BioC 3.2: CHECK report for logicFS on perceval

Package: logicFS

Version: 1.40.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings logicFS_1.40.0.tar.gz

StartedAt: 2015-11-10 06:27:12 -0800 (Tue, 10 Nov 2015)

EndedAt: 2015-11-10 06:27:44 -0800 (Tue, 10 Nov 2015)

EllapsedTime: 32.0 seconds

RetCode: 0

Status:  OK

CheckDir: logicFS.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings logicFS_1.40.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/logicFS.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘logicFS/DESCRIPTION’ ... OK
* this is package ‘logicFS’ version ‘1.40.0’
* 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 ‘logicFS’ can be installed ... [2s/2s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 dependencies in R code ... NOTE
'library' or 'require' calls in package code:
  ‘genefilter’ ‘siggenes’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘LogicReg’ ‘mcbiopi’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
adjustPval: no visible global function definition for ‘pi0.est’
adjustPval: no visible global function definition for ‘qvalue.cal’
compPermInput1: no visible global function definition for ‘eval.logreg’
compPermInput3Rebuild: no visible binding for global variable
  ‘eval.logreg’
compPermSet1: no visible global function definition for ‘eval.logreg’
compPermSet3Rebuild: no visible binding for global variable
  ‘eval.logreg’
correctPreds1: no visible global function definition for ‘eval.logreg’
correctPredsRemove1: no visible global function definition for
  ‘eval.logreg’
correctPredsRemove2: no visible binding for global variable
  ‘eval.logreg’
correctPredsRemove3: no visible binding for global variable
  ‘eval.logreg’
correctPredsRemove9: no visible binding for global variable
  ‘eval.logreg’
correctSetPermute1: no visible global function definition for
  ‘eval.logreg’
correctSetRemove1: no visible global function definition for
  ‘eval.logreg’
correctSetRemove2: no visible binding for global variable ‘eval.logreg’
correctSetRemove3: no visible binding for global variable ‘eval.logreg’
correctSetRemove9: no visible binding for global variable ‘eval.logreg’
logic.bagging.default: no visible global function definition for
  ‘logreg.anneal.control’
logic.bagging.default: no visible binding for global variable ‘logreg’
logic.pimp: no visible binding for global variable ‘getPImps’
logicFS.default: no visible global function definition for
  ‘logreg.anneal.control’
mlogreg.default: no visible global function definition for
  ‘logreg.anneal.control’
mlogreg.default: no visible global function definition for ‘logreg’
pimpMLR: no visible binding for global variable ‘getPImps’
predict.logregmodel: no visible global function definition for
  ‘eval.logreg’
standardizeMatImp: no visible global function definition for
  ‘rowttests’
vim.chisq: no visible global function definition for ‘chisqClass’
vim.ebam: no visible global function definition for ‘ebam’
vim.ebam: no visible binding for global variable ‘cat.ebam’
vim.norm: no visible global function definition for ‘rowttests’
vim.signperm: no visible global function definition for ‘rowttests’
* 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 ... [1s/1s] 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/logicFS.Rcheck/00check.log’
for details.

* installing *source* package ‘logicFS’ ...
** 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 (logicFS)

name	user	system	elapsed
logic.bagging	0.001	0.001	0.002
logicFS	0.002	0.000	0.001