BioC 3.5: CHECK report for conumee on toluca2

Package: conumee

Version: 1.9.9

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings conumee_1.9.9.tar.gz

StartedAt: 2017-04-23 02:16:46 -0400 (Sun, 23 Apr 2017)

EndedAt: 2017-04-23 02:54:35 -0400 (Sun, 23 Apr 2017)

EllapsedTime: 2269.4 seconds

RetCode: 0

Status:  OK

CheckDir: conumee.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 conumee_1.9.9.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/conumee.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘conumee/DESCRIPTION’ ... OK
* this is package ‘conumee’ version ‘1.9.9’
* 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 ... 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 ‘conumee’ 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
CNV.load,GenomicRatioSet: no visible global function definition for
  ‘assays’
CNV.load,matrix: no visible binding for global variable ‘anno’
Undefined global functions or variables:
  anno assays
* 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 R/sysdata.rda ... 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
CNV.detailplot      121.950  4.617 129.127
CNV.detailplot_wrap 119.245  4.126 125.179
CNV.genomeplot      117.232  4.787 123.061
CNV.write           117.651  3.790 123.689
CNV.analysis-class   90.452  3.851  94.442
CNV.segment          85.596  3.395  89.379
CNV.fit              65.346  3.230  69.262
CNV.detail           63.105  3.714  67.738
CNV.bin              59.472  3.640  63.643
CNV.anno-class       54.449  2.351  57.062
CNV.create_anno      53.352  2.551  56.565
read.450k.url        10.577  0.644  16.578
CNV.load              5.851  0.589   6.505
* 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/conumee.Rcheck/00check.log’
for details.

* installing *source* package ‘conumee’ ...
** 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 (conumee)

name	user	system	elapsed
CNV.analysis-class	90.452	3.851	94.442
CNV.anno-class	54.449	2.351	57.062
CNV.bin	59.472	3.640	63.643
CNV.create_anno	53.352	2.551	56.565
CNV.data-class	2.698	0.558	3.269
CNV.detail	63.105	3.714	67.738
CNV.detailplot	121.950	4.617	129.127
CNV.detailplot_wrap	119.245	4.126	125.179
CNV.fit	65.346	3.230	69.262
CNV.genomeplot	117.232	4.787	123.061
CNV.load	5.851	0.589	6.505
CNV.segment	85.596	3.395	89.379
CNV.write	117.651	3.790	123.689
read.450k.url	10.577	0.644	16.578