BioC 3.1: CHECK report for conumee on moscato2

Package: conumee

Version: 1.0.0

Command: E:\biocbld\bbs-3.1-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --no-vignettes --timings conumee_1.0.0.tar.gz

StartedAt: 2015-10-09 00:42:58 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 01:06:56 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 1437.5 seconds

RetCode: 0

Status:  OK

CheckDir: conumee.Rcheck

Warnings: 0

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### Running command:
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###   E:\biocbld\bbs-3.1-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --no-vignettes --timings conumee_1.0.0.tar.gz
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* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/conumee.Rcheck'
* using R version 3.2.2 (2015-08-14)
* 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 '1.0.0'
* 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 ... [21s] 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,matrix : .local: no visible binding for global variable 'anno'
* 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 ... [20m] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
CNV.write           165.47   0.46  166.00
CNV.detailplot_wrap 146.63   0.42  147.10
CNV.genomeplot      140.87   0.56  141.43
CNV.analysis-class  137.73   1.11  138.84
CNV.detailplot      137.25   0.56  137.95
CNV.segment         130.26   0.25  130.52
CNV.fit              72.32   0.31   72.66
CNV.detail           65.05   0.32   65.37
CNV.bin              61.93   0.37   62.30
CNV.anno-class       59.05   0.33   59.38
CNV.create_anno      55.49   0.05   55.57
read.450k.url        10.27   0.19   20.50
* 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
  'E:/biocbld/bbs-3.1-bioc/meat/conumee.Rcheck/00check.log'
for details.

* installing *source* package 'conumee' ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
* DONE (conumee)

name	user	system	elapsed
CNV.analysis-class	137.73	1.11	138.84
CNV.anno-class	59.05	0.33	59.38
CNV.bin	61.93	0.37	62.30
CNV.create_anno	55.49	0.05	55.57
CNV.data-class	2.14	0.12	2.26
CNV.detail	65.05	0.32	65.37
CNV.detailplot	137.25	0.56	137.95
CNV.detailplot_wrap	146.63	0.42	147.10
CNV.fit	72.32	0.31	72.66
CNV.genomeplot	140.87	0.56	141.43
CNV.load	2.51	0.21	2.72
CNV.segment	130.26	0.25	130.52
CNV.write	165.47	0.46	166.00
read.450k.url	10.27	0.19	20.50