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

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### Running command:
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###   rm -rf ramwas.buildbin-libdir ramwas.Rcheck && mkdir ramwas.buildbin-libdir ramwas.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ramwas.buildbin-libdir ramwas_1.2.0.tar.gz >ramwas.Rcheck\00install.out 2>&1 && cp ramwas.Rcheck\00install.out ramwas-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=ramwas.buildbin-libdir --install="check:ramwas-install.out" --force-multiarch --no-vignettes --timings ramwas_1.2.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/ramwas.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 'ramwas/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ramwas' version '1.2.0'
* 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 'ramwas' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp0c8OCx/R.INSTALL34c02a4430af/ramwas/man/getCpGset.Rd:16: missing file link 'BSgenome'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp0c8OCx/R.INSTALL34c02a4430af/ramwas/man/insilicoFASTQ.Rd:14: missing file link 'connection'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp0c8OCx/R.INSTALL34c02a4430af/ramwas/man/rowcolSumSq.Rd:32: missing file link 'rowSums'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/ramwas.Rcheck/00install.out' for details.
* 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 ... OK
* 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 ... 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 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/ramwas.buildbin-libdir/ramwas/libs/i386/ramwas.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
getCpGset 5.34   0.22    21.7
** 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, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/ramwas.Rcheck/00check.log'
for details.


install for i386

* installing *source* package 'ramwas' ...
** 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 rw_c_code.c -o rw_c_code.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o ramwas.dll tmp.def rw_c_code.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/ramwas.buildbin-libdir/ramwas/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'ramwas'
    finding HTML links ... done
    QCs                                     html  
    RaMWAS                                  html  
    cachedRDSload                           html  
    findBestNpvs                            html  
    getCpGset                               html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp0c8OCx/R.INSTALL34c02a4430af/ramwas/man/getCpGset.Rd:16: missing file link 'BSgenome'
    getDataByLocation                       html  
    getTestsByLocation                      html  
    injectSNPsMAF                           html  
    finding level-2 HTML links ... done

    insilicoFASTQ                           html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp0c8OCx/R.INSTALL34c02a4430af/ramwas/man/insilicoFASTQ.Rd:14: missing file link 'connection'
    isAbsolutePath                          html  
    makefullpath                            html  
    orthonormalizeCovariates                html  
    parameterDump                           html  
    parameterPreprocess                     html  
    parametersFromFile                      html  
    pipeline                                html  
    plotROC                                 html  
    processCommandLine                      html  
    pvalue2qvalue                           html  
    qqplotFast                              html  
    ramwas0createArtificialData             html  
    ramwasAnnotateLocations                 html  
    ramwasParameters                        html  
    rowcolSumSq                             html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp0c8OCx/R.INSTALL34c02a4430af/ramwas/man/rowcolSumSq.Rd:32: missing file link 'rowSums'
    testPhenotype                           html  
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'ramwas' ...
** 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 rw_c_code.c -o rw_c_code.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o ramwas.dll tmp.def rw_c_code.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/ramwas.buildbin-libdir/ramwas/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ramwas' as ramwas_1.2.0.zip
* DONE (ramwas)
In R CMD INSTALL
In R CMD INSTALL

CHECK report for ramwas on tokay1

Summary

Command output

Installation output

Tests output

Example timings