BioC 3.2: CHECK report for conumee on moscato1

Package: conumee

Version: 1.1.0

Command: D:\biocbld\bbs-3.2-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --no-vignettes --timings conumee_1.1.0.tar.gz

StartedAt: 2015-08-20 03:06:23 -0700 (Thu, 20 Aug 2015)

EndedAt: 2015-08-20 03:33:09 -0700 (Thu, 20 Aug 2015)

EllapsedTime: 1606.5 seconds

RetCode: 0

Status:  OK

CheckDir: conumee.Rcheck

Warnings: 0

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### Running command:
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###   D:\biocbld\bbs-3.2-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --no-vignettes --timings conumee_1.1.0.tar.gz
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* using log directory 'D:/biocbld/bbs-3.2-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 '1.1.0'
* 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 ... [29s] 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 ... [22m] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
CNV.detailplot_wrap 164.24   0.59  164.83
CNV.detailplot      157.67   0.50  158.45
CNV.genomeplot      154.50   0.61  156.45
CNV.analysis-class  150.86   1.25  157.34
CNV.write           146.41   0.62  147.04
CNV.segment         128.35   0.24  128.63
CNV.fit              76.38   0.38   76.75
CNV.detail           76.03   0.36   76.43
CNV.bin              74.97   0.44   75.46
CNV.create_anno      69.27   0.04   69.34
CNV.anno-class       65.46   0.17   65.64
read.450k.url         9.97   0.14   23.68
* 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
  'D:/biocbld/bbs-3.2-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)

name	user	system	elapsed
CNV.analysis-class	150.86	1.25	157.34
CNV.anno-class	65.46	0.17	65.64
CNV.bin	74.97	0.44	75.46
CNV.create_anno	69.27	0.04	69.34
CNV.data-class	2.61	0.11	2.71
CNV.detail	76.03	0.36	76.43
CNV.detailplot	157.67	0.50	158.45
CNV.detailplot_wrap	164.24	0.59	164.83
CNV.fit	76.38	0.38	76.75
CNV.genomeplot	154.50	0.61	156.45
CNV.load	2.40	0.15	2.56
CNV.segment	128.35	0.24	128.63
CNV.write	146.41	0.62	147.04
read.450k.url	9.97	0.14	23.68