Package: makecdfenv

Version: 1.35.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch makecdfenv_1.35.3.tar.gz

StartedAt: 2013-03-25 03:24:16 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 03:26:12 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 115.2 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: makecdfenv.Rcheck

Warnings: 2

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/makecdfenv.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* 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 for sufficient/correct file permissions ... OK
* checking whether package 'makecdfenv' can be installed ... [6s/6s] 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
* 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 ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [64s/64s] WARNING
Found the following significant warnings:

  Warning: '.path.package' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
                   user system elapsed
make.cdf.package 22.422  0.297  22.730
make.cdf.env     21.871  0.350  22.231
read.cdffile     16.924  0.139  17.066
* 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 were 2 warnings.
NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/makecdfenv.Rcheck/00check.log'
for details.

* installing *source* package 'makecdfenv' ...
creating cache ./config.cache
checking how to run the C preprocessor... cc -E
checking for main in -lz... yes
checking for zlib.h... yes
checking if zlib version >= 1.1.3... yes
updating cache ./config.cache
creating ./config.status
creating src/Makevars
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -DHAVE_ZLIB=1  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c read_cdffile.c -o read_cdffile.o
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o makecdfenv.so read_cdffile.o -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/makecdfenv.Rcheck/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
* DONE (makecdfenv)

name	user	system	elapsed
make.cdf.env	21.871	0.350	22.231
make.cdf.package	22.422	0.297	22.730
read.cdffile	16.924	0.139	17.066