Package: HybridMTest

Version: 1.22.0

Command: rm -rf HybridMTest.buildbin-libdir HybridMTest.Rcheck && mkdir HybridMTest.buildbin-libdir HybridMTest.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=HybridMTest.buildbin-libdir HybridMTest_1.22.0.tar.gz >HybridMTest.Rcheck\00install.out 2>&1 && cp HybridMTest.Rcheck\00install.out HybridMTest-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=HybridMTest.buildbin-libdir --install="check:HybridMTest-install.out" --force-multiarch --no-vignettes --timings HybridMTest_1.22.0.tar.gz

StartedAt: 2018-04-12 00:45:34 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 00:46:47 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 73.8 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: HybridMTest.Rcheck

Warnings: 1

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### Running command:
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###   rm -rf HybridMTest.buildbin-libdir HybridMTest.Rcheck && mkdir HybridMTest.buildbin-libdir HybridMTest.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=HybridMTest.buildbin-libdir HybridMTest_1.22.0.tar.gz >HybridMTest.Rcheck\00install.out 2>&1 && cp HybridMTest.Rcheck\00install.out HybridMTest-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=HybridMTest.buildbin-libdir --install="check:HybridMTest-install.out" --force-multiarch --no-vignettes --timings HybridMTest_1.22.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/HybridMTest.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'HybridMTest/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'HybridMTest' version '1.22.0'
* 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 'HybridMTest' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpqmja7Q/R.INSTALL22cc492cc98/HybridMTest/man/GroupComp.data.Rd:30: missing file link 'ExpressionSet'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpqmja7Q/R.INSTALL22cc492cc98/HybridMTest/man/correlation.data.Rd:28: missing file link 'ExpressionSet'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/HybridMTest.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Non-standard license specification:
  GPL Version 2 or later
Standardizable: TRUE
Standardized license specification:
  GPL (>= 2)
* 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
  'Biobase' 'MASS' 'fdrtool' 'survival'
  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
bartlett.test2: no visible global function definition for
  'bartlett.test'
generate.corr.data: no visible global function definition for 'rnorm'
generate.corr.data: no visible global function definition for 'new'
generate.kgroup.data: no visible global function definition for 'new'
generate.surv.data: no visible global function definition for 'rexp'
generate.surv.data: no visible global function definition for 'runif'
generate.surv.data: no visible global function definition for 'new'
grenander: no visible global function definition for 'gcmlcm'
grenander.ebp: no visible global function definition for 'ecdf'
grenander.ebp: no visible global function definition for 'approx'
hybrid.test: no visible global function definition for 'exprs'
hybrid.test: no visible global function definition for 'pData'
ranksum.test: no visible global function definition for 'wilcox.test'
row.T.test: no visible global function definition for 'pt'
row.cox: no visible global function definition for 'Surv'
row.cox: no visible global function definition for 'coxph'
row.cox: no visible global function definition for 'cox.zph'
row.fligner: no visible global function definition for 'pnorm'
row.jung: no visible global function definition for 'pnorm'
row.kruskal.wallis: no visible global function definition for 'pchisq'
row.oneway.anova: no visible global function definition for 'pf'
row.pearson: no visible global function definition for 'pt'
row.slr.resids: no visible global function definition for 'ginv'
row.spearman: no visible global function definition for 'pt'
shapiro.test2: no visible global function definition for 'shapiro.test'
Undefined global functions or variables:
  Surv approx bartlett.test cox.zph coxph ecdf exprs gcmlcm ginv new
  pData pchisq pf pnorm pt rexp rnorm runif shapiro.test wilcox.test
Consider adding
  importFrom("methods", "new")
  importFrom("stats", "approx", "bartlett.test", "ecdf", "pchisq", "pf",
             "pnorm", "pt", "rexp", "rnorm", "runif", "shapiro.test",
             "wilcox.test")
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 installed files from 'inst/doc' ... 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: 1 WARNING, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/HybridMTest.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'HybridMTest' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'HybridMTest'
    finding HTML links ... done
    GroupComp.data                          html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpqmja7Q/R.INSTALL22cc492cc98/HybridMTest/man/GroupComp.data.Rd:30: missing file link 'ExpressionSet'
    HybridMTest-package                     html  
    correlation.data                        html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpqmja7Q/R.INSTALL22cc492cc98/HybridMTest/man/correlation.data.Rd:28: missing file link 'ExpressionSet'
    grenander.ebp                           html  
    hybrid.test                             html  
    row.kgrp.shapiro                        html  
    row.kruskal.wallis                      html  
    row.oneway.anova                        html  
    row.pearson                             html  
    row.slr.shapiro                         html  
    row.spearman                            html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'HybridMTest' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'HybridMTest' as HybridMTest_1.22.0.zip
* DONE (HybridMTest)
In R CMD INSTALL
In R CMD INSTALL