Package: conumee

Version: 1.12.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings conumee_1.12.0.tar.gz

StartedAt: 2018-04-12 02:11:35 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 02:47:35 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 2160.2 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_1.12.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/conumee.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.12.0’
* 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 104.623  3.792 110.605
CNV.write           102.311  4.502 108.555
CNV.genomeplot      100.111  4.541 106.593
CNV.detailplot       98.036  4.016 104.193
CNV.analysis-class   90.406  3.429  96.120
CNV.segment          86.172  2.941  90.472
CNV.fit              55.441  2.708  59.103
CNV.detail           53.078  3.071  57.419
CNV.bin              51.899  3.036  56.259
CNV.create_anno      43.656  2.130  47.023
CNV.anno-class       43.347  2.392  46.890
read.450k.url         6.981  0.646  20.814
* 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	90.406	3.429	96.120
CNV.anno-class	43.347	2.392	46.890
CNV.bin	51.899	3.036	56.259
CNV.create_anno	43.656	2.130	47.023
CNV.data-class	2.791	0.423	3.278
CNV.detail	53.078	3.071	57.419
CNV.detailplot	98.036	4.016	104.193
CNV.detailplot_wrap	104.623	3.792	110.605
CNV.fit	55.441	2.708	59.103
CNV.genomeplot	100.111	4.541	106.593
CNV.load	3.063	0.492	3.623
CNV.segment	86.172	2.941	90.472
CNV.write	102.311	4.502	108.555
read.450k.url	6.981	0.646	20.814