BioC 3.5: CHECK report for bigmelon on oaxaca

Package: bigmelon

Version: 1.1.9

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings bigmelon_1.1.9.tar.gz

StartedAt: 2017-03-03 23:35:38 -0800 (Fri, 03 Mar 2017)

EndedAt: 2017-03-03 23:41:53 -0800 (Fri, 03 Mar 2017)

EllapsedTime: 374.8 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: bigmelon.Rcheck

Warnings: 1

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings bigmelon_1.1.9.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/bigmelon.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 ‘bigmelon/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘bigmelon’ version ‘1.1.9’
* 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 ‘bigmelon’ 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 ... NOTE
Unexported objects imported by ':::' calls:
  ‘minfi:::pickCompProbes’ ‘minfi:::projectCellType’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
estimateCellCounts.gdsn: no visible global function definition for
  ‘colData’
estimateCellCounts.gdsn: no visible binding for global variable ‘mSet’
estimateCellCounts.gdsn: no visible global function definition for
  ‘plot’
estimateCellCounts.gdsn: no visible global function definition for
  ‘legend’
Undefined global functions or variables:
  colData legend mSet plot
Consider adding
  importFrom("graphics", "legend", "plot")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘estimateCellCounts.gdsn’ ‘getq’ ‘impose’
Undocumented S4 methods:
  generic 'fot' and siglist 'gds.class'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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
Examples with CPU or elapsed time > 5s
       user system elapsed
iadd 45.978  2.004  49.297
* 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 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/bigmelon.Rcheck/00check.log’
for details.

* installing *source* package ‘bigmelon’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘fot’ from package ‘wateRmelon’ in package ‘bigmelon’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (bigmelon)

name	user	system	elapsed
GEOtoGDS	0.001	0.000	0.001
app2gds	1.175	0.039	1.300
backupGdsn	0.507	0.050	0.568
bigmelon-accessors	2.364	0.550	2.945
bigmelon-internal	0.211	0.019	0.240
bigmelon-normalization	2.131	0.270	2.423
combogds	0.353	0.035	0.409
es2gds	0.253	0.024	0.288
finalreport2gds	0	0	0
gds2mlumi	0.574	0.019	0.602
iadd	45.978	2.004	49.297
pfiltergds	0.282	0.020	0.340
prcompgdsn	0.172	0.016	0.199
pwodgdsn	0.403	0.020	0.435
rankednorm	0.235	0.020	0.266
redirect	0.208	0.022	0.239