Package: conumee

Version: 1.16.0

Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:conumee.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings conumee_1.16.0.tar.gz

StartedAt: 2019-04-15 23:09:13 -0400 (Mon, 15 Apr 2019)

EndedAt: 2019-04-15 23:45:04 -0400 (Mon, 15 Apr 2019)

EllapsedTime: 2151.0 seconds

RetCode: 0

Status:  OK

CheckDir: conumee.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:conumee.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings conumee_1.16.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/conumee.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘conumee/DESCRIPTION’ ... OK
* this is package ‘conumee’ version ‘1.16.0’
* 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      109.112  0.460 109.725
CNV.genomeplot      100.184  0.616 101.007
CNV.detailplot_wrap  97.716  0.512  98.419
CNV.analysis-class   97.276  0.864  98.782
CNV.write            94.460  0.568  95.219
CNV.segment          78.764  0.132  78.995
CNV.fit              62.568  0.152  62.867
CNV.bin              55.308  0.168  55.574
CNV.detail           53.800  0.148  54.083
CNV.create_anno      49.240  0.000  49.365
CNV.anno-class       43.828  0.012  44.230
read.450k.url         8.692  0.220  17.826
* 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
  ‘/home/biocbuild/bbs-3.8-bioc/meat/conumee.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL conumee
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/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	97.276	0.864	98.782
CNV.anno-class	43.828	0.012	44.230
CNV.bin	55.308	0.168	55.574
CNV.create_anno	49.240	0.000	49.365
CNV.data-class	3.952	0.072	4.066
CNV.detail	53.800	0.148	54.083
CNV.detailplot	109.112	0.460	109.725
CNV.detailplot_wrap	97.716	0.512	98.419
CNV.fit	62.568	0.152	62.867
CNV.genomeplot	100.184	0.616	101.007
CNV.load	3.000	0.080	3.084
CNV.segment	78.764	0.132	78.995
CNV.write	94.460	0.568	95.219
read.450k.url	8.692	0.220	17.826