BioC 2.13: CHECK report for affy on perceval

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/affy.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘affy/DESCRIPTION’ ... OK
* this is package ‘affy’ version ‘1.40.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘affy’ can be installed ... [8s/8s] 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
* 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 ... NOTE
Unexported objects imported by ‘:::’ calls:
  ‘stats:::C_loess_raw’ ‘stats:::C_lowesp’ ‘stats:::C_lowesw’
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘bg.correct’
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... WARNING
Foreign function calls to a base package:
  .C(stats:::C_loess_raw, ...)
  .Fortran(stats:::C_lowesp, ...)
  .Fortran(stats:::C_lowesw, ...)
Packages should not make .C/.Call/.External/.Fortran calls to a base
package. They are not part of the API, for use only by R itself and
subject to change without notice.
* 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 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 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 files in ‘vignettes’ ... OK
* checking examples ... [166s/198s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
mas5                  51.543  0.753  65.550
MAplot                30.581  1.132  32.507
expresso              23.723  0.975  24.885
bgc                    9.019  0.489   9.617
AffyBatch-class        8.577  0.226   8.933
AffyRNAdeg             6.229  0.117   6.466
ProgressBarText-class  1.371  0.119  16.999
* 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

WARNING: There was 1 warning.
NOTE: There was 1 note.
See
  ‘/Users/biocbuild/bbs-2.13-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 -Wall  -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 -Wall  -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 -Wall  -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 -Wall  -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 -Wall  -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 -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-2.13-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
** testing if installed package can be loaded
* DONE (affy)

name	user	system	elapsed
AffyBatch-class	8.577	0.226	8.933
AffyRNAdeg	6.229	0.117	6.466
MAplot	30.581	1.132	32.507
ProbeSet-class	0.691	0.064	0.798
ProgressBarText-class	1.371	0.119	16.999
affy-options	0.005	0.008	0.012
barplot.ProbeSet	0.680	0.055	0.741
bgc	9.019	0.489	9.617
cleancdfname	0.01	0.01	0.02
expresso	23.723	0.975	24.885
expressoWidget	0.003	0.006	0.009
fit.li.wong	0.360	0.041	0.401
generateExprSet-methods	0.497	0.086	0.592
generateExprVal-methods	0.516	0.061	0.579
generateExprVal.method.avgdiff	0.730	0.099	0.840
list.celfiles	0.002	0.005	0.007
maffy.normalise	2.653	0.134	2.814
maffy.subset	0.058	0.009	0.066
mas5	51.543	0.753	65.550
mas5calls	3.715	0.203	4.663
mva.pairs	0.183	0.022	0.205
normalize-methods	0.373	0.028	0.401
normalize.loess	0.473	0.106	0.578
plot.ProbeSet	0.023	0.007	0.032
plot.density	0.917	0.175	1.093
plotLocation	3.284	0.327	3.688
pmcorrect	0.632	0.081	0.718
ppsetApply	0.005	0.008	0.014
read.affybatch	3.373	0.383	3.964
rma	3.279	0.093	3.482
setAffyOptions	0.002	0.005	0.007
xy2indices	3.388	0.450	3.914

BioC 2.13: CHECK report for affy on perceval

Summary

Command output