Package: conumee

Version: 1.13.0

Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --no-vignettes --timings conumee_1.13.0.tar.gz

StartedAt: 2018-02-22 00:14:37 -0500 (Thu, 22 Feb 2018)

EndedAt: 2018-02-22 00:51:58 -0500 (Thu, 22 Feb 2018)

EllapsedTime: 2240.8 seconds

RetCode: 0

Status:  OK

CheckDir: conumee.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --no-vignettes --timings conumee_1.13.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/conumee.Rcheck'
* using R Under development (unstable) (2018-01-28 r74175)
* 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 '1.13.0'
* 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      105.75   1.33  107.11
CNV.genomeplot       97.70   0.81   98.52
CNV.detailplot_wrap  86.20   0.81   87.01
CNV.write            81.22   1.32   82.58
CNV.analysis-class   79.06   1.41   81.55
CNV.segment          79.74   0.38   80.11
CNV.fit              50.36   0.41   50.77
CNV.detail           44.91   0.51   45.43
CNV.bin              39.33   0.44   39.77
CNV.create_anno      35.12   0.01   35.14
CNV.anno-class       32.02   0.17   32.18
read.450k.url         7.86   0.49   16.94
* 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-3.7-bioc/meat/conumee.Rcheck/00check.log'
for details.

* installing *source* package 'conumee' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (conumee)
In R CMD INSTALL

name	user	system	elapsed
CNV.analysis-class	79.06	1.41	81.55
CNV.anno-class	32.02	0.17	32.18
CNV.bin	39.33	0.44	39.77
CNV.create_anno	35.12	0.01	35.14
CNV.data-class	2.22	0.39	2.60
CNV.detail	44.91	0.51	45.43
CNV.detailplot	105.75	1.33	107.11
CNV.detailplot_wrap	86.20	0.81	87.01
CNV.fit	50.36	0.41	50.77
CNV.genomeplot	97.70	0.81	98.52
CNV.load	2.92	0.28	3.20
CNV.segment	79.74	0.38	80.11
CNV.write	81.22	1.32	82.58
read.450k.url	7.86	0.49	16.94