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: 2017-10-17 22:59:10 -0400 (Tue, 17 Oct 2017)

EndedAt: 2017-10-17 23:34:20 -0400 (Tue, 17 Oct 2017)

EllapsedTime: 2109.8 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 3.4.2 Patched (2017-10-07 r73498)
* 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           86.09   1.19   87.38
CNV.analysis-class  86.00   1.16   88.08
CNV.detailplot_wrap 85.29   0.86   86.20
CNV.detailplot      82.94   0.98   83.92
CNV.genomeplot      76.30   1.11   77.40
CNV.segment         69.44   0.50   69.93
CNV.bin             48.14   0.64   48.78
CNV.detail          45.26   0.61   45.87
CNV.anno-class      43.96   0.28   44.23
CNV.create_anno     42.68   0.19   42.88
CNV.fit             41.59   0.77   42.36
read.450k.url        8.69   0.62   18.08
CNV.load             6.17   0.31    6.49
* 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	86.00	1.16	88.08
CNV.anno-class	43.96	0.28	44.23
CNV.bin	48.14	0.64	48.78
CNV.create_anno	42.68	0.19	42.88
CNV.data-class	3.69	0.34	4.04
CNV.detail	45.26	0.61	45.87
CNV.detailplot	82.94	0.98	83.92
CNV.detailplot_wrap	85.29	0.86	86.20
CNV.fit	41.59	0.77	42.36
CNV.genomeplot	76.30	1.11	77.40
CNV.load	6.17	0.31	6.49
CNV.segment	69.44	0.50	69.93
CNV.write	86.09	1.19	87.38
read.450k.url	8.69	0.62	18.08