BioC 2.14: CHECK report for Rolexa on zin2

Package: Rolexa

Version: 1.20.0

Command: /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings Rolexa_1.20.0.tar.gz

StartedAt: 2014-10-08 02:31:02 -0700 (Wed, 08 Oct 2014)

EndedAt: 2014-10-08 02:33:51 -0700 (Wed, 08 Oct 2014)

EllapsedTime: 169.4 seconds

RetCode: 0

Status:  OK

CheckDir: Rolexa.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings Rolexa_1.20.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/Rolexa.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rolexa/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Rolexa’ version ‘1.20.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘fork’
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Rolexa’ can be installed ... [16s/16s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘graphics’ ‘grDevices’ ‘methods’ ‘ShortRead’
A package should be listed in only one of these fields.
* 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
ForkBatch: no visible binding for global variable ‘Rolexa.env’
ForkBatch: no visible global function definition for ‘fork’
ForkBatch: no visible global function definition for ‘wait’
QualityBoxPlots: no visible binding for global variable ‘Rolexa.env’
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [14s/14s] OK
* 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

NOTE: There were 3 notes.
See
  ‘/home/biocbuild/bbs-2.14-bioc/meat/Rolexa.Rcheck/00check.log’
for details.

* installing *source* package ‘Rolexa’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Rolexa)

name	user	system	elapsed
Batch	0.008	0.000	0.009
Model1	4.100	0.032	4.138
Model3	0.320	0.008	0.329
Plots1	1.120	0.008	1.131
Plots2	0.312	0.004	0.333
Plots3	0.212	0.008	0.230