BioC 3.5: CHECK report for MetaboSignal on oaxaca

Package: MetaboSignal

Version: 1.5.6

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MetaboSignal_1.5.6.tar.gz

StartedAt: 2017-03-04 05:33:44 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 05:40:12 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 387.6 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_1.5.6.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/MetaboSignal.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.5.6’
* 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 ... 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 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
Examples with CPU or elapsed time > 5s
                               user system elapsed
MS_FindKEGG                   0.737  0.016  51.559
MetaboSignal_NetworkCytoscape 0.653  0.006  13.665
* 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: OK

* 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	0.004	0.001	2.043
MS_FilterNetwork	0.360	0.013	0.373
MS_FindKEGG	0.737	0.016	51.559
MS_FindMappedNodes	0.002	0.001	0.002
MS_GetKEGG_GeneID	0.317	0.006	0.724
MS_GetShortestpaths	0.143	0.002	0.144
MS_NodeBW	0.047	0.003	0.050
MS_RemoveNode	0.009	0.000	0.010
MS_ReplaceNode	0.010	0.001	0.010
MS_ToCytoscape	0.001	0.000	0.000
MS_interactionType	0.000	0.000	0.001
MetaboSignal_NetworkCytoscape	0.653	0.006	13.665
MetaboSignal_distances	0.152	0.006	0.159
MetaboSignal_matrix	0	0	0