Multiple platform build/check report for BioC 3.6 - CHECK report for dexus on tokay1

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### Running command:
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###   rm -rf dexus.buildbin-libdir dexus.Rcheck && mkdir dexus.buildbin-libdir dexus.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=dexus.buildbin-libdir dexus_1.18.0.tar.gz >dexus.Rcheck\00install.out 2>&1 && cp dexus.Rcheck\00install.out dexus-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=dexus.buildbin-libdir --install="check:dexus-install.out" --force-multiarch --no-vignettes --timings dexus_1.18.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/dexus.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 'dexus/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'dexus' version '1.18.0'
* 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 'dexus' 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
** 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
'library' or 'require' calls in package code:
  'DESeq' 'parallel' 'statmod' 'stats'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: 'BiocGenerics'
  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
dexss : <anonymous>: no visible global function definition for 'hist'
dexss: no visible global function definition for 'runif'
dexss: no visible global function definition for 'new'
dexus : <anonymous>: no visible global function definition for 'hist'
dexus: no visible global function definition for 'runif'
dexus: no visible global function definition for 'new'
dexus.parallel: no visible global function definition for 'mclapply'
dexus.parallel: no visible global function definition for 'new'
getSizeNB: no visible global function definition for 'var'
initialize.clusters.kmeans: no visible global function definition for
  'kmeans'
initialize.clusters.kmeans: no visible global function definition for
  'median'
initialize.clusters.kmeans: no visible global function definition for
  'rnorm'
initialize.clusters.quantiles: no visible global function definition
  for 'rnorm'
initialize.clusters.quantiles: no visible global function definition
  for 'quantile'
initialize.clusters.quantiles : <anonymous>: no visible global function
  definition for 'rnorm'
nbinomTestForMatrices : <anonymous>: no visible global function
  definition for 'dnbinom'
normalize.rle : <anonymous>: no visible global function definition for
  'median'
normalize.uq : <anonymous>: no visible global function definition for
  'quantile'
testMulticlass : <anonymous>: no visible global function definition for
  'deviance'
testMulticlass : <anonymous>: no visible global function definition for
  'pchisq'
INIThreshold<-,DEXUSResult: no visible global function definition for
  'slot<-'
[,DEXUSResult-character: no visible global function definition for
  'new'
[,DEXUSResult-logical: no visible global function definition for 'new'
[,DEXUSResult-numeric: no visible global function definition for 'new'
plot,DEXUSResult-missing: no visible global function definition for
  'par'
plot,DEXUSResult-missing: no visible global function definition for
  'colorRampPalette'
plot,DEXUSResult-missing: no visible global function definition for
  'image'
plot,DEXUSResult-missing: no visible global function definition for
  'rect'
plot,DEXUSResult-missing: no visible global function definition for
  'points'
plot,DEXUSResult-missing: no visible global function definition for
  'axis'
Undefined global functions or variables:
  axis colorRampPalette deviance dnbinom hist image kmeans mclapply
  median new par pchisq points quantile rect rnorm runif slot<- var
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("graphics", "axis", "hist", "image", "par", "points",
             "rect")
  importFrom("methods", "new", "slot<-")
  importFrom("stats", "deviance", "dnbinom", "kmeans", "median",
             "pchisq", "quantile", "rnorm", "runif", "var")
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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.6-bioc/meat/dexus.buildbin-libdir/dexus/libs/i386/dexus.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* 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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/dexus.Rcheck/00check.log'
for details.


install for i386

* installing *source* package 'dexus' ...
** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c dexus.cpp -o dexus.o
dexus.cpp: In function 'SEXPREC* dexus_impl(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, int*, SEXP, SEXP, SEXP)':
dexus.cpp:193:15: warning: unused variable 'DEFAULT_R' [-Wunused-variable]
  const double DEFAULT_R = 20; // R value used when re-setting clusters
               ^
dexus.cpp: In function 'SEXPREC* dexss_impl(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, int*, SEXP, SEXP, SEXP)':
dexus.cpp:575:15: warning: unused variable 'DEFAULT_R' [-Wunused-variable]
  const double DEFAULT_R = 20; // R value used when re-setting clusters
               ^
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o dexus.dll tmp.def dexus.o -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/dexus.buildbin-libdir/dexus/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'dexus'
    finding HTML links ... done
    DEXUSResult-class                       html  
    DEXUSResult-subset                      html  
    INI                                     html  
    INIThreshold-set                        html  
    accessors                               html  
    countsBottomly                          html  
    countsGilad                             html  
    countsLi                                html  
    countsMontgomery                        html  
    countsPickrell                          html  
    dexss                                   html  
    dexus                                   html  
    dexus.parallel                          html  
    getSizeNB                               html  
    normalizeData                           html  
    plot                                    html  
    sort                                    html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'dexus' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c dexus.cpp -o dexus.o
dexus.cpp: In function 'SEXPREC* dexus_impl(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, int*, SEXP, SEXP, SEXP)':
dexus.cpp:193:15: warning: unused variable 'DEFAULT_R' [-Wunused-variable]
  const double DEFAULT_R = 20; // R value used when re-setting clusters
               ^
dexus.cpp: In function 'SEXPREC* dexss_impl(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, int*, SEXP, SEXP, SEXP)':
dexus.cpp:575:15: warning: unused variable 'DEFAULT_R' [-Wunused-variable]
  const double DEFAULT_R = 20; // R value used when re-setting clusters
               ^
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o dexus.dll tmp.def dexus.o -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/dexus.buildbin-libdir/dexus/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'dexus' as dexus_1.18.0.zip
* DONE (dexus)
In R CMD INSTALL
In R CMD INSTALL

CHECK report for dexus on tokay1

Summary

Command output

Installation output

Tests output

Example timings