summarizing 3 ENCODE files into 1 categories.
Metadata:
treatment treatment_amount treatment_amount_unit treatment_duration
a <NA> NA <NA> NA
treatment_duration_unit split_group
a <NA> NA;NA;NA;NA;NA
Consensus regions:
GRangesList object of length 1:
$a
GRanges object with 31922 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chr3 354378-354727 *
[2] chr3 468197-468546 *
[3] chr3 481714-482063 *
[4] chr3 632583-632932 *
[5] chr3 902188-902537 *
... ... ... ...
[31918] chrUn_GL000219v1 40145-40494 *
[31919] chrUn_GL000219v1 99577-100139 *
[31920] chrUn_GL000219v1 125366-125738 *
[31921] chr17_GL000205v2_ran.. 56276-56625 *
[31922] chr1_KI270714v1_random 35674-36023 *
-------
seqinfo: 30 sequences from an unspecified genome; no seqlengths
Results : 58 files, 3 datasets
Found the following output_type: peaks and background as input for IDR, conservative IDR thresholded peaks, optimal IDR thresholded peaks
Selecting optimal idr thresholded peaks. To choose another output_type, specify it in the 'output_type', argument or set use_interactive to TRUE.
[1] "Success downloading file : ./ENCFF356LIU.bed.gz"
[1] "Success downloading file : ./ENCFF023RJC.bed.gz"
[1] "Success downloading file : ./ENCFF960ZGP.bed.gz"
[1] "Files can be found at C:/Users/biocbuild/bbs-3.13-bioc/meat/ENCODExplorer.Rcheck/tests_x64"
Results : 58 files, 3 datasets
Found the following output_type: peaks and background as input for IDR, conservative IDR thresholded peaks, optimal IDR thresholded peaks
Selecting optimal idr thresholded peaks. To choose another output_type, specify it in the 'output_type', argument or set use_interactive to TRUE.
[1] "Success downloading file : ./ENCFF356LIU.bed.gz"
[1] "Success downloading file : ./ENCFF023RJC.bed.gz"
[1] "Success downloading file : ./ENCFF960ZGP.bed.gz"
[1] "Files can be found at C:/Users/biocbuild/bbs-3.13-bioc/meat/ENCODExplorer.Rcheck/tests_x64"
Results : 126 files, 36 datasets
Found the following assembly: GRCh38, hg19
Selecting GRCh38. To choose another assembly, specify it in the 'assembly', argument or set use_interactive to TRUE.
Found the following assay: total RNA-seq, polyA plus RNA-seq, RAMPAGE, small RNA-seq, scRNA-seq, CAGE, polyA minus RNA-seq, icSHAPE, microRNA-seq
Selecting total RNA-seq. To choose another assay, specify it in the 'assay', argument or set use_interactive to TRUE.
[1] "Success downloading file : ./ENCFF783VBA.tsv"
[1] "Success downloading file : ./ENCFF906LSJ.tsv"
[1] "Success downloading file : ./ENCFF418FIT.tsv"
[1] "Success downloading file : ./ENCFF306TLL.tsv"
[1] "Success downloading file : ./ENCFF781YWT.tsv"
[1] "Success downloading file : ./ENCFF680ZFZ.tsv"
[1] "Files can be found at C:/Users/biocbuild/bbs-3.13-bioc/meat/ENCODExplorer.Rcheck/tests_x64"
An object of class ENCODEExpressionSummary.
Summarizing 6 ENCODE files into 3 categories.
Metadata:
dataset_description
a The libraries contained in this experiment come from independent growths of cell line GM12878. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size. These data were collected as part of the RNA Evaluation Study.
b RNA Evaluation Gm12878 Long Total from Graveley
c The libraries contained in this experiment come from the nucleolar fraction of independent growths of cell line GM12878. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
treatment treatment_amount treatment_amount_unit treatment_duration
a <NA> NA <NA> NA
b <NA> NA <NA> NA
c <NA> NA <NA> NA
treatment_duration_unit
a <NA>
b <NA>
c <NA>
split_group
a The libraries contained in this experiment come from independent growths of cell line GM12878. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size. These data were collected as part of the RNA Evaluation Study.;NA;NA;NA;NA;NA
b RNA Evaluation Gm12878 Long Total from Graveley;NA;NA;NA;NA;NA
c The libraries contained in this experiment come from the nucleolar fraction of independent growths of cell line GM12878. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.;NA;NA;NA;NA;NA
Sumarizing 61471 gene expression levels.
Results : 126 files, 36 datasets
Found the following assembly: GRCh38, hg19
Selecting GRCh38. To choose another assembly, specify it in the 'assembly', argument or set use_interactive to TRUE.
Found the following assay: total RNA-seq, polyA plus RNA-seq, RAMPAGE, small RNA-seq, scRNA-seq, CAGE, polyA minus RNA-seq, icSHAPE, microRNA-seq
Selecting total RNA-seq. To choose another assay, specify it in the 'assay', argument or set use_interactive to TRUE.
[1] "Success downloading file : ./ENCFF783VBA.tsv"
[1] "Success downloading file : ./ENCFF906LSJ.tsv"
[1] "Success downloading file : ./ENCFF418FIT.tsv"
[1] "Success downloading file : ./ENCFF306TLL.tsv"
[1] "Success downloading file : ./ENCFF781YWT.tsv"
[1] "Success downloading file : ./ENCFF680ZFZ.tsv"
[1] "Files can be found at C:/Users/biocbuild/bbs-3.13-bioc/meat/ENCODExplorer.Rcheck/tests_x64"
Results : 126 files, 36 datasets
Found the following assembly: GRCh38, hg19
Selecting GRCh38. To choose another assembly, specify it in the 'assembly', argument or set use_interactive to TRUE.
Found the following assay: total RNA-seq, polyA plus RNA-seq, RAMPAGE, small RNA-seq, scRNA-seq, CAGE, polyA minus RNA-seq, icSHAPE, microRNA-seq
Selecting total RNA-seq. To choose another assay, specify it in the 'assay', argument or set use_interactive to TRUE.
[1] "Success downloading file : ./ENCFF783VBA.tsv"
[1] "Success downloading file : ./ENCFF906LSJ.tsv"
[1] "Success downloading file : ./ENCFF418FIT.tsv"
[1] "Success downloading file : ./ENCFF306TLL.tsv"
[1] "Success downloading file : ./ENCFF781YWT.tsv"
[1] "Success downloading file : ./ENCFF680ZFZ.tsv"
[1] "Files can be found at C:/Users/biocbuild/bbs-3.13-bioc/meat/ENCODExplorer.Rcheck/tests_x64"
RUNIT TEST PROTOCOL -- Thu Oct 14 22:57:21 2021
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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
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ENCODExplorer.Rcheck/examples_i386/ENCODExplorer-Ex.timings
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ENCODExplorer.Rcheck/examples_x64/ENCODExplorer-Ex.timings
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