BioC 3.3: CHECK report for ggtree on windows2.bioconductor.org
This page was generated on 2015-10-27 12:15:56 -0400 (Tue, 27 Oct 2015).
ggtree 1.3.0
Guangchuang Yu
| Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree | | Last Changed Rev: 109592 / Revision: 109948 | | Last Changed Date: 2015-10-13 15:59:53 -0400 (Tue, 13 Oct 2015) |
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | [ OK ] | OK | |
Summary
| Package: ggtree
|
| Version: 1.3.0
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| Command: rm -rf ggtree.buildbin-libdir ggtree.Rcheck && mkdir ggtree.buildbin-libdir ggtree.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ggtree.buildbin-libdir ggtree_1.3.0.tar.gz >ggtree.Rcheck\00install.out 2>&1 && cp ggtree.Rcheck\00install.out ggtree-install.out && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=ggtree.buildbin-libdir --install="check:ggtree-install.out" --force-multiarch --no-vignettes --timings ggtree_1.3.0.tar.gz
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| StartedAt: 2015-10-27 02:51:02 -0400 (Tue, 27 Oct 2015)
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| EndedAt: 2015-10-27 02:53:06 -0400 (Tue, 27 Oct 2015)
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| EllapsedTime: 124.0 seconds
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| RetCode: 0
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| Status: OK
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| CheckDir: ggtree.Rcheck
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| Warnings: 0
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Command output
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###
### Running command:
###
### rm -rf ggtree.buildbin-libdir ggtree.Rcheck && mkdir ggtree.buildbin-libdir ggtree.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ggtree.buildbin-libdir ggtree_1.3.0.tar.gz >ggtree.Rcheck\00install.out 2>&1 && cp ggtree.Rcheck\00install.out ggtree-install.out && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=ggtree.buildbin-libdir --install="check:ggtree-install.out" --force-multiarch --no-vignettes --timings ggtree_1.3.0.tar.gz
###
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* using log directory 'c:/biocbld/bbs-3.3-bioc/meat/ggtree.Rcheck'
* using R Under development (unstable) (2015-09-22 r69418)
* 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 '1.3.0'
* 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 'ggtree' can be installed ... OK
* checking installed package size ... NOTE
installed size is 7.6Mb
sub-directories of 1Mb or more:
doc 1.1Mb
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' ... [7s] OK
** running examples for arch 'x64' ... [7s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R' [3s]
[3s] OK
** running tests for arch 'x64' ...
Running 'testthat.R' [3s]
[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
'c:/biocbld/bbs-3.3-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_1.3.0.zip
* DONE (ggtree)
ggtree.Rcheck/examples_i386/ggtree-Ex.timings:
| name | user | system | elapsed
|
| NJ | 0 | 0 | 0 |
|
| add.TREEDATA | 0.26 | 0.02 | 0.29 |
|
| as.binary | 0.02 | 0.00 | 0.01 |
|
| dotFun | 0 | 0 | 0 |
|
| geom_tiplab | 0.12 | 0.00 | 0.13 |
|
| geom_tree | 0.11 | 0.00 | 0.11 |
|
| get.fields-methods | 0 | 0 | 0 |
|
| get.placements-methods | 0.01 | 0.00 | 0.02 |
|
| get.subs-methods | 0.25 | 0.00 | 0.25 |
|
| get.tree-methods | 0.02 | 0.00 | 0.01 |
|
| get.treeinfo-methods | 0.01 | 0.00 | 0.02 |
|
| get.treetext-methods | 0 | 0 | 0 |
|
| ggtree | 0.11 | 0.00 | 0.11 |
|
| gplot | 0.28 | 0.00 | 0.28 |
|
| gzoom.phylo | 0.46 | 0.00 | 0.45 |
|
| plot-methods | 0.26 | 0.00 | 0.27 |
|
| read.baseml | 0.59 | 0.00 | 0.60 |
|
| read.beast | 0.07 | 0.00 | 0.06 |
|
| read.codeml | 0.71 | 0.00 | 0.72 |
|
| read.codeml_mlc | 0.05 | 0.00 | 0.04 |
|
| read.hyphy | 0.02 | 0.00 | 0.02 |
|
| read.jplace | 0 | 0 | 0 |
|
| read.paml_rst | 0.57 | 0.00 | 0.58 |
|
| show-methods | 0 | 0 | 0 |
|
| theme_tree | 0.11 | 0.00 | 0.11 |
|
| theme_tree2 | 0.11 | 0.00 | 0.11 |
|
| update.TREE | 0.14 | 0.00 | 0.14 |
|
| write.jplace | 0 | 0 | 0 |
|
ggtree.Rcheck/examples_x64/ggtree-Ex.timings:
| name | user | system | elapsed
|
| NJ | 0 | 0 | 0 |
|
| add.TREEDATA | 0.36 | 0.00 | 0.36 |
|
| as.binary | 0.01 | 0.00 | 0.02 |
|
| dotFun | 0 | 0 | 0 |
|
| geom_tiplab | 0.19 | 0.00 | 0.19 |
|
| geom_tree | 0.13 | 0.02 | 0.14 |
|
| get.fields-methods | 0.01 | 0.00 | 0.02 |
|
| get.placements-methods | 0 | 0 | 0 |
|
| get.subs-methods | 0.25 | 0.00 | 0.25 |
|
| get.tree-methods | 0.00 | 0.02 | 0.01 |
|
| get.treeinfo-methods | 0.02 | 0.00 | 0.02 |
|
| get.treetext-methods | 0.01 | 0.00 | 0.02 |
|
| ggtree | 0.13 | 0.00 | 0.12 |
|
| gplot | 0.3 | 0.0 | 0.3 |
|
| gzoom.phylo | 0.51 | 0.01 | 0.53 |
|
| plot-methods | 0.31 | 0.00 | 0.31 |
|
| read.baseml | 0.61 | 0.00 | 0.61 |
|
| read.beast | 0.08 | 0.00 | 0.08 |
|
| read.codeml | 0.55 | 0.00 | 0.55 |
|
| read.codeml_mlc | 0.05 | 0.00 | 0.04 |
|
| read.hyphy | 0.01 | 0.00 | 0.02 |
|
| read.jplace | 0 | 0 | 0 |
|
| read.paml_rst | 0.31 | 0.00 | 0.31 |
|
| show-methods | 0.02 | 0.00 | 0.02 |
|
| theme_tree | 0.12 | 0.00 | 0.12 |
|
| theme_tree2 | 0.14 | 0.00 | 0.14 |
|
| update.TREE | 0.16 | 0.00 | 0.16 |
|
| write.jplace | 0.02 | 0.00 | 0.01 |
|