Package: conumee

Version: 1.14.0

Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:conumee.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings conumee_1.14.0.tar.gz

StartedAt: 2018-10-15 23:28:37 -0400 (Mon, 15 Oct 2018)

EndedAt: 2018-10-15 23:57:10 -0400 (Mon, 15 Oct 2018)

EllapsedTime: 1712.9 seconds

RetCode: 0

Status:  OK

CheckDir: conumee.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:conumee.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings conumee_1.14.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/conumee.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.14.0’
* 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.analysis-class  98.012  0.720  99.134
CNV.write           86.356  0.288  86.703
CNV.detailplot_wrap 82.028  0.380  82.465
CNV.detailplot      81.692  0.436  82.191
CNV.genomeplot      77.568  0.464  78.192
CNV.segment         76.144  0.024  76.226
CNV.detail          47.952  0.136  48.126
CNV.bin             44.008  0.264  44.300
CNV.fit             42.984  0.120  43.136
CNV.create_anno     38.080  0.000  38.103
CNV.anno-class      37.300  0.008  37.335
read.450k.url        7.416  0.208  18.610
* 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-3.7-bioc/meat/conumee.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL conumee
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* installing to library ‘/home/biocbuild/bbs-3.7-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	98.012	0.720	99.134
CNV.anno-class	37.300	0.008	37.335
CNV.bin	44.008	0.264	44.300
CNV.create_anno	38.080	0.000	38.103
CNV.data-class	2.440	0.108	2.551
CNV.detail	47.952	0.136	48.126
CNV.detailplot	81.692	0.436	82.191
CNV.detailplot_wrap	82.028	0.380	82.465
CNV.fit	42.984	0.120	43.136
CNV.genomeplot	77.568	0.464	78.192
CNV.load	3.232	0.052	3.400
CNV.segment	76.144	0.024	76.226
CNV.write	86.356	0.288	86.703
read.450k.url	7.416	0.208	18.610