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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).

Package 440/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
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 UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

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
StartedAt: 2016-04-23 02:58:06 -0700 (Sat, 23 Apr 2016)
EndedAt: 2016-04-23 03:05:37 -0700 (Sat, 23 Apr 2016)
EllapsedTime: 451.0 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 && 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
###
##############################################################################
##############################################################################


* 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:

nameusersystemelapsed
NJ000
add-TREEDATA0.190.000.19
as.binary0.020.000.01
dotFun000
geom_tiplab0.170.000.17
get.fields-methods000
get.placements-methods000
get.subs-methods0.390.000.39
get.tree-methods0.020.000.02
get.treeinfo-methods0.020.000.01
get.treetext-methods0.010.000.02
ggtree0.130.000.12
gzoom.phylo0.400.013.15
plot-methods0.360.000.36
read.baseml0.910.000.91
read.beast0.090.000.09
read.codeml1.230.001.23
read.codeml_mlc0.090.000.10
read.hyphy0.040.000.03
read.jplace0.010.000.01
read.paml_rst0.730.000.74
show-methods0.020.000.01
theme_tree0.140.006.13
theme_tree20.160.000.16
update-TREE0.150.000.15
write.jplace000

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

nameusersystemelapsed
NJ000
add-TREEDATA0.30.00.3
as.binary0.030.000.03
dotFun000
geom_tiplab0.320.000.31
get.fields-methods0.010.000.01
get.placements-methods0.030.000.04
get.subs-methods0.720.000.71
get.tree-methods0.030.000.03
get.treeinfo-methods0.050.000.05
get.treetext-methods0.010.000.02
ggtree0.190.000.18
gzoom.phylo0.690.000.69
plot-methods0.370.010.39
read.baseml0.980.000.98
read.beast0.10.00.1
read.codeml1.430.001.43
read.codeml_mlc0.050.000.05
read.hyphy0.020.000.01
read.jplace0.010.000.02
read.paml_rst0.530.000.53
show-methods0.020.000.02
theme_tree0.150.000.15
theme_tree20.170.000.17
update-TREE0.170.001.06
write.jplace0.020.000.02