BioC 2.12: CHECK report for sagenhaft on george2

Package: sagenhaft

Version: 1.30.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings sagenhaft_1.30.0.tar.gz

StartedAt: 2013-10-09 04:51:34 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 04:54:48 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 194.3 seconds

RetCode: 0

Status:  OK

CheckDir: sagenhaft.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/sagenhaft.Rcheck’
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘sagenhaft/DESCRIPTION’ ... OK
* this is package ‘sagenhaft’ version ‘1.30.0’
* 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 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 for unstated 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 installed files from ‘inst/doc’ ... OK
* checking examples ... [147s/152s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
error.correction        109.158  1.092 114.427
sagelibrary.simulate     29.678  0.036  30.136
sage.library.comparison   4.913  0.148   5.324
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 2 notes.
See
  ‘/home/biocbuild/bbs-2.12-bioc/meat/sagenhaft.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
error.correction	109.158	1.092	114.427
extract.lib	0.000	0.008	0.008
sage.library	0.496	0.048	0.544
sage.library.comparison	4.913	0.148	5.324
sage.test	0.008	0.008	0.020
sage.utilities	0.264	0.004	0.266
sagelibrary.simulate	29.678	0.036	30.136