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

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf zlibbioc.buildbin-libdir zlibbioc.Rcheck && mkdir zlibbioc.buildbin-libdir zlibbioc.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=zlibbioc.buildbin-libdir zlibbioc_1.24.0.tar.gz >zlibbioc.Rcheck\00install.out 2>&1 && cp zlibbioc.Rcheck\00install.out zlibbioc-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=zlibbioc.buildbin-libdir --install="check:zlibbioc-install.out" --force-multiarch --no-vignettes --timings zlibbioc_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/zlibbioc.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 'zlibbioc/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'zlibbioc' version '1.24.0'
* 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 'zlibbioc' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License components with restrictions not permitted:
  Artistic-2.0 + file LICENSE
* 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/zlibbioc.buildbin-libdir/zlibbioc/libs/i386/zlib1bioc.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.6-bioc/meat/zlibbioc.buildbin-libdir/zlibbioc/libs/i386/zlibbioc.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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/zlibbioc.Rcheck/00check.log'
for details.


install for i386

* installing *source* package 'zlibbioc' ...

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


** libs
mkdir -p "C:/Users/biocbuild/bbs-3.6-bioc/meat/zlibbioc.buildbin-libdir/zlibbioc/include" "C:/Users/biocbuild/bbs-3.6-bioc/meat/zlibbioc.buildbin-libdir/zlibbioc/libs/i386"
make -C zlib-1.2.5 -fwin32/Makefile.gcc libzbioc.a zlib1bioc.dll
make[1]: Entering directory `/cygdrive/c/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpohq3u7/R.INSTALL39285688302e/zlibbioc/src/zlib-1.2.5'
C:/Rtools/mingw_32/bin/gcc -m32  -O3 -Wall -DNO_VIZ -DZ_PREFIX -c -o adler32.o adler32.c
C:/Rtools/mingw_32/bin/gcc -m32  -O3 -Wall -DNO_VIZ -DZ_PREFIX -c -o compress.o compress.c
C:/Rtools/mingw_32/bin/gcc -m32  -O3 -Wall -DNO_VIZ -DZ_PREFIX -c -o crc32.o crc32.c
C:/Rtools/mingw_32/bin/gcc -m32  -O3 -Wall -DNO_VIZ -DZ_PREFIX -c -o deflate.o deflate.c
C:/Rtools/mingw_32/bin/gcc -m32  -O3 -Wall -DNO_VIZ -DZ_PREFIX -c -o gzclose.o gzclose.c
C:/Rtools/mingw_32/bin/gcc -m32  -O3 -Wall -DNO_VIZ -DZ_PREFIX -c -o gzlib.o gzlib.c
C:/Rtools/mingw_32/bin/gcc -m32  -O3 -Wall -DNO_VIZ -DZ_PREFIX -c -o gzread.o gzread.c
C:/Rtools/mingw_32/bin/gcc -m32  -O3 -Wall -DNO_VIZ -DZ_PREFIX -c -o gzwrite.o gzwrite.c
C:/Rtools/mingw_32/bin/gcc -m32  -O3 -Wall -DNO_VIZ -DZ_PREFIX -c -o infback.o infback.c
C:/Rtools/mingw_32/bin/gcc -m32  -O3 -Wall -DNO_VIZ -DZ_PREFIX -c -o inffast.o inffast.c
C:/Rtools/mingw_32/bin/gcc -m32  -O3 -Wall -DNO_VIZ -DZ_PREFIX -c -o inflate.o inflate.c
C:/Rtools/mingw_32/bin/gcc -m32  -O3 -Wall -DNO_VIZ -DZ_PREFIX -c -o inftrees.o inftrees.c
C:/Rtools/mingw_32/bin/gcc -m32  -O3 -Wall -DNO_VIZ -DZ_PREFIX -c -o trees.o trees.c
C:/Rtools/mingw_32/bin/gcc -m32  -O3 -Wall -DNO_VIZ -DZ_PREFIX -c -o uncompr.o uncompr.c
C:/Rtools/mingw_32/bin/gcc -m32  -O3 -Wall -DNO_VIZ -DZ_PREFIX -c -o zutil.o zutil.c
C:/Rtools/mingw_32/bin/ar rcs libzbioc.a adler32.o compress.o crc32.o deflate.o gzclose.o gzlib.o gzread.o gzwrite.o infback.o inffast.o inflate.o inftrees.o trees.o uncompr.o zutil.o 
C:/Rtools/mingw_32/bin/windres --define GCC_WINDRES --target=pe-i386 -o zlibrc.o win32/zlib1.rc
C:/Rtools/mingw_32/bin/gcc -m32 -shared -Wl,--out-implib,libzbiocdll.a  \
-o zlib1bioc.dll win32/zlib.def adler32.o compress.o crc32.o deflate.o gzclose.o gzlib.o gzread.o gzwrite.o infback.o inffast.o inflate.o inftrees.o trees.o uncompr.o zutil.o  zlibrc.o
C:/Rtools/mingw_32/bin/strip zlib1bioc.dll
make[1]: Leaving directory `/cygdrive/c/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpohq3u7/R.INSTALL39285688302e/zlibbioc/src/zlib-1.2.5'
cp zlib-1.2.5/libzbioc.a zlib-1.2.5/zlib1bioc.dll \
            "C:/Users/biocbuild/bbs-3.6-bioc/meat/zlibbioc.buildbin-libdir/zlibbioc/libs/i386"
cp zlib-1.2.5/zconf.h zlib-1.2.5/zlib.h "C:/Users/biocbuild/bbs-3.6-bioc/meat/zlibbioc.buildbin-libdir/zlibbioc/include"
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 R_init_zlibbioc.c -o R_init_zlibbioc.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o zlibbioc.dll tmp.def R_init_zlibbioc.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/zlibbioc.buildbin-libdir/zlibbioc/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'zlibbioc'
    finding HTML links ... done
    pkgconfig                               html  
    zlibbioc-package                        html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'zlibbioc' ...

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


** libs
mkdir -p "C:/Users/biocbuild/bbs-3.6-bioc/meat/zlibbioc.buildbin-libdir/zlibbioc/include" "C:/Users/biocbuild/bbs-3.6-bioc/meat/zlibbioc.buildbin-libdir/zlibbioc/libs/x64"
make -C zlib-1.2.5 -fwin32/Makefile.gcc libzbioc.a zlib1bioc.dll
make[1]: Entering directory `/cygdrive/c/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWw7OIe/R.INSTALL34502b1c1077/zlibbioc/src/zlib-1.2.5'
C:/Rtools/mingw_64/bin/gcc -m64  -O3 -Wall -DNO_VIZ -DZ_PREFIX -c -o adler32.o adler32.c
C:/Rtools/mingw_64/bin/gcc -m64  -O3 -Wall -DNO_VIZ -DZ_PREFIX -c -o compress.o compress.c
C:/Rtools/mingw_64/bin/gcc -m64  -O3 -Wall -DNO_VIZ -DZ_PREFIX -c -o crc32.o crc32.c
C:/Rtools/mingw_64/bin/gcc -m64  -O3 -Wall -DNO_VIZ -DZ_PREFIX -c -o deflate.o deflate.c
C:/Rtools/mingw_64/bin/gcc -m64  -O3 -Wall -DNO_VIZ -DZ_PREFIX -c -o gzclose.o gzclose.c
C:/Rtools/mingw_64/bin/gcc -m64  -O3 -Wall -DNO_VIZ -DZ_PREFIX -c -o gzlib.o gzlib.c
C:/Rtools/mingw_64/bin/gcc -m64  -O3 -Wall -DNO_VIZ -DZ_PREFIX -c -o gzread.o gzread.c
C:/Rtools/mingw_64/bin/gcc -m64  -O3 -Wall -DNO_VIZ -DZ_PREFIX -c -o gzwrite.o gzwrite.c
C:/Rtools/mingw_64/bin/gcc -m64  -O3 -Wall -DNO_VIZ -DZ_PREFIX -c -o infback.o infback.c
C:/Rtools/mingw_64/bin/gcc -m64  -O3 -Wall -DNO_VIZ -DZ_PREFIX -c -o inffast.o inffast.c
C:/Rtools/mingw_64/bin/gcc -m64  -O3 -Wall -DNO_VIZ -DZ_PREFIX -c -o inflate.o inflate.c
C:/Rtools/mingw_64/bin/gcc -m64  -O3 -Wall -DNO_VIZ -DZ_PREFIX -c -o inftrees.o inftrees.c
C:/Rtools/mingw_64/bin/gcc -m64  -O3 -Wall -DNO_VIZ -DZ_PREFIX -c -o trees.o trees.c
C:/Rtools/mingw_64/bin/gcc -m64  -O3 -Wall -DNO_VIZ -DZ_PREFIX -c -o uncompr.o uncompr.c
C:/Rtools/mingw_64/bin/gcc -m64  -O3 -Wall -DNO_VIZ -DZ_PREFIX -c -o zutil.o zutil.c
C:/Rtools/mingw_64/bin/ar rcs libzbioc.a adler32.o compress.o crc32.o deflate.o gzclose.o gzlib.o gzread.o gzwrite.o infback.o inffast.o inflate.o inftrees.o trees.o uncompr.o zutil.o 
C:/Rtools/mingw_64/bin/windres --define GCC_WINDRES --target=pe-x86-64 -o zlibrc.o win32/zlib1.rc
C:/Rtools/mingw_64/bin/gcc -m64 -shared -Wl,--out-implib,libzbiocdll.a  \
-o zlib1bioc.dll win32/zlib.def adler32.o compress.o crc32.o deflate.o gzclose.o gzlib.o gzread.o gzwrite.o infback.o inffast.o inflate.o inftrees.o trees.o uncompr.o zutil.o  zlibrc.o
C:/Rtools/mingw_64/bin/strip zlib1bioc.dll
make[1]: Leaving directory `/cygdrive/c/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWw7OIe/R.INSTALL34502b1c1077/zlibbioc/src/zlib-1.2.5'
cp zlib-1.2.5/libzbioc.a zlib-1.2.5/zlib1bioc.dll \
            "C:/Users/biocbuild/bbs-3.6-bioc/meat/zlibbioc.buildbin-libdir/zlibbioc/libs/x64"
cp zlib-1.2.5/zconf.h zlib-1.2.5/zlib.h "C:/Users/biocbuild/bbs-3.6-bioc/meat/zlibbioc.buildbin-libdir/zlibbioc/include"
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 R_init_zlibbioc.c -o R_init_zlibbioc.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o zlibbioc.dll tmp.def R_init_zlibbioc.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/zlibbioc.buildbin-libdir/zlibbioc/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'zlibbioc' as zlibbioc_1.24.0.zip
* DONE (zlibbioc)
In R CMD INSTALL
In R CMD INSTALL

CHECK report for zlibbioc on tokay1

Summary

Command output

Installation output

Tests output

Example timings