BioC 2.12: CHECK report for affy on pelham

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/affy.Rcheck'
* using R version 3.0.0 beta (2013-03-21 r62346)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'affy/DESCRIPTION' ... OK
* this is package 'affy' version '1.37.4'
* 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 'affy' can be installed ... [9s/9s] 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 ... NOTE
Foreign function calls with 'PACKAGE' argument in a different package:
  .Call("read_abatch", ..., PACKAGE = "affyio")
  .Call("read_abatch_stddev", ..., PACKAGE = "affyio")
See the chapter 'System and foreign language interfaces' of the
'Writing R Extensions' manual.
* checking R code for possible problems ... NOTE
featureNames,AffyBatch: warning in ls(env = cdf.envir): partial
  argument match of 'env' to 'envir'
geneNames,AffyBatch: warning in ls(env = cdf.envir): partial argument
  match of 'env' to 'envir'
show,AffyBatch: warning in ls(env = cdf.env): partial argument match of
  'env' to 'envir'
cleancdfname: no visible binding for global variable 'mapCdfName'
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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 installed files from 'inst/doc' ... OK
* checking examples ... [182s/208s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
mas5                  58.056  0.658  59.427
MAplot                31.910  1.100  35.867
expresso              27.373  0.954  32.688
bgc                    8.836  0.471  10.322
AffyBatch-class        8.313  0.248   8.654
AffyRNAdeg             6.568  0.169   6.785
xy2indices             4.968  0.440   5.582
ProgressBarText-class  1.625  0.121  17.308
* 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

NOTE: There were 2 notes.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/affy.Rcheck/00check.log'
for details.

* installing *source* package 'affy' ...
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
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DHAVE_ZLIB=1  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/preprocessCore/include"   -fPIC  -mtune=core2 -g -O2  -c chipbackground.c -o chipbackground.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DHAVE_ZLIB=1  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/preprocessCore/include"   -fPIC  -mtune=core2 -g -O2  -c getall_locations.c -o getall_locations.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DHAVE_ZLIB=1  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/preprocessCore/include"   -fPIC  -mtune=core2 -g -O2  -c mas5calls.c -o mas5calls.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DHAVE_ZLIB=1  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/preprocessCore/include"   -fPIC  -mtune=core2 -g -O2  -c rma2.c -o rma2.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DHAVE_ZLIB=1  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/preprocessCore/include"   -fPIC  -mtune=core2 -g -O2  -c rma_common.c -o rma_common.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o affy.so chipbackground.o getall_locations.o mas5calls.o rma2.o rma_common.o -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/affy.Rcheck/affy/libs
** R
** data
** demo
** inst
** preparing package for lazy loading
Creating a generic function for 'open' from package 'base' in package 'affy'
Creating a generic function for 'close' from package 'base' in package 'affy'
Creating a generic function for 'barplot' from package 'graphics' in package 'affy'
** help
*** installing help indices
** building package indices
** installing vignettes
   'affy.Rnw' 
   'builtinMethods.Rnw' 
   'customMethods.Rnw' 
   'vim.Rnw' 
** testing if installed package can be loaded
* DONE (affy)

name	user	system	elapsed
AffyBatch-class	8.313	0.248	8.654
AffyRNAdeg	6.568	0.169	6.785
MAplot	31.910	1.100	35.867
ProbeSet-class	0.652	0.052	0.704
ProgressBarText-class	1.625	0.121	17.308
affy-options	0.004	0.010	0.015
barplot.ProbeSet	0.748	0.071	0.821
bgc	8.836	0.471	10.322
cleancdfname	0.013	0.009	0.023
expresso	27.373	0.954	32.688
expressoWidget	0.005	0.008	0.012
fit.li.wong	0.444	0.043	0.567
generateExprSet-methods	0.628	0.082	0.947
generateExprVal-methods	0.693	0.056	0.962
generateExprVal.method.avgdiff	0.862	0.117	1.181
list.celfiles	0.003	0.005	0.009
maffy.normalise	3.884	0.100	4.199
maffy.subset	0.042	0.008	0.050
mas5	58.056	0.658	59.427
mas5calls	2.933	0.205	3.142
mva.pairs	0.179	0.011	0.191
normalize-methods	0.474	0.040	0.519
normalize.loess	0.046	0.010	0.102
plot.ProbeSet	0.028	0.009	0.070
plot.density	0.970	0.185	1.157
plotLocation	3.163	0.346	3.739
pmcorrect	0.632	0.052	0.686
ppsetApply	0.007	0.012	0.019
read.affybatch	4.114	0.433	4.583
rma	3.636	0.118	3.761
setAffyOptions	0.003	0.004	0.007
xy2indices	4.968	0.440	5.582

Summary

Command output