BioC 3.6: CHECK report for conumee on veracruz1

Package: conumee

Version: 1.11.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings conumee_1.11.0.tar.gz

StartedAt: 2017-08-16 01:38:19 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 02:13:33 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 2113.5 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_1.11.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-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 ‘1.11.0’
* 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      103.805  3.483 110.674
CNV.detailplot_wrap 103.286  3.457 109.967
CNV.write           102.488  3.550 109.335
CNV.genomeplot       94.850  3.533 101.229
CNV.segment          83.361  3.030  89.018
CNV.analysis-class   82.430  3.505  88.606
CNV.bin              54.484  2.676  59.212
CNV.fit              54.795  2.360  58.764
CNV.detail           53.034  2.849  57.644
CNV.anno-class       48.011  1.728  51.566
CNV.create_anno      43.444  2.131  47.082
read.450k.url         8.365  0.452  16.904
* 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-3.6-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	82.430	3.505	88.606
CNV.anno-class	48.011	1.728	51.566
CNV.bin	54.484	2.676	59.212
CNV.create_anno	43.444	2.131	47.082
CNV.data-class	2.503	0.452	3.027
CNV.detail	53.034	2.849	57.644
CNV.detailplot	103.805	3.483	110.674
CNV.detailplot_wrap	103.286	3.457	109.967
CNV.fit	54.795	2.360	58.764
CNV.genomeplot	94.850	3.533	101.229
CNV.load	2.916	0.463	3.482
CNV.segment	83.361	3.030	89.018
CNV.write	102.488	3.550	109.335
read.450k.url	8.365	0.452	16.904