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BioC 2.13: CHECK report for sagenhaft on perceval

This page was generated on 2014-04-05 09:51:44 -0700 (Sat, 05 Apr 2014).

Package 640/750HostnameOS / ArchBUILDCHECKBUILD BIN
sagenhaft 1.32.0
Tim Beissbarth
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/sagenhaft
Last Changed Rev: 81642 / Revision: 88450
Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

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

Command output

* 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.

sagenhaft.Rcheck/00install.out:

* 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)

sagenhaft.Rcheck/sagenhaft-Ex.timings:

nameusersystemelapsed
error.correction81.732 4.15887.559
extract.lib0.0020.0050.008
sage.library0.4130.0310.445
sage.library.comparison4.0020.3494.575
sage.test0.0120.0080.020
sage.utilities0.1620.0350.202
sagelibrary.simulate25.591 1.26428.029