BioC 2.13: CHECK report for simpleaffy on perceval

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/simpleaffy.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 ‘simpleaffy/DESCRIPTION’ ... OK
* this is package ‘simpleaffy’ version ‘2.38.0’
* 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 ‘simpleaffy’ can be installed ... [23s/23s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘methods’ ‘utils’ ‘grDevices’ ‘graphics’ ‘stats’ ‘BiocGenerics’ ‘Biobase’ ‘affy’ ‘genefilter’ ‘gcrma’
A package should be listed in only one of these fields.
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* 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 for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File ‘/Users/biocbuild/bbs-2.13-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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘simpleAffy.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 3 notes.
See
  ‘/Users/biocbuild/bbs-2.13-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 -Wall  -c simpleaffy.c -o simpleaffy.o
simpleaffy.c: In function ‘bgmas’:
simpleaffy.c:440: warning: passing argument 1 of ‘REprintf’ from incompatible pointer type
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 simpleaffy.so simpleaffy.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.13-bioc/meat/simpleaffy.Rcheck/simpleaffy/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (simpleaffy)

name	user	system	elapsed
all.present	0.333	0.004	0.338
all.present.in.group	0.006	0.002	0.008
bg.correct.sa	0.362	0.003	0.365
call.exprs	0.012	0.003	0.016
detection.p.val	0.005	0.001	0.007
get.annotation	0.005	0.002	0.007
get.array.indices	0.007	0.002	0.010
get.array.subset	0.008	0.003	0.011
get.array.subset.affy	0.008	0.002	0.010
get.fold.change.and.t.test	0.008	0.002	0.010
hmap.colors	0.010	0.003	0.013
hmap.eset	0.013	0.005	0.018
hmap.pc	0.006	0.002	0.008
journalpng	0.009	0.003	0.012
justMAS	0.006	0.003	0.009
pairwise.comparison	0.009	0.002	0.011
pairwise.filter	0.006	0.003	0.010
plot.pairwise.comparison	0.007	0.002	0.011
plot.qc.stats	0.080	0.008	0.090
qc	0.067	0.011	0.079
qc.affy	0.069	0.010	0.081
qc.get.alpha1	0.014	0.004	0.017
qc.get.array	0.005	0.001	0.007
qc.get.probes	0.020	0.005	0.025
qc.get.ratios	0.016	0.004	0.020
qc.get.spikes	0.012	0.002	0.014
qc.have.params	0.033	0.007	0.061
qc.ok	0.017	0.002	0.020
qc.read.file	0.029	0.002	0.032
qc.stats	0.042	0.003	0.045
read.affy	0.011	0.003	0.013
read.affy.mixed	0.012	0.004	0.015
setQCEnvironment	0.022	0.006	0.032
simpleaffy-deprecated	0.039	0.010	0.050
standard.pearson	0.006	0.002	0.008
trad.scatter.plot	0.007	0.002	0.009

BioC 2.13: CHECK report for simpleaffy on perceval

Summary

Command output