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CHECK report for philr on tokay1

This page was generated on 2021-05-06 12:32:45 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the philr package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1340/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
philr 1.16.0  (landing page)
Justin Silverman
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/philr
Branch: RELEASE_3_12
Last Commit: 686f4ac
Last Changed Date: 2020-10-27 11:17:22 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: philr
Version: 1.16.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:philr.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings philr_1.16.0.tar.gz
StartedAt: 2021-05-06 05:31:36 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 05:33:32 -0400 (Thu, 06 May 2021)
EllapsedTime: 116.4 seconds
RetCode: 0
Status:   OK   
CheckDir: philr.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:philr.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings philr_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/philr.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'philr/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'philr' version '1.16.0'
* 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 'philr' 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
name.balance: no visible global function definition for 'as'
vote.annotation: no visible global function definition for 'is'
Undefined global functions or variables:
  as is
Consider adding
  importFrom("methods", "as", "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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* 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: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/philr.Rcheck/00check.log'
for details.



Installation output

philr.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/philr_1.16.0.tar.gz && rm -rf philr.buildbin-libdir && mkdir philr.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=philr.buildbin-libdir philr_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL philr_1.16.0.zip && rm philr_1.16.0.tar.gz philr_1.16.0.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 53921  100 53921    0     0  1133k      0 --:--:-- --:--:-- --:--:-- 1170k

install for i386

* installing *source* package 'philr' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'philr'
    finding HTML links ... done
    annotate_balance                        html  
    buildilrBasep                           html  
    calculate.blw                           html  
    convert_to_long                         html  
    g.colMeans                              html  
    g.rowMeans                              html  
    mean_dist_to_tips                       html  
    miniclo                                 html  
    name.balance                            html  
    name_nodenumber_conversion              html  
    named_rtree                             html  
    philr                                   html  
    philrInv                                html  
    phylo2sbp                               html  
    shift                                   html  
    weighted_clr                            html  
    weighted_ilr                            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 'philr' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'philr' as philr_1.16.0.zip
* DONE (philr)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'philr' successfully unpacked and MD5 sums checked

Tests output

philr.Rcheck/tests_i386/testthat.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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.

> library(testthat)
> library(philr)
> 
> test_check("philr")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 33 ]
> 
> proc.time()
   user  system elapsed 
   3.07    0.23    3.39 

philr.Rcheck/tests_x64/testthat.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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.

> library(testthat)
> library(philr)
> 
> test_check("philr")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 33 ]
> 
> proc.time()
   user  system elapsed 
   4.96    0.31    5.37 

Example timings

philr.Rcheck/examples_i386/philr-Ex.timings

nameusersystemelapsed
annotate_balance1.130.061.19
buildilrBasep000
calculate.blw000
convert_to_long0.030.000.04
g.colMeans000
g.rowMeans000
mean_dist_to_tips000
miniclo000
name.balance0.020.000.01
name_nodenumber_conversion000
named_rtree000
philr000
philrInv0.020.000.02
phylo2sbp000
shift000
weighted_clr000
weighted_ilr000

philr.Rcheck/examples_x64/philr-Ex.timings

nameusersystemelapsed
annotate_balance1.090.051.14
buildilrBasep000
calculate.blw0.000.000.23
convert_to_long0.020.000.02
g.colMeans0.000.010.01
g.rowMeans000
mean_dist_to_tips000
miniclo000
name.balance0.020.000.02
name_nodenumber_conversion000
named_rtree000
philr000
philrInv000
phylo2sbp000
shift000
weighted_clr000
weighted_ilr000