BioC 3.2: CHECK report for ggtree on moscato1
This page was generated on 2016-04-23 10:21:19 -0700 (Sat, 23 Apr 2016).
ggtree 1.2.17
Guangchuang Yu
| Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/ggtree | | Last Changed Rev: 114635 / Revision: 116712 | | Last Changed Date: 2016-03-10 22:37:59 -0800 (Thu, 10 Mar 2016) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | NotNeeded | OK | [ OK ] | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
Summary
| Package: ggtree
|
| Version: 1.2.17
|
| Command: rm -rf ggtree.buildbin-libdir ggtree.Rcheck && mkdir ggtree.buildbin-libdir ggtree.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ggtree.buildbin-libdir ggtree_1.2.17.tar.gz >ggtree.Rcheck\00install.out 2>&1 && cp ggtree.Rcheck\00install.out ggtree-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=ggtree.buildbin-libdir --install="check:ggtree-install.out" --force-multiarch --no-vignettes --timings ggtree_1.2.17.tar.gz
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| StartedAt: 2016-04-23 02:58:06 -0700 (Sat, 23 Apr 2016)
|
| EndedAt: 2016-04-23 03:05:37 -0700 (Sat, 23 Apr 2016)
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| EllapsedTime: 451.0 seconds
|
| RetCode: 0
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| Status: OK
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| CheckDir: ggtree.Rcheck
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| Warnings: 0
|
Command output
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###
### Running command:
###
### rm -rf ggtree.buildbin-libdir ggtree.Rcheck && mkdir ggtree.buildbin-libdir ggtree.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ggtree.buildbin-libdir ggtree_1.2.17.tar.gz >ggtree.Rcheck\00install.out 2>&1 && cp ggtree.Rcheck\00install.out ggtree-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=ggtree.buildbin-libdir --install="check:ggtree-install.out" --force-multiarch --no-vignettes --timings ggtree_1.2.17.tar.gz
###
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* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/ggtree.Rcheck'
* using R version 3.2.4 (2016-03-10)
* 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 '1.2.17'
* 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 15.2Mb
sub-directories of 1Mb or more:
doc 8.7Mb
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
* 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
** checking loading without being on the library search path ... 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 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 ...
** running examples for arch 'i386' ... [50s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
theme_tree 0.14 0 6.13
** running examples for arch 'x64' ... [12s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R' [5s]
[5s] OK
** running tests for arch 'x64' ...
Running 'testthat.R' [6s]
[7s] 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
'D:/biocbld/bbs-3.2-bioc/meat/ggtree.Rcheck/00check.log'
for details.
ggtree.Rcheck/00install.out:
install for i386
* installing *source* package 'ggtree' ...
** R
** inst
** preparing package for lazy loading
** 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_1.2.17.zip
* DONE (ggtree)
ggtree.Rcheck/examples_i386/ggtree-Ex.timings:
| name | user | system | elapsed
|
| NJ | 0 | 0 | 0 |
|
| add-TREEDATA | 0.19 | 0.00 | 0.19 |
|
| as.binary | 0.02 | 0.00 | 0.01 |
|
| dotFun | 0 | 0 | 0 |
|
| geom_tiplab | 0.17 | 0.00 | 0.17 |
|
| get.fields-methods | 0 | 0 | 0 |
|
| get.placements-methods | 0 | 0 | 0 |
|
| get.subs-methods | 0.39 | 0.00 | 0.39 |
|
| get.tree-methods | 0.02 | 0.00 | 0.02 |
|
| get.treeinfo-methods | 0.02 | 0.00 | 0.01 |
|
| get.treetext-methods | 0.01 | 0.00 | 0.02 |
|
| ggtree | 0.13 | 0.00 | 0.12 |
|
| gzoom.phylo | 0.40 | 0.01 | 3.15 |
|
| plot-methods | 0.36 | 0.00 | 0.36 |
|
| read.baseml | 0.91 | 0.00 | 0.91 |
|
| read.beast | 0.09 | 0.00 | 0.09 |
|
| read.codeml | 1.23 | 0.00 | 1.23 |
|
| read.codeml_mlc | 0.09 | 0.00 | 0.10 |
|
| read.hyphy | 0.04 | 0.00 | 0.03 |
|
| read.jplace | 0.01 | 0.00 | 0.01 |
|
| read.paml_rst | 0.73 | 0.00 | 0.74 |
|
| show-methods | 0.02 | 0.00 | 0.01 |
|
| theme_tree | 0.14 | 0.00 | 6.13 |
|
| theme_tree2 | 0.16 | 0.00 | 0.16 |
|
| update-TREE | 0.15 | 0.00 | 0.15 |
|
| write.jplace | 0 | 0 | 0 |
|
ggtree.Rcheck/examples_x64/ggtree-Ex.timings:
| name | user | system | elapsed
|
| NJ | 0 | 0 | 0 |
|
| add-TREEDATA | 0.3 | 0.0 | 0.3 |
|
| as.binary | 0.03 | 0.00 | 0.03 |
|
| dotFun | 0 | 0 | 0 |
|
| geom_tiplab | 0.32 | 0.00 | 0.31 |
|
| get.fields-methods | 0.01 | 0.00 | 0.01 |
|
| get.placements-methods | 0.03 | 0.00 | 0.04 |
|
| get.subs-methods | 0.72 | 0.00 | 0.71 |
|
| get.tree-methods | 0.03 | 0.00 | 0.03 |
|
| get.treeinfo-methods | 0.05 | 0.00 | 0.05 |
|
| get.treetext-methods | 0.01 | 0.00 | 0.02 |
|
| ggtree | 0.19 | 0.00 | 0.18 |
|
| gzoom.phylo | 0.69 | 0.00 | 0.69 |
|
| plot-methods | 0.37 | 0.01 | 0.39 |
|
| read.baseml | 0.98 | 0.00 | 0.98 |
|
| read.beast | 0.1 | 0.0 | 0.1 |
|
| read.codeml | 1.43 | 0.00 | 1.43 |
|
| read.codeml_mlc | 0.05 | 0.00 | 0.05 |
|
| read.hyphy | 0.02 | 0.00 | 0.01 |
|
| read.jplace | 0.01 | 0.00 | 0.02 |
|
| read.paml_rst | 0.53 | 0.00 | 0.53 |
|
| show-methods | 0.02 | 0.00 | 0.02 |
|
| theme_tree | 0.15 | 0.00 | 0.15 |
|
| theme_tree2 | 0.17 | 0.00 | 0.17 |
|
| update-TREE | 0.17 | 0.00 | 1.06 |
|
| write.jplace | 0.02 | 0.00 | 0.02 |
|