BioC 2.12: CHECK report for affy on petty

Package: affy

Version: 1.38.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch affy_1.38.1.tar.gz

StartedAt: 2013-10-08 21:26:57 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 21:32:22 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 324.3 seconds

RetCode: 0

Status:  OK

CheckDir: affy.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/affy.Rcheck'
* using R version 3.0.1 (2013-05-16)
* 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 '1.38.1'
* 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 ... [10s/11s] 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [207s/227s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
mas5                  74.181  0.559  76.154
expresso              33.165  0.850  34.310
MAplot                32.670  1.144  34.881
AffyBatch-class        9.031  0.219   9.302
bgc                    8.156  0.449   8.804
AffyRNAdeg             7.899  0.152   8.080
ProgressBarText-class  1.581  0.123  17.188
* 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 -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
** testing if installed package can be loaded
* DONE (affy)

name	user	system	elapsed
AffyBatch-class	9.031	0.219	9.302
AffyRNAdeg	7.899	0.152	8.080
MAplot	32.670	1.144	34.881
ProbeSet-class	0.797	0.053	0.860
ProgressBarText-class	1.581	0.123	17.188
affy-options	0.005	0.009	0.014
barplot.ProbeSet	0.935	0.064	1.045
bgc	8.156	0.449	8.804
cleancdfname	0.012	0.006	0.021
expresso	33.165	0.850	34.310
expressoWidget	0.003	0.006	0.008
fit.li.wong	0.479	0.040	0.521
generateExprSet-methods	0.769	0.071	0.853
generateExprVal-methods	0.882	0.054	0.943
generateExprVal.method.avgdiff	1.011	0.094	1.111
list.celfiles	0.002	0.004	0.007
maffy.normalise	3.825	0.096	3.957
maffy.subset	0.049	0.010	0.059
mas5	74.181	0.559	76.154
mas5calls	3.109	0.156	3.301
mva.pairs	0.221	0.008	0.245
normalize-methods	0.566	0.032	0.658
normalize.loess	0.052	0.008	0.065
plot.ProbeSet	0.029	0.006	0.036
plot.density	1.026	0.137	1.270
plotLocation	3.482	0.375	4.390
pmcorrect	0.761	0.048	0.872
ppsetApply	0.005	0.008	0.012
read.affybatch	3.785	0.360	4.476
rma	3.885	0.083	4.060
setAffyOptions	0.003	0.004	0.007
xy2indices	3.951	0.408	4.583