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

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### Running command:
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###   rm -rf JunctionSeq.buildbin-libdir JunctionSeq.Rcheck && mkdir JunctionSeq.buildbin-libdir JunctionSeq.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=JunctionSeq.buildbin-libdir JunctionSeq_1.8.0.tar.gz >JunctionSeq.Rcheck\00install.out 2>&1 && cp JunctionSeq.Rcheck\00install.out JunctionSeq-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=JunctionSeq.buildbin-libdir --install="check:JunctionSeq-install.out" --force-multiarch --no-vignettes --timings JunctionSeq_1.8.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/JunctionSeq.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 'JunctionSeq/DESCRIPTION' ... OK
* this is package 'JunctionSeq' version '1.8.0'
* 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 'JunctionSeq' 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
Packages in Depends field not imported from:
  'Rcpp' 'RcppArmadillo'
  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 ... OK
* checking Rd files ... NOTE
prepare_Rd: setJunctionSeqCompiledSourcePackage.Rd:23-25: Dropping empty section \examples
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... 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/JunctionSeq.buildbin-libdir/JunctionSeq/libs/i386/JunctionSeq.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
Examples with CPU or elapsed time > 5s
                      user system elapsed
buildAllPlots        10.79  47.87   59.17
buildAllPlotsForGene  1.11   5.39    6.50
defaultColorList      1.00   4.41    5.41
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
buildAllPlots        10.75  44.94   56.12
defaultColorList      1.34   4.69    6.06
buildAllPlotsForGene  1.05   4.53    5.69
* 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/JunctionSeq.Rcheck/00check.log'
for details.


install for i386

* installing *source* package 'JunctionSeq' ...
** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RcppArmadillo/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c DESeq2.cpp -o DESeq2.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RcppArmadillo/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o JunctionSeq.dll tmp.def DESeq2.o RcppExports.o -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -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/JunctionSeq.buildbin-libdir/JunctionSeq/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'JunctionSeq'
    finding HTML links ... done
    JunctionSeqCountSet-class               html  
    finding level-2 HTML links ... done

    buildAllPlots                           html  
    buildAllPlotsForGene                    html  
    defaultColorList                        html  
    estimateEffectSizes                     html  
    estimateJunctionSeqDispersions          html  
    estimateJunctionSeqSizeFactors          html  
    fitJunctionSeqDispersionFunction        html  
    plotDispEsts                            html  
    plotJunctionSeqResultsForGene           html  
    plotMA                                  html  
    readAnnotationData                      html  
    readJunctionSeqCounts                   html  
    runJunctionSeqAnalyses                  html  
    setJunctionSeqCompiledSourcePackage     html  
    testForDiffUsage                        html  
    writeBedTrack                           html  
    writeCompleteResults                    html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'JunctionSeq' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RcppArmadillo/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c DESeq2.cpp -o DESeq2.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RcppArmadillo/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o JunctionSeq.dll tmp.def DESeq2.o RcppExports.o -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -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/JunctionSeq.buildbin-libdir/JunctionSeq/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'JunctionSeq' as JunctionSeq_1.8.0.zip
* DONE (JunctionSeq)
In R CMD INSTALL
In R CMD INSTALL

CHECK report for JunctionSeq on tokay1

Summary

Command output

Installation output

Tests output

Example timings