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CHECK report for brainflowprobes on tokay1

This page was generated on 2020-08-10 12:27:46 -0400 (Mon, 10 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE brainflowprobes PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 192/1882HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
brainflowprobes 1.3.1
Amanda Price
Snapshot Date: 2020-08-09 14:51:29 -0400 (Sun, 09 Aug 2020)
URL: https://git.bioconductor.org/packages/brainflowprobes
Branch: master
Last Commit: 8556164
Last Changed Date: 2020-05-27 01:09:22 -0400 (Wed, 27 May 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  ERROR 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: brainflowprobes
Version: 1.3.1
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:brainflowprobes.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings brainflowprobes_1.3.1.tar.gz
StartedAt: 2020-08-10 05:58:53 -0400 (Mon, 10 Aug 2020)
EndedAt: 2020-08-10 06:14:33 -0400 (Mon, 10 Aug 2020)
EllapsedTime: 940.3 seconds
RetCode: 0
Status:  OK  
CheckDir: brainflowprobes.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:brainflowprobes.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings brainflowprobes_1.3.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/brainflowprobes.Rcheck'
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'brainflowprobes/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'brainflowprobes' version '1.3.1'
* package encoding: UTF-8
* 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 'brainflowprobes' 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 ... OK
* 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 ... OK
* checking data for ASCII and uncompressed saves ... 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
region_info            51.64   5.71   58.34
plot_coverage          41.69   1.12   43.95
four_panels            26.73   4.63   34.56
get_nearest_annotation 28.94   1.75   31.05
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
region_info            51.76   1.49   54.32
plot_coverage          33.44   0.84   37.51
get_nearest_annotation 22.05   0.58   23.05
four_panels            18.83   1.24   24.61
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.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: OK


Installation output

brainflowprobes.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/brainflowprobes_1.3.1.tar.gz && rm -rf brainflowprobes.buildbin-libdir && mkdir brainflowprobes.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=brainflowprobes.buildbin-libdir brainflowprobes_1.3.1.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL brainflowprobes_1.3.1.zip && rm brainflowprobes_1.3.1.tar.gz brainflowprobes_1.3.1.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
 81 1609k   81 1312k    0     0  4568k      0 --:--:-- --:--:-- --:--:-- 4619k
100 1609k  100 1609k    0     0  4208k      0 --:--:-- --:--:-- --:--:-- 4246k

install for i386

* installing *source* package 'brainflowprobes' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
No methods found in package 'IRanges' for request: 'values<-' when loading 'derfinder'
No methods found in package 'IRanges' for request: 'values' when loading 'derfinder'
** help
*** installing help indices
  converting help for package 'brainflowprobes'
    finding HTML links ... done
    brainflowprobes-package                 html  
    brainflowprobes_cov                     html  
    check_pdf                               html  
    four_panels                             html  
    four_panels_example_cov                 html  
    get_nearest_annotation                  html  
    get_region_cov                          html  
    pd                                      html  
    plot_coverage                           html  
    region_info                             html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
No methods found in package 'IRanges' for request: 'values<-' when loading 'derfinder'
No methods found in package 'IRanges' for request: 'values' when loading 'derfinder'
** testing if installed package can be loaded from final location
No methods found in package 'IRanges' for request: 'values<-' when loading 'derfinder'
No methods found in package 'IRanges' for request: 'values' when loading 'derfinder'
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'brainflowprobes' ...
** testing if installed package can be loaded
No methods found in package 'IRanges' for request: 'values<-' when loading 'derfinder'
No methods found in package 'IRanges' for request: 'values' when loading 'derfinder'
* MD5 sums
packaged installation of 'brainflowprobes' as brainflowprobes_1.3.1.zip
* DONE (brainflowprobes)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'brainflowprobes' successfully unpacked and MD5 sums checked

Tests output

brainflowprobes.Rcheck/tests_i386/testthat.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 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.

> library(testthat)
> library(brainflowprobes)
No methods found in package 'IRanges' for request: 'values<-' when loading 'derfinder'
No methods found in package 'IRanges' for request: 'values' when loading 'derfinder'
> 
> test_check("brainflowprobes")
== testthat results  ===========================================================
[ OK: 26 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  58.87    4.90   69.82 

brainflowprobes.Rcheck/tests_x64/testthat.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 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.

> library(testthat)
> library(brainflowprobes)
No methods found in package 'IRanges' for request: 'values<-' when loading 'derfinder'
No methods found in package 'IRanges' for request: 'values' when loading 'derfinder'
> 
> test_check("brainflowprobes")
== testthat results  ===========================================================
[ OK: 26 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  54.34    2.89   62.03 

Example timings

brainflowprobes.Rcheck/examples_i386/brainflowprobes-Ex.timings

nameusersystemelapsed
brainflowprobes_cov0.010.000.01
check_pdf0.100.000.09
four_panels26.73 4.6334.56
four_panels_example_cov000
get_nearest_annotation28.94 1.7531.05
get_region_cov000
pd000
plot_coverage41.69 1.1243.95
region_info51.64 5.7158.34

brainflowprobes.Rcheck/examples_x64/brainflowprobes-Ex.timings

nameusersystemelapsed
brainflowprobes_cov000
check_pdf0.080.010.63
four_panels18.83 1.2424.61
four_panels_example_cov000
get_nearest_annotation22.05 0.5823.05
get_region_cov000
pd000
plot_coverage33.44 0.8437.51
region_info51.76 1.4954.32