BioC 3.1: CHECK report for sagenhaft on petty
This page was generated on 2015-10-09 09:32:45 -0700 (Fri, 09 Oct 2015).
sagenhaft 1.38.1 Tim Beissbarth
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015) | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/sagenhaft | Last Changed Rev: 105889 / Revision: 109384 | Last Changed Date: 2015-07-07 14:52:07 -0700 (Tue, 07 Jul 2015) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK |  |
petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | [ OK ] | OK |  |
morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK |  |
Summary
Package: sagenhaft |
Version: 1.38.1 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings sagenhaft_1.38.1.tar.gz |
StartedAt: 2015-10-09 01:52:02 -0700 (Fri, 09 Oct 2015) |
EndedAt: 2015-10-09 01:54:09 -0700 (Fri, 09 Oct 2015) |
EllapsedTime: 127.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: sagenhaft.Rcheck |
Warnings: 0 |
Command output
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings sagenhaft_1.38.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/sagenhaft.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* 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 ‘1.38.1’
* 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 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
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 files in ‘vignettes’ ... OK
* checking examples ... [90s/90s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
error.correction 63.797 2.444 66.289
sagelibrary.simulate 17.447 0.844 18.298
* 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
* DONE
Status: 3 NOTEs
See
‘/Users/biocbuild/bbs-3.1-bioc/meat/sagenhaft.Rcheck/00check.log’
for details.
sagenhaft.Rcheck/00install.out:
* installing *source* package ‘sagenhaft’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (sagenhaft)
sagenhaft.Rcheck/sagenhaft-Ex.timings:
name | user | system | elapsed
|
error.correction | 63.797 | 2.444 | 66.289 |
|
extract.lib | 0.001 | 0.000 | 0.001 |
|
sage.library | 0.505 | 0.021 | 0.529 |
|
sage.library.comparison | 3.494 | 0.211 | 3.715 |
|
sage.test | 0.012 | 0.001 | 0.013 |
|
sage.utilities | 0.001 | 0.000 | 0.002 |
|
sagelibrary.simulate | 17.447 | 0.844 | 18.298 |
|