Charles Joly Beauparlant
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/ENCODExplorer |
| Branch: RELEASE_3_7 |
| Last Commit: 1f7053f |
| Last Changed Date: 2018-04-30 10:35:36 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:40:29 -0400 (Wed, 17 Oct 2018).
| Package 444/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| ENCODExplorer 2.6.0 Charles Joly Beauparlant
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: ENCODExplorer |
| Version: 2.6.0 |
| Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ENCODExplorer.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings ENCODExplorer_2.6.0.tar.gz |
| StartedAt: 2018-10-17 01:48:12 -0400 (Wed, 17 Oct 2018) |
| EndedAt: 2018-10-17 01:51:11 -0400 (Wed, 17 Oct 2018) |
| EllapsedTime: 178.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ENCODExplorer.Rcheck |
| Warnings: 0 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ENCODExplorer.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings ENCODExplorer_2.6.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/ENCODExplorer.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* 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 '2.6.0'
* 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 72.2Mb
sub-directories of 1Mb or more:
data 23.9Mb
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 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
createDesign 4.74 0.50 5.24
searchToquery 3.86 0.25 5.75
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
searchToquery 5.34 0.22 7.15
* 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-3.7-bioc/meat/ENCODExplorer.Rcheck/00check.log'
for details.
ENCODExplorer.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/ENCODExplorer_2.6.0.tar.gz && rm -rf ENCODExplorer.buildbin-libdir && mkdir ENCODExplorer.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ENCODExplorer.buildbin-libdir ENCODExplorer_2.6.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL ENCODExplorer_2.6.0.zip && rm ENCODExplorer_2.6.0.tar.gz ENCODExplorer_2.6.0.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
99 66.2M 99 66.1M 0 0 98.6M 0 --:--:-- --:--:-- --:--:-- 99.6M
100 66.2M 100 66.2M 0 0 98.6M 0 --:--:-- --:--:-- --:--:-- 99.6M
install for i386
* installing *source* package 'ENCODExplorer' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare 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_2.6.0.zip
* DONE (ENCODExplorer)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'ENCODExplorer' successfully unpacked and MD5 sums checked
In R CMD INSTALL
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ENCODExplorer.Rcheck/tests_i386/runTests.Rout
R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
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 Oct 17 01:50:36 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
20.68 1.95 25.46
|
ENCODExplorer.Rcheck/tests_x64/runTests.Rout
R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
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 Oct 17 01:51:05 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
23.70 2.07 28.98
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ENCODExplorer.Rcheck/examples_i386/ENCODExplorer-Ex.timings
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ENCODExplorer.Rcheck/examples_x64/ENCODExplorer-Ex.timings
|