Multiple platform build/check report for BioC 3.6 - CHECK report for treeio on tokay1

Package: treeio

Version: 1.2.2

Command: rm -rf treeio.buildbin-libdir treeio.Rcheck && mkdir treeio.buildbin-libdir treeio.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=treeio.buildbin-libdir treeio_1.2.2.tar.gz >treeio.Rcheck\00install.out 2>&1 && cp treeio.Rcheck\00install.out treeio-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=treeio.buildbin-libdir --install="check:treeio-install.out" --force-multiarch --no-vignettes --timings treeio_1.2.2.tar.gz

StartedAt: 2018-04-12 03:39:59 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 03:41:15 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 75.4 seconds

RetCode: 0

Status: WARNINGS

CheckDir: treeio.Rcheck

Warnings: 1

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### Running command:
###
###   rm -rf treeio.buildbin-libdir treeio.Rcheck && mkdir treeio.buildbin-libdir treeio.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=treeio.buildbin-libdir treeio_1.2.2.tar.gz >treeio.Rcheck\00install.out 2>&1 && cp treeio.Rcheck\00install.out treeio-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=treeio.buildbin-libdir --install="check:treeio-install.out" --force-multiarch --no-vignettes --timings treeio_1.2.2.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/treeio.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 'treeio/DESCRIPTION' ... OK
* this is package 'treeio' version '1.2.2'
* 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 'treeio' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpcn1Fo2/R.INSTALL3c6469c581d/treeio/man/reexports.Rd:19: missing file link '%>%'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/treeio.Rcheck/00install.out' for details.
* 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 installed files from 'inst/doc' ... 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 WARNING
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/treeio.Rcheck/00check.log'
for details.


install for i386

* installing *source* package 'treeio' ...
** R
** inst
** byte-compile and prepare package for lazy loading
Note: wrong number of arguments to '>' 
** help
*** installing help indices
  converting help for package 'treeio'
    finding HTML links ... done
    Nnode                                   html  
    Ntip                                    html  
    as.treedata                             html  
    beast-class                             html  
    codeml-class                            html  
    codeml_mlc-class                        html  
    drop.tip-methods                        html  
    get.fields-methods                      html  
    get.placements-methods                  html  
    get.subs-methods                        html  
    get.tipseq-methods                      html  
    get.tree-methods                        html  
    get.treetext-methods                    html  
    getNodeNum                              html  
    getRoot                                 html  
    groupClade-methods                      html  
    groupOTU-methods                        html  
    groupOTU.phylo                          html  
    hyphy-class                             html  
    is.ggtree                               html  
    jplace-class                            html  
    label_branch_paml                       html  
    mask                                    html  
    merge_tree                              html  
    paml_rst-class                          html  
    phangorn-class                          html  
    phyPML                                  html  
    phylip-class                            html  
    pmlToSeq                                html  
    print.beastList                         html  
    r8s-class                               html  
    raxml2nwk                               html  
    read.baseml                             html  
    read.beast                              html  
    read.codeml                             html  
    read.codeml_mlc                         html  
    read.hyphy                              html  
    read.jplace                             html  
    read.newick                             html  
    read.nhx                                html  
    read.paml_rst                           html  
    read.phylip                             html  
    read.phyloT                             html  
    read.r8s                                html  
    read.raxml                              html  
    reexports                               html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpcn1Fo2/R.INSTALL3c6469c581d/treeio/man/reexports.Rd:19: missing file link '%>%'
    show-methods                            html  
    taxa_rename                             html  
    treedata-class                          html  
    write.jplace                            html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'treeio' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'treeio' as treeio_1.2.2.zip
* DONE (treeio)
In R CMD INSTALL
In R CMD INSTALL


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.

> library(testthat)
> library(treeio)
> 
> test_check("treeio")
== testthat results  ===========================================================
OK: 17 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   3.62    0.10    3.71


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.

> library(testthat)
> library(treeio)
> 
> test_check("treeio")
== testthat results  ===========================================================
OK: 17 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   4.90    0.15    5.04

name	user	system	elapsed
Nnode	0.03	0.00	0.03
Ntip	0.10	0.00	0.09
drop.tip-methods	0.22	0.00	0.22
get.fields-methods	0.11	0.00	0.11
get.placements-methods	0.06	0.00	0.06
get.subs-methods	2.66	0.13	2.78
get.tree-methods	0.03	0.00	0.03
get.treetext-methods	0	0	0
getNodeNum	0	0	0
getRoot	0	0	0
is.ggtree	0.62	0.01	0.73
read.baseml	1.24	0.03	1.27
read.beast	0.11	0.00	0.11
read.codeml	1.15	0.03	1.18
read.codeml_mlc	0.05	0.00	0.05
read.hyphy	0	0	0
read.jplace	0.01	0.00	0.02
read.nhx	0	0	0
read.paml_rst	0.66	0.04	0.68
read.phylip	0	0	0
read.r8s	0.02	0.00	0.02
read.raxml	0	0	0
show-methods	0.01	0.00	0.02
write.jplace	0	0	0

name	user	system	elapsed
Nnode	0.03	0.00	0.03
Ntip	0.11	0.00	0.11
drop.tip-methods	0.2	0.0	0.2
get.fields-methods	0.11	0.00	0.11
get.placements-methods	0.05	0.00	0.05
get.subs-methods	2.92	0.02	2.93
get.tree-methods	0.03	0.00	0.03
get.treetext-methods	0	0	0
getNodeNum	0	0	0
getRoot	0	0	0
is.ggtree	0.5	0.0	0.5
read.baseml	0.75	0.02	0.77
read.beast	0.06	0.00	0.06
read.codeml	0.82	0.01	0.83
read.codeml_mlc	0.03	0.00	0.03
read.hyphy	0	0	0
read.jplace	0	0	0
read.nhx	0	0	0
read.paml_rst	0.47	0.01	0.48
read.phylip	0.01	0.00	0.02
read.r8s	0	0	0
read.raxml	0.02	0.00	0.01
show-methods	0	0	0
write.jplace	0.01	0.00	0.02

CHECK report for treeio on tokay1

Summary

Command output

Installation output

Tests output

Example timings