Charles Joly Beauparlant
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/ENCODExplorer |
| Branch: RELEASE_3_6 |
| Last Commit: af73611 |
| Last Changed Date: 2017-10-30 12:40:51 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:26:13 -0400 (Thu, 12 Apr 2018).
| Package 420/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| ENCODExplorer 2.4.0 Charles Joly Beauparlant
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: ENCODExplorer |
| Version: 2.4.0 |
| Command: rm -rf ENCODExplorer.buildbin-libdir ENCODExplorer.Rcheck && mkdir ENCODExplorer.buildbin-libdir ENCODExplorer.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ENCODExplorer.buildbin-libdir ENCODExplorer_2.4.0.tar.gz >ENCODExplorer.Rcheck\00install.out 2>&1 && cp ENCODExplorer.Rcheck\00install.out ENCODExplorer-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=ENCODExplorer.buildbin-libdir --install="check:ENCODExplorer-install.out" --force-multiarch --no-vignettes --timings ENCODExplorer_2.4.0.tar.gz |
| StartedAt: 2018-04-11 23:45:17 -0400 (Wed, 11 Apr 2018) |
| EndedAt: 2018-04-11 23:49:24 -0400 (Wed, 11 Apr 2018) |
| EllapsedTime: 247.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ENCODExplorer.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### rm -rf ENCODExplorer.buildbin-libdir ENCODExplorer.Rcheck && mkdir ENCODExplorer.buildbin-libdir ENCODExplorer.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ENCODExplorer.buildbin-libdir ENCODExplorer_2.4.0.tar.gz >ENCODExplorer.Rcheck\00install.out 2>&1 && cp ENCODExplorer.Rcheck\00install.out ENCODExplorer-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=ENCODExplorer.buildbin-libdir --install="check:ENCODExplorer-install.out" --force-multiarch --no-vignettes --timings ENCODExplorer_2.4.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/ENCODExplorer.Rcheck'
* using R version 3.4.4 (2018-03-15)
* 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 '2.4.0'
* 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 ... NOTE
installed size is 73.6Mb
sub-directories of 1Mb or more:
data 23.9Mb
doc 1.5Mb
extdata 48.0Mb
* 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 global function definition for 'data'
createDesign: no visible binding for global variable 'encode_df'
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 global function definition for 'data'
downloadEncode: no visible binding for global variable 'encode_df'
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'
download_single_file: no visible global function definition for
'download.file'
export_ENCODEdb_matrix: no visible binding for global variable
'accession'
fuzzySearch: no visible global function definition for 'data'
queryEncode: no visible global function definition for 'data'
queryEncode: no visible binding for global variable 'encode_df'
searchToquery: no visible global function definition for 'data'
shinyEncode: no visible binding for global variable 'ui'
shinyEncode: no visible binding for global variable 'server'
step11: no visible binding for global variable 'submitted_by'
step3: no visible binding for global variable 'project'
step3: no visible binding for global variable 'platform'
step3: no visible binding for global variable 'lab'
step4: no visible binding for global variable
'biological_replicate_number'
step4: no visible binding for global variable 'replicate_library'
step4: no visible binding for global variable 'replicate_antibody'
step4: no visible binding for global variable 'antibody_target'
step4: no visible binding for global variable
'antibody_characterization'
step4: no visible binding for global variable 'antibody_caption'
step4: no visible binding for global variable
'technical_replicate_number'
step4: no visible binding for global variable 'treatment'
step4: no visible binding for global variable 'nucleic_acid_term'
step6_assay: no visible binding for global variable 'assay'
step6_biosample_name: no visible binding for global variable
'biosample_name'
step6_biosample_type: no visible binding for global variable
'biosample_type'
step6_control: no visible binding for global variable 'controls'
step6_date_released: no visible binding for global variable
'date_released'
step6_status: no visible binding for global variable 'status'
step6_target: no visible binding for global variable 'target'
step7: no visible binding for global variable 'organism'
step8: no visible binding for global variable 'investigated_as'
step8: no visible binding for global variable 'target'
step9: no visible binding for global variable 'organism'
Undefined global functions or variables:
. Experiment Value accession antibody_caption
antibody_characterization antibody_target assay
biological_replicate_number biosample_name biosample_type col_name
controls data date_released download.file encode_df file_accession
file_format href investigated_as lab nucleic_acid_term organism
platform project replicate_antibody replicate_library server status
submitted_by target technical_replicate_number treatment ui value
Consider adding
importFrom("utils", "data", "download.file")
to your NAMESPACE file.
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... NOTE
Note: found 771 marked UTF-8 strings
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
createDesign 5.48 0.36 5.85
searchToquery 3.25 0.27 5.03
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
createDesign 6.43 0.33 6.81
* 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: 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.6-bioc/meat/ENCODExplorer.Rcheck/00check.log'
for details.
ENCODExplorer.Rcheck/00install.out
install for i386
* installing *source* package 'ENCODExplorer' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
converting help for package 'ENCODExplorer'
finding HTML links ... done
ENCODExplorer html
clean_column html
clean_table html
createDesign html
downloadEncode html
download_dt_file html
download_single_file html
encode_df html
export_ENCODEdb_matrix html
extract_table html
fuzzySearch html
get_encode_types html
get_schemas html
prepare_ENCODEdb html
queryEncode html
searchEncode html
searchToquery html
shinyEncode html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'ENCODExplorer' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ENCODExplorer' as ENCODExplorer_2.4.0.zip
* DONE (ENCODExplorer)
In R CMD INSTALL
In R CMD INSTALL
|
ENCODExplorer.Rcheck/tests_i386/runTests.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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")
Attaching package: 'DT'
The following objects are masked from 'package:shiny':
dataTableOutput, renderDataTable
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
Results : 30 files, 10 datasets
results : 4
RUNIT TEST PROTOCOL -- Wed Apr 11 23:48:45 2018
***********************************************
Number of test functions: 31
Number of errors: 0
Number of failures: 0
1 Test Suite :
ENCODExplorer RUnit Tests - 31 test functions, 0 errors, 0 failures
Number of test functions: 31
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
31.29 1.90 35.56
|
ENCODExplorer.Rcheck/tests_x64/runTests.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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")
Attaching package: 'DT'
The following objects are masked from 'package:shiny':
dataTableOutput, renderDataTable
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
Results : 30 files, 10 datasets
results : 4
RUNIT TEST PROTOCOL -- Wed Apr 11 23:49:20 2018
***********************************************
Number of test functions: 31
Number of errors: 0
Number of failures: 0
1 Test Suite :
ENCODExplorer RUnit Tests - 31 test functions, 0 errors, 0 failures
Number of test functions: 31
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
31.09 1.67 34.95
|
|
ENCODExplorer.Rcheck/examples_i386/ENCODExplorer-Ex.timings
|
ENCODExplorer.Rcheck/examples_x64/ENCODExplorer-Ex.timings
|