BioC 3.2: CHECK report for conumee on moscato1

Package: conumee

Version: 1.2.0

Command: D:\biocbld\bbs-3.2-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --no-vignettes --timings conumee_1.2.0.tar.gz

StartedAt: 2016-04-23 01:06:18 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 01:33:29 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 1631.7 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: conumee.Rcheck

Warnings: 1

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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_1.2.0.tar.gz
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* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/conumee.Rcheck'
* using R version 3.2.4 (2016-03-10)
* 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 '1.2.0'
* 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 ... [36s] 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 ... WARNING
Undocumented S4 methods:
  generic '[' and siglist 'CNV.data,ANY,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 ... [21m] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
CNV.detailplot_wrap 177.41   0.50  177.94
CNV.write           165.16   1.09  166.26
CNV.detailplot      149.76   0.62  150.69
CNV.genomeplot      144.05   0.91  145.03
CNV.analysis-class  141.75   1.09  145.80
CNV.segment         130.83   0.47  131.34
CNV.fit              81.95   0.67   82.64
CNV.detail           65.05   0.31   65.38
CNV.bin              64.67   0.37   65.05
CNV.create_anno      59.27   0.10   59.39
CNV.anno-class       52.30   0.25   52.54
read.450k.url         9.61   0.21   22.75
* 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: 1 WARNING, 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	141.75	1.09	145.80
CNV.anno-class	52.30	0.25	52.54
CNV.bin	64.67	0.37	65.05
CNV.create_anno	59.27	0.10	59.39
CNV.data-class	1.85	0.14	2.00
CNV.detail	65.05	0.31	65.38
CNV.detailplot	149.76	0.62	150.69
CNV.detailplot_wrap	177.41	0.50	177.94
CNV.fit	81.95	0.67	82.64
CNV.genomeplot	144.05	0.91	145.03
CNV.load	2.83	0.15	2.98
CNV.segment	130.83	0.47	131.34
CNV.write	165.16	1.09	166.26
read.450k.url	9.61	0.21	22.75