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

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### Running command:
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###   rm -rf makecdfenv.buildbin-libdir makecdfenv.Rcheck && mkdir makecdfenv.buildbin-libdir makecdfenv.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=makecdfenv.buildbin-libdir makecdfenv_1.54.0.tar.gz >makecdfenv.Rcheck\00install.out 2>&1 && cp makecdfenv.Rcheck\00install.out makecdfenv-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=makecdfenv.buildbin-libdir --install="check:makecdfenv-install.out" --force-multiarch --no-vignettes --timings makecdfenv_1.54.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/makecdfenv.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 'makecdfenv/DESCRIPTION' ... OK
* this is package 'makecdfenv' version '1.54.0'
* 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 'makecdfenv' 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 ... NOTE
Foreign function calls to a different package:
  .Call("CheckCDFXDA", ..., PACKAGE = "affyio")
  .Call("ReadCDFFile", ..., PACKAGE = "affyio")
See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.
* 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/makecdfenv.buildbin-libdir/makecdfenv/libs/i386/makecdfenv.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
make.cdf.env     5.78   0.12    5.94
make.cdf.package 5.77   0.05    5.81
** 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/makecdfenv.Rcheck/00check.log'
for details.


install for i386

* installing *source* package 'makecdfenv' ...

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


** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DHAVE_ZLIB    -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c read_cdffile.c -o read_cdffile.o
read_cdffile.c: In function 'readQC':
read_cdffile.c:576:7: warning: variable 'typeQC' set but not used [-Wunused-but-set-variable]
   int typeQC;
       ^
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o makecdfenv.dll tmp.def read_cdffile.o -LC:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -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/makecdfenv.buildbin-libdir/makecdfenv/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'makecdfenv'
    finding HTML links ... done
    Cdf-class                               html  
    getInfoInAffyFile                       html  
    make.cdf.env                            html  
    make.cdf.package                        html  
    pmormm                                  html  
    read.cdffile                            html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'makecdfenv' ...

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


** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DHAVE_ZLIB    -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c read_cdffile.c -o read_cdffile.o
read_cdffile.c: In function 'readQC':
read_cdffile.c:576:7: warning: variable 'typeQC' set but not used [-Wunused-but-set-variable]
   int typeQC;
       ^
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o makecdfenv.dll tmp.def read_cdffile.o -LC:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -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/makecdfenv.buildbin-libdir/makecdfenv/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'makecdfenv' as makecdfenv_1.54.0.zip
* DONE (makecdfenv)
In R CMD INSTALL
In R CMD INSTALL

CHECK report for makecdfenv on tokay1

Summary

Command output

Installation output

Tests output

Example timings