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BioC 3.5: CHECK report for philr on toluca2

This page was generated on 2017-04-23 14:42:05 -0400 (Sun, 23 Apr 2017).

Package 973/1377HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
philr 1.1.1
Justin Silverman
Snapshot Date: 2017-04-22 17:18:01 -0400 (Sat, 22 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/philr
Last Changed Rev: 128284 / Revision: 129046
Last Changed Date: 2017-04-07 09:46:40 -0400 (Fri, 07 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK 
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: philr
Version: 1.1.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings philr_1.1.1.tar.gz
StartedAt: 2017-04-23 07:57:07 -0400 (Sun, 23 Apr 2017)
EndedAt: 2017-04-23 07:58:22 -0400 (Sun, 23 Apr 2017)
EllapsedTime: 74.3 seconds
RetCode: 0
Status:  OK 
CheckDir: philr.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings philr_1.1.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/philr.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘philr/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘philr’ version ‘1.1.1’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘philr’ can be installed ... OK
* checking installed package size ... OK
* 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 ... NOTE
name.balance: no visible global function definition for ‘as’
vote.annotation: no visible global function definition for ‘is’
Undefined global functions or variables:
  as is
Consider adding
  importFrom("methods", "as", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/philr.Rcheck/00check.log’
for details.


philr.Rcheck/00install.out:

* installing *source* package ‘philr’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (philr)

philr.Rcheck/philr-Ex.timings:

nameusersystemelapsed
annotate_balance3.0860.0283.134
buildilrBasep0.1570.0010.160
calculate.blw0.0200.0010.020
convert_to_long0.0760.0010.078
g.colMeans0.0010.0000.000
g.rowMeans0.0010.0000.001
mean_dist_to_tips0.0380.0010.037
miniclo0.0010.0000.001
name.balance0.1010.0010.102
name_nodenumber_conversion0.0010.0000.001
named_rtree0.0010.0010.001
philr0.0950.0000.096
philrInv0.0060.0000.006
phylo2sbp0.0010.0000.002
shift0.0010.0010.001
weighted_clr0.0020.0000.002
weighted_ilr0.0030.0010.004