BioC 2.12: CHECK report for makecdfenv on moscato2

Package: makecdfenv

Version: 1.35.3

Command: rm -rf makecdfenv.buildbin-libdir && mkdir makecdfenv.buildbin-libdir && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=makecdfenv.buildbin-libdir makecdfenv_1.35.3.tar.gz >makecdfenv-install.out 2>&1 && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD check --library=makecdfenv.buildbin-libdir --install="check:makecdfenv-install.out" --force-multiarch --no-vignettes --timings makecdfenv_1.35.3.tar.gz && mv makecdfenv.buildbin-libdir/* makecdfenv.Rcheck/ && rmdir makecdfenv.buildbin-libdir

StartedAt: 2013-03-25 03:22:02 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 03:23:50 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 108.0 seconds

RetCode: 0

Status: WARNINGS

CheckDir: makecdfenv.Rcheck

Warnings: 1

* using log directory 'E:/biocbld/bbs-2.12-bioc/meat/makecdfenv.Rcheck'
* using R version 3.0.0 beta (2013-03-19 r62328)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'makecdfenv/DESCRIPTION' ... OK
* this is package 'makecdfenv' version '1.35.3'
* 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 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 for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... WARNING
Foreign function calls with 'PACKAGE' argument in a different package:
  .Call("CheckCDFXDA", ..., PACKAGE = "affyio")
  .Call("ReadCDFFile", ..., PACKAGE = "affyio")
Undeclared package in foreign function calls:
   'affyio'
See the chapter 'System and foreign language interfaces' of the
'Writing R Extensions' manual.
* checking R code for possible problems ... NOTE
make.cdf.package: warning in packageDescription("makecdfenv", field =
  "Version"): partial argument match of 'field' to 'fields'
* 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 for portable compilation flags in Makevars ... 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 'E:/biocbld/bbs-2.12-bioc/meat/makecdfenv.buildbin-libdir/makecdfenv/libs/i386/makecdfenv.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'E:/biocbld/bbs-2.12-bioc/meat/makecdfenv.buildbin-libdir/makecdfenv/libs/x64/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.  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 examples ...
** running examples for arch 'i386' ... [23s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
make.cdf.package  8.1   0.05    8.18
make.cdf.env      6.9   0.07    6.97
read.cdffile      6.0   0.03    6.03
** running examples for arch 'x64' ... [24s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
make.cdf.env     8.29   0.11    8.39
make.cdf.package 7.80   0.09    7.90
read.cdffile     5.59   0.05    5.63
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning.
NOTE: There were 2 notes.
See
  'E:/biocbld/bbs-2.12-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
gcc -m32 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -DHAVE_ZLIB    -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -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]
gcc -m32 -shared -s -static-libgcc -o makecdfenv.dll tmp.def read_cdffile.o -LE:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -Ld:/RCompile/CRANpkg/extralibs64/local/lib/i386 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LE:/biocbld/BBS-2˜1.12-/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.12-bioc/meat/makecdfenv.buildbin-libdir/makecdfenv/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'makecdfenv.Rnw' 
** testing if installed package can be loaded

install for x64

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

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


** libs
gcc -m64 -I"E:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG -DHAVE_ZLIB    -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -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]
gcc -m64 -shared -s -static-libgcc -o makecdfenv.dll tmp.def read_cdffile.o -LE:/biocbld/bbs-2.12-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LE:/biocbld/BBS-2˜1.12-/R/bin/x64 -lR
installing to E:/biocbld/bbs-2.12-bioc/meat/makecdfenv.buildbin-libdir/makecdfenv/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'makecdfenv' as makecdfenv_1.35.3.zip
* DONE (makecdfenv)

Summary

Command output