BioC 3.5: CHECK report for conumee on veracruz2

Package: conumee

Version: 1.10.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings conumee_1.10.0.tar.gz

StartedAt: 2017-08-16 01:24:06 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 02:00:05 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 2159.3 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_1.10.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/conumee.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘conumee/DESCRIPTION’ ... OK
* this is package ‘conumee’ version ‘1.10.0’
* 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 ‘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 loading without being on the library search path ... 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_wrap 110.870  3.750 118.240
CNV.genomeplot      104.625  3.464 111.507
CNV.write           103.239  3.562 109.986
CNV.detailplot       98.165  3.524 104.658
CNV.analysis-class   80.903  3.512  86.613
CNV.segment          81.419  2.979  87.120
CNV.bin              57.636  2.791  62.332
CNV.detail           53.060  3.072  58.012
CNV.anno-class       50.184  1.921  53.991
CNV.fit              48.496  2.540  52.214
CNV.create_anno      44.093  2.297  47.893
read.450k.url         8.409  0.578  17.524
CNV.load              6.773  0.601   7.645
* 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	80.903	3.512	86.613
CNV.anno-class	50.184	1.921	53.991
CNV.bin	57.636	2.791	62.332
CNV.create_anno	44.093	2.297	47.893
CNV.data-class	1.783	0.376	2.217
CNV.detail	53.060	3.072	58.012
CNV.detailplot	98.165	3.524	104.658
CNV.detailplot_wrap	110.87	3.75	118.24
CNV.fit	48.496	2.540	52.214
CNV.genomeplot	104.625	3.464	111.507
CNV.load	6.773	0.601	7.645
CNV.segment	81.419	2.979	87.120
CNV.write	103.239	3.562	109.986
read.450k.url	8.409	0.578	17.524