BioC 2.12: CHECK report for simpleaffy on petty

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/simpleaffy.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 'simpleaffy/DESCRIPTION' ... OK
* this is package 'simpleaffy' version '2.36.1'
* 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 ... [24s/24s] 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 ... 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-2.12-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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [12s/12s] 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 2 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 -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
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (simpleaffy)

name	user	system	elapsed
all.present	0.275	0.003	0.282
all.present.in.group	0.005	0.001	0.007
bg.correct.sa	0.006	0.002	0.007
call.exprs	0.005	0.002	0.007
detection.p.val	0.005	0.001	0.007
get.annotation	0.005	0.001	0.007
get.array.indices	0.006	0.003	0.009
get.array.subset	0.006	0.002	0.008
get.array.subset.affy	0.006	0.003	0.010
get.fold.change.and.t.test	0.006	0.002	0.008
hmap.colors	0.005	0.002	0.007
hmap.eset	0.005	0.001	0.006
hmap.pc	0.005	0.001	0.007
journalpng	0.005	0.002	0.007
justMAS	0.006	0.002	0.008
pairwise.comparison	0.004	0.001	0.007
pairwise.filter	0.005	0.002	0.008
plot.pairwise.comparison	0.006	0.002	0.007
plot.qc.stats	0.123	0.009	0.131
qc	0.091	0.008	0.100
qc.affy	0.086	0.010	0.100
qc.get.alpha1	0.017	0.003	0.020
qc.get.array	0.010	0.002	0.012
qc.get.probes	0.019	0.004	0.023
qc.get.ratios	0.014	0.003	0.017
qc.get.spikes	0.009	0.002	0.011
qc.have.params	0.033	0.007	0.040
qc.ok	0.014	0.002	0.015
qc.read.file	0.015	0.004	0.019
qc.stats	0.070	0.002	0.072
read.affy	0.284	0.002	0.287
read.affy.mixed	0.010	0.002	0.013
setQCEnvironment	0.024	0.006	0.030
simpleaffy-deprecated	0.048	0.011	0.061
standard.pearson	0.010	0.003	0.012
trad.scatter.plot	0.008	0.001	0.009

BioC 2.12: CHECK report for simpleaffy on petty

Summary

Command output