Package: DeMAND

Version: 1.10.0

Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DeMAND.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings DeMAND_1.10.0.tar.gz

StartedAt: 2018-10-17 01:31:29 -0400 (Wed, 17 Oct 2018)

EndedAt: 2018-10-17 01:31:59 -0400 (Wed, 17 Oct 2018)

EllapsedTime: 30.4 seconds

RetCode: 0

Status:  OK

CheckDir: DeMAND.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:DeMAND.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings DeMAND_1.10.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/DeMAND.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 'DeMAND/DESCRIPTION' ... OK
* this is package 'DeMAND' version '1.10.0'
* 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 'DeMAND' 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' call to 'KernSmooth' which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: 'KernSmooth'
  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
.ks.dist.fixed.pareto: no visible global function definition for
  'ks.test'
.ks.resimulate.pareto.tail: no visible global function definition for
  'rbinom'
.pareto.fit.regression.cdf: no visible global function definition for
  'lm'
.pareto.fit.regression.cdf: no visible global function definition for
  'coef'
KLD2D: no visible global function definition for 'bw.nrd'
KLD2D: no visible global function definition for 'bkde2D'
eucdf: no visible global function definition for 'ecdf'
eucdf : at.knot.prob.jump: no visible global function definition for
  'knots'
eucdf : x.eucdf: no visible global function definition for 'knots'
integratePvalues: no visible global function definition for 'lm'
integratePvalues: no visible global function definition for 'cov'
integratePvalues: no visible global function definition for 'pchisq'
plot.eucdf.loglog: no visible global function definition for 'plot'
printDeMAND: no visible global function definition for 'head'
rpareto: no visible global function definition for 'runif'
runDeMAND: no visible global function definition for 'na.exclude'
runDeMAND: no visible global function definition for 'quantile'
runDeMAND: no visible global function definition for 'p.adjust'
Undefined global functions or variables:
  bkde2D bw.nrd coef cov ecdf head knots ks.test lm na.exclude p.adjust
  pchisq plot quantile rbinom runif
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "bw.nrd", "coef", "cov", "ecdf", "knots",
             "ks.test", "lm", "na.exclude", "p.adjust", "pchisq",
             "quantile", "rbinom", "runif")
  importFrom("utils", "head")
to your NAMESPACE file.
* 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/DeMAND.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/DeMAND_1.10.0.tar.gz && rm -rf DeMAND.buildbin-libdir && mkdir DeMAND.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DeMAND.buildbin-libdir DeMAND_1.10.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL DeMAND_1.10.0.zip && rm DeMAND_1.10.0.tar.gz DeMAND_1.10.0.zip
###
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install for i386

* installing *source* package 'DeMAND' ...
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'DeMAND'
    finding HTML links ... done
    bcellAnno                               html  
    bcellExp                                html  
    bcellNetwork                            html  
    caseIndex                               html  
    controlIndex                            html  
    demand-instance                         html  
    demandClass                             html  
    printDeMAND                             html  
    runDeMAND                               html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'DeMAND' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DeMAND' as DeMAND_1.10.0.zip
* DONE (DeMAND)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'DeMAND' successfully unpacked and MD5 sums checked
In R CMD INSTALL