BioC 2.13: CHECK report for clst on zin1

Package: clst

Version: 1.10.0

Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings clst_1.10.0.tar.gz

StartedAt: 2014-04-05 00:23:45 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 00:24:20 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 35.7 seconds

RetCode: 0

Status:  OK

CheckDir: clst.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/clst.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘clst/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘clst’ version ‘1.10.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘clst’ can be installed ... [1s/1s] 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 dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function call to a different package:
  .C("ROC", ..., PACKAGE = "ROC")
See the chapter ‘System and foreign language interfaces’ of the
‘Writing R Extensions’ manual.
* checking R code for possible problems ... OK
* 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 installed files from ‘inst/doc’ ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘clstDemo.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [12s/12s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
scaleDistPlot 10.444  0.036  10.523
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runalltests.R’ [7s/8s]
 [8s/8s] 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 2 notes.
See
  ‘/home/biocbuild/bbs-2.13-bioc/meat/clst.Rcheck/00check.log’
for details.

* installing *source* package ‘clst’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (clst)

name	user	system	elapsed
actino	0.020	0.004	0.020
bvseqs	0.000	0.004	0.004
classify	0.224	0.000	0.225
clst-package	0.200	0.004	0.207
findThreshold	0.088	0.004	0.093
plotDistances	0.256	0.000	0.259
printClst	0.004	0.004	0.007
scaleDistPlot	10.444	0.036	10.523
strep	0.000	0.000	0.002