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

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### Running command:
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###   rm -rf hapFabia.buildbin-libdir hapFabia.Rcheck && mkdir hapFabia.buildbin-libdir hapFabia.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=hapFabia.buildbin-libdir hapFabia_1.20.0.tar.gz >hapFabia.Rcheck\00install.out 2>&1 && cp hapFabia.Rcheck\00install.out hapFabia-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=hapFabia.buildbin-libdir --install="check:hapFabia-install.out" --force-multiarch --no-vignettes --timings hapFabia_1.20.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/hapFabia.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 'hapFabia/DESCRIPTION' ... OK
* this is package 'hapFabia' version '1.20.0'
* 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 'hapFabia' 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
File 'hapFabia/R/zzz.R':
  .onLoad calls:
    packageStartupMessage("+--------------------------+          #    #    ##    #####     \n",     "|#.....#...#.......#.#....#|          #    #   #  #   #    #    \n",     "|#.....#...#.......#.#....#|          ######  #    #  #    #    \n",     "|#.....#...#...............|          #    #  ######  #####     \n",     "|#.....#...#.......#.#....#|          #    #  #    #  #         \n",     "|#.....#...#...............|          #    #  #    #  #         \n",     "|#.....#...#.......#.#....#|  #######                           \n",     "|..................#.#....#|  #         ##    #####   #    ##   \n",     "|#.....#...#.......#.#....#|  #        #  #   #    #  #   #  #  \n",     "|..................#.#....#|  #####   #    #  #####   #  #    # \n",     "|#.....#...#.......#.#....#|  #       ######  #    #  #  ###### \n",     "|#.....#...#.......#.#....#|  #       #    #  #    #  #  #    # \n",     "+--------------------------+  #       #    #  #####   #  #    # \n")
    packageStartupMessage("Citation: S. Hochreiter,", "\n", "HapFABIA: Identification of very short segments of identity by descent characterized by rare variants in large sequencing data,",     "\n", "Nucleic Acids Research, 2013, doi: 10.1093/nar/gkt1013.",     "\n", "BibTex: enter 'toBibtex(citation(\"hapFabia\"))'",     "\n\n", "Homepage: http://www.bioinf.jku.at/software/hapFabia/index.html",     "\n\n", "hapFabia Package Version ", version, "\n")

See section 'Good practice' in '?.onAttach'.
* 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 shell scripts ... 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/hapFabia.buildbin-libdir/hapFabia/libs/i386/hapFabia.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
iterateIntervals 6.56   0.45    7.06
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
iterateIntervals 9.04   0.61    9.66
* 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-3.6-bioc/meat/hapFabia.Rcheck/00check.log'
for details.


install for i386

* installing *source* package 'hapFabia' ...
** 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 interfaceR.c -o interfaceR.o
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 split_sparse_matrixB.c -o split_sparse_matrixB.o
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 vcftoFABIAB.c -o vcftoFABIAB.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o hapFabia.dll tmp.def interfaceR.o split_sparse_matrixB.o vcftoFABIAB.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/hapFabia.buildbin-libdir/hapFabia/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'hapFabia'
    finding HTML links ... done
    IBDsegment-class                        html  
    IBDsegmentList-class                    html  
    IBDsegmentList2excel                    html  
    analyzeIBDsegments                      html  
    chr1ASW1000G                            html  
    compareIBDsegmentLists                  html  
    extractIBDsegments                      html  
    findDenseRegions                        html  
    hapFabia                                html  
    hapFabiaVersion                         html  
    hapRes                                  html  
    identifyDuplicates                      html  
    iterateIntervals                        html  
    makePipelineFile                        html  
    matrixPlot                              html  
    mergeIBDsegmentLists                    html  
    mergedIBDsegmentList                    html  
    plotIBDsegment                          html  
    res                                     html  
    setAnnotation                           html  
    setStatistics                           html  
    sim                                     html  
    simu                                    html  
    simulateIBDsegments                     html  
    simulateIBDsegmentsFabia                html  
    split_sparse_matrix                     html  
    toolsFactorizationClass                 html  
    vcftoFABIA                              html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'hapFabia' ...
** 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 interfaceR.c -o interfaceR.o
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 split_sparse_matrixB.c -o split_sparse_matrixB.o
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 vcftoFABIAB.c -o vcftoFABIAB.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o hapFabia.dll tmp.def interfaceR.o split_sparse_matrixB.o vcftoFABIAB.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/hapFabia.buildbin-libdir/hapFabia/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'hapFabia' as hapFabia_1.20.0.zip
* DONE (hapFabia)
In R CMD INSTALL
In R CMD INSTALL

CHECK report for hapFabia on tokay1

Summary

Command output

Installation output

Tests output

Example timings