BioC 2.13: CHECK report for sagenhaft on perceval

Package: sagenhaft

Version: 1.32.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch sagenhaft_1.32.0.tar.gz

StartedAt: 2014-04-05 04:13:59 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 04:16:38 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 159.3 seconds

RetCode: 0

Status:  OK

CheckDir: sagenhaft.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/sagenhaft.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘sagenhaft/DESCRIPTION’ ... OK
* this is package ‘sagenhaft’ version ‘1.32.0’
* 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 ‘sagenhaft’ can be installed ... [2s/3s] OK
* checking installed package size ... NOTE
  installed size is  7.2Mb
  sub-directories of 1Mb or more:
    extdata   7.0Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘methods’ ‘SparseM’
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 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
sage.test: warning in dbinom(0:isize, p = (prob[i])[1], size = isize):
  partial argument match of 'p' to 'prob'
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘SAGEnhaft.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [119s/122s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
error.correction     81.732  4.158  87.559
sagelibrary.simulate 25.591  1.264  28.029
* 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 4 notes.
See
  ‘/Users/biocbuild/bbs-2.13-bioc/meat/sagenhaft.Rcheck/00check.log’
for details.

* installing *source* package ‘sagenhaft’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import by ‘SparseM::coerce’ when loading ‘sagenhaft’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import by ‘SparseM::coerce’ when loading ‘sagenhaft’
* DONE (sagenhaft)

name	user	system	elapsed
error.correction	81.732	4.158	87.559
extract.lib	0.002	0.005	0.008
sage.library	0.413	0.031	0.445
sage.library.comparison	4.002	0.349	4.575
sage.test	0.012	0.008	0.020
sage.utilities	0.162	0.035	0.202
sagelibrary.simulate	25.591	1.264	28.029