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: 2017-10-18 02:08:25 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 02:45:15 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 2210.5 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_1.10.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/conumee.Rcheck’
* using R version 3.4.2 (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 ‘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.genomeplot      106.948  4.505 114.547
CNV.detailplot      105.090  4.543 112.881
CNV.write           103.708  3.719 110.448
CNV.detailplot_wrap  98.334  3.921 105.642
CNV.analysis-class   82.482  3.749  89.088
CNV.segment          81.333  3.093  86.730
CNV.fit              62.785  2.492  67.312
CNV.detail           54.707  2.849  59.740
CNV.bin              52.121  2.579  56.788
CNV.anno-class       46.454  1.876  50.235
CNV.create_anno      45.700  2.262  49.670
CNV.load              7.632  0.811   8.681
read.450k.url         7.940  0.500  16.028
* 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	82.482	3.749	89.088
CNV.anno-class	46.454	1.876	50.235
CNV.bin	52.121	2.579	56.788
CNV.create_anno	45.700	2.262	49.670
CNV.data-class	2.822	0.393	3.298
CNV.detail	54.707	2.849	59.740
CNV.detailplot	105.090	4.543	112.881
CNV.detailplot_wrap	98.334	3.921	105.642
CNV.fit	62.785	2.492	67.312
CNV.genomeplot	106.948	4.505	114.547
CNV.load	7.632	0.811	8.681
CNV.segment	81.333	3.093	86.730
CNV.write	103.708	3.719	110.448
read.450k.url	7.940	0.500	16.028