BioC 3.5: CHECK report for conumee on tokay2

Package: conumee

Version: 1.10.0

Command: C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --no-vignettes --timings conumee_1.10.0.tar.gz

StartedAt: 2017-08-15 22:56:10 -0400 (Tue, 15 Aug 2017)

EndedAt: 2017-08-15 23:34:09 -0400 (Tue, 15 Aug 2017)

EllapsedTime: 2278.8 seconds

RetCode: 0

Status:  OK

CheckDir: conumee.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --no-vignettes --timings conumee_1.10.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/conumee.Rcheck'
* using R version 3.4.1 (2017-06-30)
* 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 '1.10.0'
* 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.write           131.18   1.03  132.22
CNV.detailplot_wrap 112.27   1.31  113.58
CNV.detailplot      101.98   1.37  103.36
CNV.segment          96.93   0.68   97.64
CNV.genomeplot       94.22   1.09   95.31
CNV.analysis-class   83.74   1.43   85.48
CNV.detail           55.88   0.83   56.71
CNV.fit              54.17   1.18   55.34
CNV.create_anno      51.39   0.19   51.58
CNV.bin              50.50   0.45   50.95
CNV.anno-class       37.25   0.16   37.41
read.450k.url        10.73   0.66   20.17
* 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-3.5-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	83.74	1.43	85.48
CNV.anno-class	37.25	0.16	37.41
CNV.bin	50.50	0.45	50.95
CNV.create_anno	51.39	0.19	51.58
CNV.data-class	2.84	0.33	3.17
CNV.detail	55.88	0.83	56.71
CNV.detailplot	101.98	1.37	103.36
CNV.detailplot_wrap	112.27	1.31	113.58
CNV.fit	54.17	1.18	55.34
CNV.genomeplot	94.22	1.09	95.31
CNV.load	3.22	0.30	3.52
CNV.segment	96.93	0.68	97.64
CNV.write	131.18	1.03	132.22
read.450k.url	10.73	0.66	20.17