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BioC 3.2: CHECK report for LedPred on zin1

This page was generated on 2015-08-24 10:50:43 -0700 (Mon, 24 Aug 2015).

Package 544/1071HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
LedPred 1.0.0
Aitor Gonzalez
Snapshot Date: 2015-08-23 16:24:14 -0700 (Sun, 23 Aug 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/LedPred
Last Changed Rev: 106728 / Revision: 107696
Last Changed Date: 2015-07-24 06:44:00 -0700 (Fri, 24 Jul 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: LedPred
Version: 1.0.0
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings LedPred_1.0.0.tar.gz
StartedAt: 2015-08-24 01:08:07 -0700 (Mon, 24 Aug 2015)
EndedAt: 2015-08-24 01:13:48 -0700 (Mon, 24 Aug 2015)
EllapsedTime: 341.3 seconds
RetCode: 0
Status:  OK 
CheckDir: LedPred.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings LedPred_1.0.0.tar.gz
###
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##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/LedPred.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘LedPred/DESCRIPTION’ ... OK
* this is package ‘LedPred’ version ‘1.0.0’
* 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 ‘LedPred’ can be installed ... [6s/6s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License components which are templates and need '+ file LICENSE':
  MIT
* 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 ... NOTE
'library' or 'require' call to ‘e1071’ which was already attached by Depends.
  Please remove these calls from your code.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... NOTE
The following files look like leftovers/mistakes:
  ‘LedPred.dvi’
Please remove them from your package.
* checking examples ... [666s/212s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
LedPred       422.976  1.515 123.495
tuneFeatureNb 135.062  0.549  47.951
rankFeatures   82.181  0.608  28.075
mcTune         18.821  0.536   8.734
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [102s/63s]
 [102s/63s] 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
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.2-bioc/meat/LedPred.Rcheck/00check.log’
for details.


LedPred.Rcheck/00install.out:

* installing *source* package ‘LedPred’ ...
** R
** data
*** moving datasets to lazyload DB
Note: the specification for S3 class “AsIs” in package ‘jsonlite’ seems equivalent to one from package ‘BiocGenerics’: not turning on duplicate class definitions for this class.
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Note: the specification for S3 class “AsIs” in package ‘jsonlite’ seems equivalent to one from package ‘BiocGenerics’: not turning on duplicate class definitions for this class.
* DONE (LedPred)

LedPred.Rcheck/LedPred-Ex.timings:

nameusersystemelapsed
LedPred422.976 1.515123.495
createModel0.4020.0120.418
evaluateModelPerformance0.3460.1440.338
mapFeaturesToSeqs0.0010.0000.001
mcTune18.821 0.536 8.734
rankFeatures82.181 0.60828.075
scoreData0.1530.0120.164
tuneFeatureNb135.062 0.549 47.951