Package: conumee

Version: 1.17.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:conumee.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings conumee_1.17.0.tar.gz

StartedAt: 2019-04-09 00:07:55 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 00:44:26 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 2191.5 seconds

RetCode: 0

Status:  OK

CheckDir: conumee.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:conumee.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings conumee_1.17.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/conumee.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* 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 ‘1.17.0’
* 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 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
CNV.detailplot_wrap 110.547  5.057 116.779
CNV.detailplot      103.532  4.472 109.116
CNV.genomeplot       97.981  4.720 103.382
CNV.write            97.235  4.538 102.658
CNV.analysis-class   95.977  4.471 101.347
CNV.segment          80.571  3.028  84.111
CNV.fit              70.219  3.439  74.349
CNV.detail           61.703  3.462  72.706
CNV.bin              55.759  3.409  60.090
CNV.anno-class       50.311  2.659  53.470
CNV.create_anno      50.402  2.562  53.550
read.450k.url         7.080  0.923  14.769
* 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-3.9-bioc/meat/conumee.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL conumee
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘conumee’ ...
** R
** data
** inst
** byte-compile and prepare 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	95.977	4.471	101.347
CNV.anno-class	50.311	2.659	53.470
CNV.bin	55.759	3.409	60.090
CNV.create_anno	50.402	2.562	53.550
CNV.data-class	3.411	0.533	3.979
CNV.detail	61.703	3.462	72.706
CNV.detailplot	103.532	4.472	109.116
CNV.detailplot_wrap	110.547	5.057	116.779
CNV.fit	70.219	3.439	74.349
CNV.genomeplot	97.981	4.720	103.382
CNV.load	3.020	0.499	3.545
CNV.segment	80.571	3.028	84.111
CNV.write	97.235	4.538	102.658
read.450k.url	7.080	0.923	14.769