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BioC 3.6: CHECK report for metagene on veracruz1

This page was generated on 2017-08-16 13:45:42 -0400 (Wed, 16 Aug 2017).

Package 799/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
metagene 2.9.1
Charles Joly Beauparlant
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagene
Last Changed Rev: 129289 / Revision: 131943
Last Changed Date: 2017-04-29 17:09:18 -0400 (Sat, 29 Apr 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: metagene
Version: 2.9.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings metagene_2.9.1.tar.gz
StartedAt: 2017-08-16 05:21:09 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 05:28:13 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 423.5 seconds
RetCode: 0
Status:  OK 
CheckDir: metagene.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings metagene_2.9.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/metagene.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘metagene/DESCRIPTION’ ... OK
* this is package ‘metagene’ version ‘2.9.1’
* 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 ‘metagene’ 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 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
get_demo_design: no visible global function definition for ‘read.table’
get_promoters_txdb: no visible global function definition for ‘is’
plot_metagene: no visible binding for global variable ‘position’
plot_metagene: no visible binding for global variable ‘value’
plot_metagene: no visible binding for global variable ‘qinf’
plot_metagene: no visible binding for global variable ‘qsup’
plot_metagene: no visible binding for global variable ‘group’
Undefined global functions or variables:
  group is position qinf qsup read.table value
Consider adding
  importFrom("methods", "is")
  importFrom("utils", "read.table")
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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... 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 ‘runTests.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-3.6-bioc/meat/metagene.Rcheck/00check.log’
for details.


metagene.Rcheck/00install.out:

* installing *source* package ‘metagene’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (metagene)

metagene.Rcheck/metagene-Ex.timings:

nameusersystemelapsed
Bam_Handler0.9510.0461.033
get_demo_bam_files0.0040.0000.005
get_demo_design0.0030.0000.003
get_demo_metagene3.1630.0493.310
get_demo_regions0.0020.0000.002
get_promoters_txdb0.0000.0000.001
metagene0.4300.0070.449
permutation_test2.2450.0432.361
plot_metagene0.8590.0770.964
promoters_hg180.0030.0010.004
promoters_hg190.0020.0010.002
promoters_mm100.0020.0010.002
promoters_mm90.0020.0010.002