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

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### Running command:
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###   rm -rf BayesPeak.buildbin-libdir BayesPeak.Rcheck && mkdir BayesPeak.buildbin-libdir BayesPeak.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BayesPeak.buildbin-libdir BayesPeak_1.30.0.tar.gz >BayesPeak.Rcheck\00install.out 2>&1 && cp BayesPeak.Rcheck\00install.out BayesPeak-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=BayesPeak.buildbin-libdir --install="check:BayesPeak-install.out" --force-multiarch --no-vignettes --timings BayesPeak_1.30.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/BayesPeak.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 'BayesPeak/DESCRIPTION' ... OK
* this is package 'BayesPeak' version '1.30.0'
* 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 'BayesPeak' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpSKd1so/R.INSTALL1d682c425d11/BayesPeak/man/bayespeak.Rd:72: missing file link 'mclapply'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpSKd1so/R.INSTALL1d682c425d11/BayesPeak/man/bayespeak.Rd:76: missing file link 'mclapply'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/BayesPeak.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
  installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data      1.0Mb
    extdata   5.0Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'IRanges'
A package should be listed in only one of these fields.
* 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' call to 'parallel' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
identify.overfitdiag: no visible global function definition for
  'identify'
plot.job: no visible global function definition for 'plot'
plot.overfitdiag: no visible global function definition for 'plot'
region.overfitdiag: no visible global function definition for 'locator'
region.overfitdiag: no visible global function definition for 'polygon'
Undefined global functions or variables:
  identify locator plot polygon
Consider adding
  importFrom("graphics", "identify", "locator", "plot", "polygon")
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 ... NOTE
S3 methods shown with full name in documentation object 'overfittingDiagnostics':
  'plot.overfitdiag' 'identify.overfitdiag'

S3 methods shown with full name in documentation object 'plot.PP':
  'plot.PP'

S3 methods shown with full name in documentation object 'plot.bed':
  'plot.bed'

S3 methods shown with full name in documentation object 'plot.job':
  'plot.job'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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/BayesPeak.buildbin-libdir/BayesPeak/libs/i386/BayesPeak.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

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
summarise.peaks 164.59   0.04  164.65
bayespeak       163.45   0.05  163.50
plot.job         13.36   0.00   13.40
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
bayespeak       151.90   0.05  151.97
summarise.peaks 151.22   0.03  151.25
plot.job         12.84   0.01   12.86
* 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, 6 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/BayesPeak.Rcheck/00check.log'
for details.


install for i386

* installing *source* package 'BayesPeak' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c bayespeak.c -o bayespeak.o
bayespeak.c: In function 'bayespeak':
bayespeak.c:176:27: warning: variable 'M' set but not used [-Wunused-but-set-variable]
   double  M1, M2, M3, M4, M, a, b;
                           ^
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o BayesPeak.dll tmp.def bayespeak.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/BayesPeak.buildbin-libdir/BayesPeak/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'BayesPeak'
    finding HTML links ... done
    bayespeak                               html  
    finding level-2 HTML links ... done

Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpSKd1so/R.INSTALL1d682c425d11/BayesPeak/man/bayespeak.Rd:72: missing file link 'mclapply'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpSKd1so/R.INSTALL1d682c425d11/BayesPeak/man/bayespeak.Rd:76: missing file link 'mclapply'
    overfitting                             html  
    plot.PP                                 html  
    plot.bed                                html  
    plot.job                                html  
    raw.output.H3K4me3                      html  
    raw.output                              html  
    read.bed                                html  
    summarise.peaks                         html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'BayesPeak' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c bayespeak.c -o bayespeak.o
bayespeak.c: In function 'bayespeak':
bayespeak.c:176:27: warning: variable 'M' set but not used [-Wunused-but-set-variable]
   double  M1, M2, M3, M4, M, a, b;
                           ^
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o BayesPeak.dll tmp.def bayespeak.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/BayesPeak.buildbin-libdir/BayesPeak/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BayesPeak' as BayesPeak_1.30.0.zip
* DONE (BayesPeak)
In R CMD INSTALL
In R CMD INSTALL

CHECK report for BayesPeak on tokay1

Summary

Command output

Installation output

Tests output

Example timings