Package: simpleaffy

Version: 2.35.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch simpleaffy_2.35.1.tar.gz

StartedAt: 2013-03-24 10:18:38 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 10:22:18 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 220.4 seconds

RetCode: 0

Status:  OK

CheckDir: simpleaffy.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/simpleaffy.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 'simpleaffy/DESCRIPTION' ... OK
* this is package 'simpleaffy' version '2.35.1'
* 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 'simpleaffy' can be installed ... [22s/22s] 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 ... OK
* checking R code for possible problems ... NOTE
File 'simpleaffy/R/zzz.R':
  .onLoad calls:
    require("methods", quietly = TRUE)

Package startup functions should not change the search path.
See section 'Good practice' in '?.onAttach'.
* 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 ... NOTE
  No methods found in "Biobase" for requests: geneNames
* 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 use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File '/Users/biocbuild/bbs-2.12-bioc/meat/simpleaffy.Rcheck/simpleaffy/libs/simpleaffy.so':
  Found '___stderrp', possibly from 'stderr' (C)
    Object: 'simpleaffy.o'

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking examples ... [11s/11s] OK
* 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 3 notes.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/simpleaffy.Rcheck/00check.log'
for details.

* installing *source* package 'simpleaffy' ...
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c simpleaffy.c -o simpleaffy.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 simpleaffy.so simpleaffy.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/simpleaffy.Rcheck/simpleaffy/libs
** R
** data
** inst
** preparing package for lazy loading
No methods found in "Biobase" for requests: geneNames
** help
*** installing help indices
** building package indices
** installing vignettes
   'simpleAffy.Rnw' 
** testing if installed package can be loaded
No methods found in "Biobase" for requests: geneNames
* DONE (simpleaffy)

name	user	system	elapsed
all.present	0.268	0.005	0.329
all.present.in.group	0.009	0.003	0.013
bg.correct.sa	0.009	0.004	0.012
call.exprs	0.010	0.004	0.013
detection.p.val	0.009	0.003	0.012
get.annotation	0.009	0.003	0.012
get.array.indices	0.008	0.003	0.011
get.array.subset	0.008	0.003	0.012
get.array.subset.affy	0.009	0.003	0.013
get.fold.change.and.t.test	0.009	0.004	0.012
hmap.colors	0.006	0.002	0.008
hmap.eset	0.011	0.003	0.015
hmap.pc	0.008	0.003	0.011
journalpng	0.009	0.003	0.012
justMAS	0.008	0.002	0.011
pairwise.comparison	0.008	0.003	0.011
pairwise.filter	0.009	0.002	0.013
plot.pairwise.comparison	0.006	0.002	0.009
plot.qc.stats	0.099	0.009	0.117
qc	0.072	0.012	0.085
qc.affy	0.074	0.012	0.086
qc.get.alpha1	0.019	0.004	0.023
qc.get.array	0.009	0.001	0.010
qc.get.probes	0.020	0.003	0.024
qc.get.ratios	0.016	0.003	0.020
qc.get.spikes	0.010	0.003	0.014
qc.have.params	0.032	0.009	0.042
qc.ok	0.014	0.002	0.015
qc.read.file	0.017	0.003	0.021
qc.stats	0.057	0.003	0.064
read.affy	0.010	0.003	0.013
read.affy.mixed	0.013	0.002	0.016
setQCEnvironment	0.021	0.004	0.025
simpleaffy-deprecated	0.048	0.008	0.060
standard.pearson	0.009	0.002	0.011
trad.scatter.plot	0.008	0.002	0.012