Package: conumee

Version: 1.12.0

Command: C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --no-vignettes --timings conumee_1.12.0.tar.gz

StartedAt: 2018-02-21 23:24:22 -0500 (Wed, 21 Feb 2018)

EndedAt: 2018-02-22 00:00:58 -0500 (Thu, 22 Feb 2018)

EllapsedTime: 2195.9 seconds

RetCode: 0

Status:  OK

CheckDir: conumee.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --no-vignettes --timings conumee_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/conumee.Rcheck'
* using R version 3.4.3 (2017-11-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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      107.33   1.41  108.73
CNV.detailplot_wrap 106.43   1.37  107.81
CNV.genomeplot       93.05   1.77   94.81
CNV.write            90.83   1.70   92.55
CNV.segment          86.16   1.08   87.23
CNV.analysis-class   79.50   1.37   80.89
CNV.fit              56.33   0.84   57.18
CNV.detail           45.13   0.39   45.52
CNV.create_anno      43.98   0.09   44.08
CNV.bin              41.97   0.53   42.50
CNV.anno-class       34.67   0.24   34.90
read.450k.url         8.00   0.85   18.51
* 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
  'C:/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)
In R CMD INSTALL

name	user	system	elapsed
CNV.analysis-class	79.50	1.37	80.89
CNV.anno-class	34.67	0.24	34.90
CNV.bin	41.97	0.53	42.50
CNV.create_anno	43.98	0.09	44.08
CNV.data-class	3.11	0.16	3.26
CNV.detail	45.13	0.39	45.52
CNV.detailplot	107.33	1.41	108.73
CNV.detailplot_wrap	106.43	1.37	107.81
CNV.fit	56.33	0.84	57.18
CNV.genomeplot	93.05	1.77	94.81
CNV.load	2.04	0.25	2.30
CNV.segment	86.16	1.08	87.23
CNV.write	90.83	1.70	92.55
read.450k.url	8.00	0.85	18.51