BioC 3.5: CHECK report for bigmelon on veracruz2

Package: bigmelon

Version: 1.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings bigmelon_1.2.0.tar.gz

StartedAt: 2017-10-18 00:55:01 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 01:01:32 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 391.2 seconds

RetCode: 0

Status:  OK

CheckDir: bigmelon.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 bigmelon_1.2.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/bigmelon.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.2.0’
* 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 ‘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
es2gds: no visible global function definition for ‘colData’
estimateCellCounts.gds: no visible global function definition for
  ‘colData’
Undefined global functions or variables:
  colData
* 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
Examples with CPU or elapsed time > 5s
       user system elapsed
iadd 48.104  1.955  52.193
* 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: 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 new generic function for ‘fot’ 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	0.000	0.000	0.001
app2gds	1.351	0.045	1.435
backupGdsn	0.384	0.022	0.416
bigmelon-accessors	2.848	0.815	3.870
bigmelon-internal	0.219	0.023	0.253
bigmelon-normalization	2.880	0.269	3.261
combogds	0.389	0.034	0.437
es2gds	0.202	0.019	0.224
finalreport2gds	0.000	0.000	0.001
gds2mlumi	0.694	0.029	0.742
getquantilesandranks	0.462	0.039	0.514
iadd	48.104	1.955	52.193
pfiltergds	0.359	0.024	0.399
prcompgdsn	0.215	0.022	0.244
pwodgdsn	0.518	0.027	0.605
rankednorm	0.213	0.022	0.247
redirect	0.209	0.020	0.244