BioC 3.6: CHECK report for conumee on malbec1

Package: conumee

Version: 1.11.0

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings conumee_1.11.0.tar.gz

StartedAt: 2017-08-15 22:14:54 -0400 (Tue, 15 Aug 2017)

EndedAt: 2017-08-15 22:48:15 -0400 (Tue, 15 Aug 2017)

EllapsedTime: 2001.1 seconds

RetCode: 0

Status:  OK

CheckDir: conumee.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings conumee_1.11.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/conumee.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... 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.analysis-class  95.768  2.116  98.487
CNV.detailplot      83.744  0.764  84.567
CNV.detailplot_wrap 81.376  0.720  82.143
CNV.genomeplot      80.096  0.836  81.027
CNV.write           77.920  1.164  79.138
CNV.segment         69.536  0.548  70.124
CNV.detail          44.036  0.764  44.935
CNV.fit             42.416  0.720  43.164
CNV.bin             39.444  0.828  40.291
CNV.create_anno     37.992  0.040  38.051
CNV.anno-class      34.728  0.040  34.790
read.450k.url        8.428  0.224  19.312
* 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
  ‘/home/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	95.768	2.116	98.487
CNV.anno-class	34.728	0.040	34.790
CNV.bin	39.444	0.828	40.291
CNV.create_anno	37.992	0.040	38.051
CNV.data-class	2.732	0.364	3.101
CNV.detail	44.036	0.764	44.935
CNV.detailplot	83.744	0.764	84.567
CNV.detailplot_wrap	81.376	0.720	82.143
CNV.fit	42.416	0.720	43.164
CNV.genomeplot	80.096	0.836	81.027
CNV.load	2.744	0.156	2.900
CNV.segment	69.536	0.548	70.124
CNV.write	77.920	1.164	79.138
read.450k.url	8.428	0.224	19.312