Package: logicFS

Version: 1.50.0

Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:logicFS.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings logicFS_1.50.0.tar.gz

StartedAt: 2018-10-17 02:59:02 -0400 (Wed, 17 Oct 2018)

EndedAt: 2018-10-17 03:00:06 -0400 (Wed, 17 Oct 2018)

EllapsedTime: 64.5 seconds

RetCode: 0

Status:  OK

CheckDir: logicFS.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:logicFS.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings logicFS_1.50.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/logicFS.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'logicFS/DESCRIPTION' ... OK
* this is package 'logicFS' version '1.50.0'
* 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 whether package 'logicFS' can be installed ... 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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
.onAttach: no visible global function definition for 'winMenuAddItem'
adjustPval: no visible global function definition for 'pi0.est'
adjustPval: no visible global function definition for 'qvalue.cal'
adjustPval: no visible global function definition for 'p.adjust'
check.mat.imp: no visible global function definition for 'is'
checkDataCl: no visible global function definition for 'is'
checkSet: no visible global function definition for 'na.exclude'
checkSet: no visible global function definition for 'na.omit'
compMatProbMLR: no visible global function definition for 'predict'
compNb: no visible global function definition for 'predict'
compPermInput1: no visible global function definition for 'eval.logreg'
compPermInput3Fast: no visible global function definition for 'predict'
compPermInput3Rebuild: no visible binding for global variable
  'eval.logreg'
compPermInput3Rebuild: no visible global function definition for
  'glm.fit'
compPermInput3Rebuild: no visible global function definition for
  'binomial'
compPermSet1: no visible global function definition for 'eval.logreg'
compPermSet3Fast: no visible global function definition for 'predict'
compPermSet3Rebuild: no visible binding for global variable
  'eval.logreg'
compPermSet3Rebuild: no visible global function definition for
  'glm.fit'
compPermSet3Rebuild: no visible global function definition for
  'binomial'
contr.none: no visible global function definition for 'contr.treatment'
contr.snps: no visible global function definition for 'contr.treatment'
correctPreds1: no visible global function definition for 'eval.logreg'
correctPredsPermute2: no visible global function definition for
  'predict'
correctPredsPermute3: no visible global function definition for
  'predict'
correctPredsPermute9: no visible global function definition for
  'predict'
correctPredsRemove1: no visible global function definition for
  'eval.logreg'
correctPredsRemove2: no visible global function definition for
  'predict'
correctPredsRemove2: no visible binding for global variable
  'eval.logreg'
correctPredsRemove2: no visible global function definition for 'lm.fit'
correctPredsRemove3: no visible global function definition for
  'predict'
correctPredsRemove3: no visible binding for global variable
  'eval.logreg'
correctPredsRemove3: no visible global function definition for
  'glm.fit'
correctPredsRemove3: no visible global function definition for
  'binomial'
correctPredsRemove9: no visible global function definition for
  'predict'
correctPredsRemove9: no visible binding for global variable
  'eval.logreg'
correctPredsRemove9: no visible global function definition for
  'glm.fit'
correctPredsRemove9: no visible global function definition for
  'binomial'
correctSetPermute1: no visible global function definition for
  'eval.logreg'
correctSetPermute2: no visible global function definition for 'predict'
correctSetPermute3: no visible global function definition for 'predict'
correctSetPermute9: no visible global function definition for 'predict'
correctSetRemove1: no visible global function definition for
  'eval.logreg'
correctSetRemove2: no visible global function definition for 'predict'
correctSetRemove2: no visible binding for global variable 'eval.logreg'
correctSetRemove2: no visible global function definition for 'lm.fit'
correctSetRemove3: no visible global function definition for 'predict'
correctSetRemove3: no visible binding for global variable 'eval.logreg'
correctSetRemove3: no visible global function definition for 'glm.fit'
correctSetRemove3: no visible global function definition for 'binomial'
correctSetRemove9: no visible global function definition for 'predict'
correctSetRemove9: no visible binding for global variable 'eval.logreg'
correctSetRemove9: no visible global function definition for 'glm.fit'
correctSetRemove9: no visible global function definition for 'binomial'
findB: no visible global function definition for 'qt'
findB: no visible global function definition for 'qf'
getKnots: no visible global function definition for 'is'
getNewProbsMLR: no visible global function definition for 'glm.fit'
getNewProbsMLR: no visible global function definition for 'binomial'
getTree: no visible global function definition for 'is'
getXy: no visible global function definition for 'model.frame'
getXy: no visible global function definition for 'model.matrix'
getXyPred: no visible global function definition for 'delete.response'
getY: no visible global function definition for 'model.response'
logic.bagging.default: no visible global function definition for
  'logreg.anneal.control'
logic.bagging.default: no visible binding for global variable 'logreg'
logic.oob: no visible global function definition for 'is'
logic.oob: no visible global function definition for 'predict'
logic.pimp: no visible global function definition for 'is'
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'
modelMat: no visible global function definition for 'model.matrix'
pimpMLR: no visible binding for global variable 'getPImps'
plot.logicBagg: no visible global function definition for 'plot'
plot.logicFS: no visible global function definition for 'dotchart'
plot.logicFS: no visible global function definition for 'abline'
predict.logicBagg: no visible global function definition for 'predict'
predict.logregmodel: no visible global function definition for
  'eval.logreg'
standardizeMatImp: no visible global function definition for
  'rowttests'
vim.MLR: no visible global function definition for 'predict'
vim.approxPval: no visible global function definition for 'is'
vim.approxPval: no visible global function definition for 'pt'
vim.approxPval: no visible global function definition for 'pf'
vim.chisq: no visible global function definition for 'chisqClass'
vim.chisq: no visible global function definition for 'qchisq'
vim.ebam: no visible global function definition for 'ebam'
vim.ebam: no visible binding for global variable 'cat.ebam'
vim.input: no visible global function definition for 'is'
vim.input: no visible global function definition for 'qt'
vim.input: no visible global function definition for 'qf'
vim.lm: no visible global function definition for 'lm'
vim.lm: no visible global function definition for 'predict'
vim.lm.oneprime: no visible global function definition for 'lm'
vim.lm.oneprime: no visible global function definition for 'predict'
vim.multiple: no visible global function definition for 'glm'
vim.multiple: no visible global function definition for 'predict'
vim.multiple.oneprime: no visible global function definition for 'glm'
vim.multiple.oneprime: no visible global function definition for
  'predict'
vim.norm: no visible global function definition for 'rowttests'
vim.norm: no visible global function definition for 'qt'
vim.permInput: no visible global function definition for 'is'
vim.permSet: no visible global function definition for 'is'
vim.set: no visible global function definition for 'is'
vim.set: no visible global function definition for 'qt'
vim.set: no visible global function definition for 'qf'
vim.signperm: no visible global function definition for 'rowttests'
Undefined global functions or variables:
  abline binomial cat.ebam chisqClass contr.treatment delete.response
  dotchart ebam eval.logreg getPImps glm glm.fit is lm lm.fit logreg
  logreg.anneal.control model.frame model.matrix model.response
  na.exclude na.omit p.adjust pf pi0.est plot predict pt qchisq qf qt
  qvalue.cal rowttests winMenuAddItem
Consider adding
  importFrom("graphics", "abline", "dotchart", "plot")
  importFrom("methods", "is")
  importFrom("stats", "binomial", "contr.treatment", "delete.response",
             "glm", "glm.fit", "lm", "lm.fit", "model.frame",
             "model.matrix", "model.response", "na.exclude", "na.omit",
             "p.adjust", "pf", "predict", "pt", "qchisq", "qf", "qt")
  importFrom("utils", "winMenuAddItem")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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
  'C:/Users/biocbuild/bbs-3.7-bioc/meat/logicFS.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/logicFS_1.50.0.tar.gz && rm -rf logicFS.buildbin-libdir && mkdir logicFS.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=logicFS.buildbin-libdir logicFS_1.50.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL logicFS_1.50.0.zip && rm logicFS_1.50.0.tar.gz logicFS_1.50.0.zip
###
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install for i386

* installing *source* package 'logicFS' ...
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'logicFS'
    finding HTML links ... done
    data.logicfs                            html  
    getMatEval                              html  
    logic.bagging                           html  
    logic.oob                               html  
    logic.pimp                              html  
    finding level-2 HTML links ... done

    logicFS-internal                        html  
    logicFS                                 html  
    make.snp.dummy                          html  
    mlogreg                                 html  
    plot.logicFS                            html  
    predict.logicBagg                       html  
    predict.mlogreg                         html  
    print.logicFS                           html  
    vim.approxPval                          html  
    vim.chisq                               html  
    vim.ebam                                html  
    vim.individual                          html  
    vim.logicFS                             html  
    vim.norm                                html  
    vim.permSet                             html  
    vim.set                                 html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'logicFS' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'logicFS' as logicFS_1.50.0.zip
* DONE (logicFS)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'logicFS' successfully unpacked and MD5 sums checked
In R CMD INSTALL