Multiple platform build/check report for BioC 3.8 - CHECK report for spliceSites on tokay1

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### Running command:
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###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:spliceSites.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings spliceSites_1.30.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/spliceSites.Rcheck'
* using R version 3.5.2 (2018-12-20)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'spliceSites/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'spliceSites' 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 'spliceSites' 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 ... 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 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-3.8-bioc/R/library/spliceSites/libs/i386/spliceSites.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 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: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/spliceSites.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/spliceSites_1.30.0.tar.gz && rm -rf spliceSites.buildbin-libdir && mkdir spliceSites.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=spliceSites.buildbin-libdir spliceSites_1.30.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL spliceSites_1.30.0.zip && rm spliceSites_1.30.0.tar.gz spliceSites_1.30.0.zip
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 2645k  100 2645k    0     0  41.0M      0 --:--:-- --:--:-- --:--:-- 43.7M

install for i386

* installing *source* package 'spliceSites' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c spliceSites.c -o spliceSites.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o spliceSites.dll tmp.def spliceSites.o -lm -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/spliceSites.buildbin-libdir/spliceSites/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'spliceSites'
    finding HTML links ... done
    SpliceCountSet-class                    html  
    aaGapSites-class                        html  
    addGeneAligns                           html  
    addGenomeData-ExpressionSet             html  
    addGenomeData-gapSites                  html  
    addHbond                                html  
    addMaxEnt                               html  
    alt_X_ranks                             html  
    annGapSites-class                       html  
    annotate-ExpressionSet                  html  
    annotation                              html  
    as.data.frame-methods                   html  
    c-methods                               html  
    cRanges-class                           html  
    caRanges-class                          html  
    cdRanges-class                          html  
    countByGeneName                         html  
    dim-methods                             html  
    dnaGapSites-class                       html  
    dnaRanges                               html  
    extractByGeneName                       html  
    extractRange                            html  
    gapSites-class                          html  
    gapSites                                html  
    getGapSites                             html  
    hbond-class                             html  
    head-methods                            html  
    initialize-methods                      html  
    keyProfiler-class                       html  
    lrCodons                                html  
    maxEnt-class                            html  
    merge-methods                           html  
    plotGeneAlignDepth                      html  
    rangeByGeneName                         html  
    readCuffGeneFpkm                        html  
    readExpSet                              html  
    readMergedBamGaps                       html  
    readTabledBamGaps                       html  
    seqlogo                                 html  
    silic_tryp                              html  
    sortTable-methods                       html  
    spliceSites-package                     html  
    trim                                    html  
    truncateSeq                             html  
    truncate_seq                            html  
    trypsinCleave                           html  
    uniqueJuncAnn                           html  
    write.files                             html  
    xCodons                                 html  
    xJunc                                   html  
    xJuncStrand                             html  
    z[-methods                              html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'spliceSites' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c spliceSites.c -o spliceSites.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o spliceSites.dll tmp.def spliceSites.o -lm -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/spliceSites.buildbin-libdir/spliceSites/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'spliceSites' as spliceSites_1.30.0.zip
* DONE (spliceSites)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'spliceSites' successfully unpacked and MD5 sums checked
In R CMD INSTALL

CHECK report for spliceSites on tokay1

Summary

Command output

Installation output

Tests output

Example timings