BioC 3.2: CHECK report for conumee on linux1.bioconductor.org

Package: conumee

Version: 1.2.0

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings conumee_1.2.0.tar.gz

StartedAt: 2015-10-27 02:28:31 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 02:45:47 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 1035.9 seconds

RetCode: 0

Status:  OK

CheckDir: conumee.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings conumee_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-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 ‘1.2.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘conumee’ can be installed ... [18s/18s] 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/14m] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
CNV.detailplot      107.341  0.331 107.829
CNV.detailplot_wrap 101.314  0.336 101.960
CNV.analysis-class   97.064  0.896  98.032
CNV.write            95.537  0.324  95.956
CNV.genomeplot       94.518  0.328  94.880
CNV.segment          93.817  0.004  93.903
CNV.bin              51.319  0.188  51.546
CNV.detail           51.449  0.024  51.526
CNV.create_anno      46.934  0.000  47.001
CNV.anno-class       44.675  0.008  44.710
CNV.fit              43.675  0.024  43.730
read.450k.url         4.205  0.028   6.708
* 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-3.2-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	97.064	0.896	98.032
CNV.anno-class	44.675	0.008	44.710
CNV.bin	51.319	0.188	51.546
CNV.create_anno	46.934	0.000	47.001
CNV.data-class	1.418	0.068	1.490
CNV.detail	51.449	0.024	51.526
CNV.detailplot	107.341	0.331	107.829
CNV.detailplot_wrap	101.314	0.336	101.960
CNV.fit	43.675	0.024	43.730
CNV.genomeplot	94.518	0.328	94.880
CNV.load	1.561	0.004	1.565
CNV.segment	93.817	0.004	93.903
CNV.write	95.537	0.324	95.956
read.450k.url	4.205	0.028	6.708