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

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### Running command:
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###   rm -rf Rhtslib.buildbin-libdir Rhtslib.Rcheck && mkdir Rhtslib.buildbin-libdir Rhtslib.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Rhtslib.buildbin-libdir Rhtslib_1.10.0.tar.gz >Rhtslib.Rcheck\00install.out 2>&1 && cp Rhtslib.Rcheck\00install.out Rhtslib-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=Rhtslib.buildbin-libdir --install="check:Rhtslib-install.out" --force-multiarch --no-vignettes --timings Rhtslib_1.10.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/Rhtslib.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 'Rhtslib/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Rhtslib' version '1.10.0'
* 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 ... NOTE
Found the following hidden files and directories:
  src/htslib/.travis.yml
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... WARNING
Found the following file with a non-portable file name:
  src/htslib/m4/lt˜obsolete.m4
These are not fully portable file names.
See section 'Package structure' in the 'Writing R Extensions' manual.
* checking whether package 'Rhtslib' 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 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/Rhtslib.buildbin-libdir/Rhtslib/libs/i386/Rhtslib.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
** 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, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/Rhtslib.Rcheck/00check.log'
for details.


install for i386

* installing *source* package 'Rhtslib' ...

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
cp "winlib/i386/libhts.a" "C:/Users/biocbuild/bbs-3.6-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/lib/i386"/libhts.a
cp ./htslib/htslib/bgzf.h ./htslib/htslib/faidx.h ./htslib/htslib/hfile.h ./htslib/htslib/hts.h ./htslib/htslib/hts_defs.h ./htslib/htslib/kfunc.h ./htslib/htslib/khash.h ./htslib/htslib/khash_str2int.h ./htslib/htslib/klist.h ./htslib/htslib/knetfile.h ./htslib/htslib/kseq.h ./htslib/htslib/ksort.h ./htslib/htslib/kstring.h ./htslib/htslib/regidx.h ./htslib/htslib/sam.h ./htslib/htslib/synced_bcf_reader.h ./htslib/htslib/tbx.h ./htslib/htslib/vcf.h ./htslib/htslib/vcf_sweep.h ./htslib/htslib/vcfutils.h ""C:/Users/biocbuild/bbs-3.6-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/include""
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c Rhtslib.c -o Rhtslib.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o Rhtslib.dll tmp.def Rhtslib.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/Rhtslib.buildbin-libdir/Rhtslib/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'Rhtslib'
    finding HTML links ... done
    Rhtslib-package                         html  
    pkgconfig                               html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'Rhtslib' ...

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
cp "winlib/x64/libhts.a" "C:/Users/biocbuild/bbs-3.6-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/lib/x64"/libhts.a
cp ./htslib/htslib/bgzf.h ./htslib/htslib/faidx.h ./htslib/htslib/hfile.h ./htslib/htslib/hts.h ./htslib/htslib/hts_defs.h ./htslib/htslib/kfunc.h ./htslib/htslib/khash.h ./htslib/htslib/khash_str2int.h ./htslib/htslib/klist.h ./htslib/htslib/knetfile.h ./htslib/htslib/kseq.h ./htslib/htslib/ksort.h ./htslib/htslib/kstring.h ./htslib/htslib/regidx.h ./htslib/htslib/sam.h ./htslib/htslib/synced_bcf_reader.h ./htslib/htslib/tbx.h ./htslib/htslib/vcf.h ./htslib/htslib/vcf_sweep.h ./htslib/htslib/vcfutils.h ""C:/Users/biocbuild/bbs-3.6-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/include""
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c Rhtslib.c -o Rhtslib.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o Rhtslib.dll tmp.def Rhtslib.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/Rhtslib.buildbin-libdir/Rhtslib/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Rhtslib' as Rhtslib_1.10.0.zip
* DONE (Rhtslib)
In R CMD INSTALL
In R CMD INSTALL

CHECK report for Rhtslib on tokay1

Summary

Command output

Installation output

Tests output

Example timings