Package: RamiGO

Version: 1.29.0

Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:RamiGO.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings RamiGO_1.29.0.tar.gz

StartedAt: 2018-05-11 02:42:47 -0400 (Fri, 11 May 2018)

EndedAt: 2018-05-11 02:43:27 -0400 (Fri, 11 May 2018)

EllapsedTime: 40.5 seconds

RetCode: 0

Status:  OK

CheckDir: RamiGO.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:RamiGO.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings RamiGO_1.29.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/RamiGO.Rcheck’
* using R version 3.5.0 Patched (2018-05-03 r74699)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RamiGO/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RamiGO’ version ‘1.29.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘RamiGO’ 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 ... NOTE
Package in Depends field not imported from: ‘gsubfn’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
adjM2gml : convCol: no visible global function definition for ‘col2rgb’
getAmigoTree: no visible global function definition for
  ‘colorRampPalette’
readAmigoDot : <anonymous>: no visible global function definition for
  ‘strapply’
show,AmigoDot: no visible global function definition for ‘str’
Undefined global functions or variables:
  col2rgb colorRampPalette str strapply
Consider adding
  importFrom("grDevices", "col2rgb", "colorRampPalette")
  importFrom("utils", "str")
to your NAMESPACE file.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
getAmigoTree 1.156  0.112    6.07
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.8-bioc/meat/RamiGO.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL RamiGO
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘RamiGO’ ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (RamiGO)

name	user	system	elapsed
AmigoDot-class	0.000	0.000	0.002
AmigoDot	0.600	0.032	3.517
AmigoDot.to.Cyto	0.400	0.024	1.476
AmigoDot.to.graphAM	0.000	0.000	0.001
AmigoDot.to.graphNEL	0.000	0.000	0.001
adjM2gml	0	0	0
c5.go.mapping	0.028	0.000	0.027
exportCytoGML	0.384	0.016	1.494
getAmigoTree	1.156	0.112	6.070
readAmigoDot	0.448	0.016	1.683