BioC 3.1: CHECK report for conumee on zin2

Package: conumee

Version: 1.0.0

Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings conumee_1.0.0.tar.gz

StartedAt: 2015-10-08 23:55:38 -0700 (Thu, 08 Oct 2015)

EndedAt: 2015-10-09 00:19:14 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 1416.0 seconds

RetCode: 0

Status:  OK

CheckDir: conumee.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings conumee_1.0.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/conumee.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.0.0’
* 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 ... [16s/23s] 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 ... 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 ... [14m/20m] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
CNV.analysis-class  101.419  0.579 130.928
CNV.genomeplot      100.188  0.490 145.627
CNV.detailplot_wrap  99.496  0.341 148.162
CNV.write            98.136  0.360 136.352
CNV.detailplot       94.659  0.406 138.984
CNV.segment          88.898  0.107 133.136
CNV.fit              48.720  0.045  72.303
CNV.bin              45.093  0.072  71.724
CNV.detail           43.747  0.032  60.070
CNV.anno-class       40.775  0.129  59.550
CNV.create_anno      40.804  0.011  56.790
read.450k.url         4.365  0.104  14.867
* 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-3.1-bioc/meat/conumee.Rcheck/00check.log’
for details.

* installing *source* package ‘conumee’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (conumee)

name	user	system	elapsed
CNV.analysis-class	101.419	0.579	130.928
CNV.anno-class	40.775	0.129	59.550
CNV.bin	45.093	0.072	71.724
CNV.create_anno	40.804	0.011	56.790
CNV.data-class	1.335	0.004	1.890
CNV.detail	43.747	0.032	60.070
CNV.detailplot	94.659	0.406	138.984
CNV.detailplot_wrap	99.496	0.341	148.162
CNV.fit	48.720	0.045	72.303
CNV.genomeplot	100.188	0.490	145.627
CNV.load	1.605	0.096	1.873
CNV.segment	88.898	0.107	133.136
CNV.write	98.136	0.360	136.352
read.450k.url	4.365	0.104	14.867