BioC 3.1: CHECK report for ggtree on morelia
This page was generated on 2015-10-09 09:42:37 -0700 (Fri, 09 Oct 2015).
ggtree 1.0.21 Guangchuang Yu
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015) | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/ggtree | Last Changed Rev: 109054 / Revision: 109384 | Last Changed Date: 2015-09-30 22:34:07 -0700 (Wed, 30 Sep 2015) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK |  |
petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | OK | OK |  |
morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | [ OK ] | OK |  |
Summary
Package: ggtree |
Version: 1.0.21 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ggtree_1.0.21.tar.gz |
StartedAt: 2015-10-09 02:26:54 -0700 (Fri, 09 Oct 2015) |
EndedAt: 2015-10-09 02:29:01 -0700 (Fri, 09 Oct 2015) |
EllapsedTime: 126.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ggtree.Rcheck |
Warnings: 0 |
Command output
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ggtree_1.0.21.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/ggtree.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ggtree/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ggtree’ version ‘1.0.21’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘ggtree’ can be installed ... [11s/11s] OK
* checking installed package size ... NOTE
installed size is 17.3Mb
sub-directories of 1Mb or more:
doc 10.9Mb
examples 3.7Mb
extdata 2.3Mb
* 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
* 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 loading without being on the library search path ... 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 ... [13s/14s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [4s/4s]
[4s/4s] 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
‘/Users/biocbuild/bbs-3.1-bioc/meat/ggtree.Rcheck/00check.log’
for details.
ggtree.Rcheck/00install.out:
* installing *source* package ‘ggtree’ ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
Note: the specification for S3 class “AsIs” in package ‘jsonlite’ seems equivalent to one from package ‘BiocGenerics’: not turning on duplicate class definitions for this class.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
Note: the specification for S3 class “AsIs” in package ‘jsonlite’ seems equivalent to one from package ‘BiocGenerics’: not turning on duplicate class definitions for this class.
* DONE (ggtree)
ggtree.Rcheck/ggtree-Ex.timings:
name | user | system | elapsed
|
NJ | 0.001 | 0.000 | 0.001 |
|
add.TREEDATA | 0.366 | 0.066 | 0.476 |
|
as.binary | 0.024 | 0.000 | 0.024 |
|
dotFun | 0.001 | 0.000 | 0.001 |
|
geom_tiplab | 0.202 | 0.001 | 0.203 |
|
geom_tree | 0.159 | 0.001 | 0.161 |
|
get.fields-methods | 0.011 | 0.001 | 0.043 |
|
get.placements-methods | 0.011 | 0.000 | 0.012 |
|
get.subs-methods | 0.555 | 0.005 | 0.561 |
|
get.tree-methods | 0.011 | 0.001 | 0.011 |
|
get.treeinfo-methods | 0.021 | 0.001 | 0.022 |
|
get.treetext-methods | 0.007 | 0.000 | 0.007 |
|
ggtree | 0.164 | 0.021 | 0.190 |
|
gplot | 0.340 | 0.012 | 0.352 |
|
gzoom.phylo | 0.673 | 0.079 | 0.773 |
|
plot-methods | 0.352 | 0.012 | 0.365 |
|
read.baseml | 1.810 | 0.045 | 1.856 |
|
read.beast | 0.111 | 0.012 | 0.123 |
|
read.codeml | 2.155 | 0.149 | 2.306 |
|
read.codeml_mlc | 0.095 | 0.013 | 0.109 |
|
read.hyphy | 0.015 | 0.000 | 0.016 |
|
read.jplace | 0.011 | 0.001 | 0.013 |
|
read.paml_rst | 1.178 | 0.014 | 1.192 |
|
show-methods | 0.005 | 0.000 | 0.005 |
|
theme_tree | 0.165 | 0.025 | 0.190 |
|
theme_tree2 | 0.159 | 0.001 | 0.161 |
|
update.TREE | 0.223 | 0.001 | 0.225 |
|
write.jplace | 0.006 | 0.000 | 0.007 |
|