BioC 3.6: CHECK report for conumee on tokay1

Package: conumee

Version: 1.11.0

Command: C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --no-vignettes --timings conumee_1.11.0.tar.gz

StartedAt: 2017-08-15 22:39:45 -0400 (Tue, 15 Aug 2017)

EndedAt: 2017-08-15 23:18:28 -0400 (Tue, 15 Aug 2017)

EllapsedTime: 2322.9 seconds

RetCode: 0

Status:  OK

CheckDir: conumee.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --no-vignettes --timings conumee_1.11.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.6-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 '1.11.0'
* 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_wrap 102.81   0.83  103.65
CNV.genomeplot      100.02   1.36  101.38
CNV.detailplot       95.15   1.14   96.29
CNV.write            95.03   1.02   96.04
CNV.segment          86.76   0.57   87.35
CNV.analysis-class   83.56   1.06  103.74
CNV.bin              60.74   0.19   60.92
CNV.fit              56.72   0.58   57.29
CNV.detail           56.07   0.34   56.41
CNV.create_anno      48.98   0.06   49.05
CNV.anno-class       47.25   0.12   47.37
read.450k.url         8.72   0.37   19.14
* 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)

name	user	system	elapsed
CNV.analysis-class	83.56	1.06	103.74
CNV.anno-class	47.25	0.12	47.37
CNV.bin	60.74	0.19	60.92
CNV.create_anno	48.98	0.06	49.05
CNV.data-class	2.89	0.13	3.01
CNV.detail	56.07	0.34	56.41
CNV.detailplot	95.15	1.14	96.29
CNV.detailplot_wrap	102.81	0.83	103.65
CNV.fit	56.72	0.58	57.29
CNV.genomeplot	100.02	1.36	101.38
CNV.load	3.42	0.33	3.75
CNV.segment	86.76	0.57	87.35
CNV.write	95.03	1.02	96.04
read.450k.url	8.72	0.37	19.14