BioC 3.6: CHECK report for MetaboSignal on veracruz1

Package: MetaboSignal

Version: 1.7.11

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MetaboSignal_1.7.11.tar.gz

StartedAt: 2017-08-16 05:20:48 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 05:26:44 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 356.0 seconds

RetCode: 0

Status:  OK

CheckDir: MetaboSignal.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MetaboSignal_1.7.11.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/MetaboSignal.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 ‘MetaboSignal/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MetaboSignal’ version ‘1.7.11’
* package encoding: UTF-8
* 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 ‘MetaboSignal’ 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
MS_tissueFilter: no visible binding for global variable
  'hpaNormalTissue'
Undefined global functions or variables:
  hpaNormalTissue
* 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 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/MetaboSignal.Rcheck/00check.log’
for details.

* installing *source* package ‘MetaboSignal’ ...
** 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 (MetaboSignal)

name	user	system	elapsed
MS_changeNames	0.001	0.000	0.000
MS_convertGene	0.299	0.003	0.932
MS_distances	0.196	0.008	0.210
MS_exportCytoscape	0.000	0.000	0.001
MS_findMappedNodes	0.004	0.001	0.006
MS_getPathIds	0	0	0
MS_keggFinder	0.418	0.009	4.014
MS_keggNetwork	0	0	0
MS_nodeBW	0.117	0.004	0.123
MS_removeDrugs	0.005	0.001	0.006
MS_removeNode	0.017	0.001	0.022
MS_replaceNode	0.014	0.001	0.015
MS_shortestPaths	0.157	0.004	0.163
MS_shortestPathsNetwork	0	0	0
MS_tissueFilter	0	0	0
MS_topologyFilter	0.869	0.018	0.928