BioC 3.4: CHECK report for conumee on malbec1

Package: conumee

Version: 1.8.0

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings conumee_1.8.0.tar.gz

StartedAt: 2017-04-14 21:46:56 -0400 (Fri, 14 Apr 2017)

EndedAt: 2017-04-14 22:17:47 -0400 (Fri, 14 Apr 2017)

EllapsedTime: 1850.9 seconds

RetCode: 0

Status:  OK

CheckDir: conumee.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings conumee_1.8.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/conumee.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.8.0’
* 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,matrix: no visible binding for global variable ‘anno’
Undefined global functions or variables:
  anno
* 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  95.212  0.708  96.256
CNV.detailplot_wrap 82.100  0.260  82.420
CNV.write           79.280  0.340  79.670
CNV.detailplot      77.596  0.264  77.927
CNV.genomeplot      74.828  0.236  75.107
CNV.segment         67.064  0.124  67.231
CNV.bin             46.480  0.380  46.910
CNV.fit             41.680  0.004  41.716
CNV.detail          38.468  0.096  38.590
CNV.anno-class      34.752  0.056  34.840
CNV.create_anno     33.040  0.024  33.087
read.450k.url        8.720  0.208  19.761
* 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-3.4-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	95.212	0.708	96.256
CNV.anno-class	34.752	0.056	34.840
CNV.bin	46.48	0.38	46.91
CNV.create_anno	33.040	0.024	33.087
CNV.data-class	1.380	0.008	1.390
CNV.detail	38.468	0.096	38.590
CNV.detailplot	77.596	0.264	77.927
CNV.detailplot_wrap	82.10	0.26	82.42
CNV.fit	41.680	0.004	41.716
CNV.genomeplot	74.828	0.236	75.107
CNV.load	1.956	0.008	1.967
CNV.segment	67.064	0.124	67.231
CNV.write	79.28	0.34	79.67
read.450k.url	8.720	0.208	19.761