BioC 2.12: CHECK report for netresponse on pelham

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/netresponse.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 'netresponse/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'netresponse' version '1.11.24'
* 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 'netresponse' can be installed ... [19s/22s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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 'netresponse/R/firstlib.R':
  .onLoad calls:
    packageStartupMessage("\nnetresponse Copyright (C) 2008-2013 Leo Lahti.\nThis program comes with ABSOLUTELY NO WARRANTY.\nThis is free software, and you are welcome to redistribute it under GNU GPL >=2, see the licensing terms for details.\n")

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 compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [142s/144s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
ICMg.combined.sampler 96.210  0.375  97.749
detect.responses      16.081  1.998  19.204
netresponse-package    9.246  1.073  10.348
ICMg.links.sampler     6.527  0.146   6.930
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'ICMg.test.R' [26s/27s]
  Running 'bicmixture.R' [8s/8s]
  Running 'mixture.model.test.R' [8s/9s]
  Running 'mixture.model.test.multimodal.R' [12s/13s]
  Running 'mixture.model.test.singlemode.R' [9s/9s]
  Running 'timing.R' [0s/0s]
  Running 'toydata2.R' [0s/0s]
  Running 'validate.netresponse.R' [24s/24s]
  Running 'validate.pca.basis.R' [38s/38s]
  Running 'vdpmixture.R' [8s/8s]
 [133s/138s] 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/netresponse.Rcheck/00check.log'
for details.

* installing *source* package 'netresponse' ...
** 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 netresponse.c -o netresponse.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 netresponse.so netresponse.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/netresponse.Rcheck/netresponse/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'netresponse.Rnw' 
** testing if installed package can be loaded
* DONE (netresponse)

name	user	system	elapsed
ICMg.combined.sampler	96.210	0.375	97.749
ICMg.links.sampler	6.527	0.146	6.930
NetResponseModel-class	0.008	0.007	0.016
PlotMixture	0.006	0.005	0.011
PlotMixtureBivariate	0.005	0.003	0.009
PlotMixtureMultivariate	0.003	0.002	0.005
PlotMixtureMultivariate.deprecated	0.006	0.004	0.009
PlotMixtureUnivariate	0.002	0.002	0.004
add.ellipse	0.006	0.005	0.010
centerData	0.007	0.003	0.010
check.matrix	0.002	0.002	0.004
check.network	0.006	0.004	0.010
detect.responses	16.081	1.998	19.204
dna	0.047	0.015	0.062
enrichment.list.factor	0.002	0.004	0.006
filter.netw	0.003	0.005	0.008
filter.network	0.009	0.004	0.012
find.similar.features	1.040	0.147	1.193
generate.toydata	0.002	0.004	0.007
get.dat	0.008	0.006	0.015
get.mis	0.002	0.003	0.006
get.model.parameters	0.014	0.009	0.025
get.subnets	0.009	0.006	0.015
getqofz	0.002	0.002	0.004
independent.models	0.012	0.004	0.016
list.significant.responses	0.010	0.004	0.014
model.stats	0.015	0.007	0.022
netresponse-package	9.246	1.073	10.348
order.responses	0.002	0.004	0.007
osmo	0.069	0.015	0.085
pick.model.pairs	0.005	0.003	0.009
pick.model.parameters	0.005	0.003	0.009
plot.data	0.002	0.002	0.005
plot.expression	0.002	0.004	0.006
plot.response	0.002	0.004	0.007
plot.responses	0.003	0.004	0.007
plot.scale	0.006	0.006	0.012
plot.subnet	0.006	0.004	0.011
plotAssociations	0.006	0.004	0.009
plotPCA	0.005	0.004	0.010
read.sif	0.006	0.004	0.010
remove.negative.edges	0.006	0.004	0.011
response.enrichment	0.006	0.004	0.010
response2sample	0.015	0.009	0.025
sample2response	0.007	0.006	0.014
set.breaks	0.007	0.004	0.012
toydata	0.007	0.005	0.013
update.model.pair	0.005	0.005	0.011
vdp.mixt	0.156	0.027	0.182
write.netresponse.results	0.002	0.002	0.004

Summary

Command output