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BioC 3.5: CHECK report for ggtree on tokay2

This page was generated on 2017-08-16 13:24:09 -0400 (Wed, 16 Aug 2017).

Package 561/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ggtree 1.8.1
Guangchuang Yu
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/ggtree
Last Changed Rev: 129275 / Revision: 131943
Last Changed Date: 2017-04-29 09:07:29 -0400 (Sat, 29 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ggtree
Version: 1.8.1
Command: rm -rf ggtree.buildbin-libdir ggtree.Rcheck && mkdir ggtree.buildbin-libdir ggtree.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ggtree.buildbin-libdir ggtree_1.8.1.tar.gz >ggtree.Rcheck\00install.out 2>&1 && cp ggtree.Rcheck\00install.out ggtree-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=ggtree.buildbin-libdir --install="check:ggtree-install.out" --force-multiarch --no-vignettes --timings ggtree_1.8.1.tar.gz
StartedAt: 2017-08-16 00:10:39 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 00:12:29 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 109.9 seconds
RetCode: 0
Status:  OK  
CheckDir: ggtree.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf ggtree.buildbin-libdir ggtree.Rcheck && mkdir ggtree.buildbin-libdir ggtree.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ggtree.buildbin-libdir ggtree_1.8.1.tar.gz >ggtree.Rcheck\00install.out 2>&1 && cp ggtree.Rcheck\00install.out ggtree-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=ggtree.buildbin-libdir --install="check:ggtree-install.out" --force-multiarch --no-vignettes --timings ggtree_1.8.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/ggtree.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ggtree/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ggtree' version '1.8.1'
* 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 'ggtree' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  9.4Mb
  sub-directories of 1Mb or more:
    doc        5.1Mb
    examples   3.7Mb
* 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 NOTE
See
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/ggtree.Rcheck/00check.log'
for details.


ggtree.Rcheck/00install.out:


install for i386

* installing *source* package 'ggtree' ...
** R
** inst
** byte-compile and prepare package for lazy loading
Note: wrong number of arguments to '>' 
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'ggtree' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ggtree' as ggtree_1.8.1.zip
* DONE (ggtree)

ggtree.Rcheck/examples_i386/ggtree-Ex.timings:

nameusersystemelapsed
NJ000
add-TREEDATA000
as.binary0.070.000.08
dotFun000
geom_tiplab1.020.001.02
ggtree0.530.000.53
gzoom.phylo0.530.020.61
theme_tree0.140.000.14
theme_tree20.160.000.16
update-TREE000

ggtree.Rcheck/examples_x64/ggtree-Ex.timings:

nameusersystemelapsed
NJ000
add-TREEDATA000
as.binary0.130.000.12
dotFun000
geom_tiplab2.240.022.25
ggtree1.020.001.02
gzoom.phylo0.500.020.57
theme_tree0.200.000.21
theme_tree20.20.00.2
update-TREE000