Charles Joly Beauparlant
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/ENCODExplorer |
| Branch: RELEASE_3_9 |
| Last Commit: a360412 |
| Last Changed Date: 2019-05-02 11:53:55 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:33:12 -0400 (Wed, 16 Oct 2019).
| Package 497/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| ENCODExplorer 2.10.0 Charles Joly Beauparlant
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | ERROR | skipped | skipped |
| Package: ENCODExplorer |
| Version: 2.10.0 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ENCODExplorer.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings ENCODExplorer_2.10.0.tar.gz |
| StartedAt: 2019-10-16 03:29:48 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 03:37:17 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 449.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ENCODExplorer.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ENCODExplorer.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings ENCODExplorer_2.10.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/ENCODExplorer.Rcheck'
* using R version 3.6.1 (2019-07-05)
* 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 '2.10.0'
* 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 ... NOTE
Package in Depends field not imported from: 'DT'
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* 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'
clean_column: no visible global function definition for 'is'
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 'is'
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 is server status ui value
Consider adding
importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 or elapsed time > 5s
user system elapsed
get_encode_df_full 59.28 5.42 65.63
get_encode_df 31.62 1.21 33.17
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
get_encode_df_full 67.79 1.17 69.25
get_encode_df 26.88 0.66 27.86
queryEncodeGeneric 5.31 0.06 5.33
* 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: 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.9-bioc/meat/ENCODExplorer.Rcheck/00check.log'
for details.
ENCODExplorer.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/ENCODExplorer_2.10.0.tar.gz && rm -rf ENCODExplorer.buildbin-libdir && mkdir ENCODExplorer.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ENCODExplorer.buildbin-libdir ENCODExplorer_2.10.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL ENCODExplorer_2.10.0.zip && rm ENCODExplorer_2.10.0.tar.gz ENCODExplorer_2.10.0.zip
###
##############################################################################
##############################################################################
% 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 745k 100 745k 0 0 10.0M 0 --:--:-- --:--:-- --:--:-- 11.0M
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
ENCODExplorer html
clean_column html
clean_table 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
queryEncode html
queryEncodeGeneric html
searchEncode html
searchToquery html
shinyEncode 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_2.10.0.zip
* DONE (ENCODExplorer)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'ENCODExplorer' successfully unpacked and MD5 sums checked
|
ENCODExplorer.Rcheck/tests_i386/runTests.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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
snapshotDate(): 2019-05-02
downloading 0 resources
loading from cache
'AH69290 : 76036'
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-3.9-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-3.9-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-3.9-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
|
ENCODExplorer.Rcheck/tests_x64/runTests.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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
snapshotDate(): 2019-05-02
downloading 0 resources
loading from cache
'AH69290 : 76036'
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-3.9-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-3.9-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-3.9-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
|
|
ENCODExplorer.Rcheck/examples_i386/ENCODExplorer-Ex.timings
|
ENCODExplorer.Rcheck/examples_x64/ENCODExplorer-Ex.timings
|