BioC 3.5: CHECK report for geneplotter on oaxaca

Package: geneplotter

Version: 1.53.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings geneplotter_1.53.0.tar.gz

StartedAt: 2017-03-04 03:21:40 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 03:23:29 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 109.3 seconds

RetCode: 0

Status:  OK

CheckDir: geneplotter.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings geneplotter_1.53.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/geneplotter.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 ‘geneplotter/DESCRIPTION’ ... OK
* this is package ‘geneplotter’ version ‘1.53.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘geneplotter’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
'library' or 'require' call to ‘annotate’ which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' call to ‘Rgraphviz’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘lattice’
  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
plotExpressionGraph: no visible global function definition for
  ‘selectMethod’
Undefined global functions or variables:
  selectMethod
Consider adding
  importFrom("methods", "selectMethod")
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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/geneplotter.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
GetColor	0.019	0.000	0.020
Makesense	2.557	0.077	2.860
alongChrom	3.426	0.060	3.544
amplicon.plot	0.000	0.000	0.001
cColor	3.192	0.020	3.214
cPlot	2.753	0.016	2.774
cScale	2.538	0.014	2.553
eset133a	0.125	0.009	0.134
groupedHeatmap	0.064	0.002	0.065
histStack	0.039	0.001	0.048
imageMap	0.068	0.011	0.551
make.chromOrd	0.146	0.028	0.222
multiecdf	0.949	0.007	0.958
openHtmlPage	0.001	0.000	0.001
plotChr	1.766	0.041	1.809
plotExpressionGraph	1.229	0.025	1.354
plotMA	0.014	0.001	0.016
savepng	0.194	0.082	3.636