BioC 2.12: CHECK report for netresponse on petty

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/netresponse.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 'netresponse/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'netresponse' version '1.12.0'
* 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 'netresponse' can be installed ... [21s/23s] 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [159s/176s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
ICMg.combined.sampler 111.561  0.346 126.648
detect.responses       18.229  1.374  20.631
netresponse-package    11.102  0.843  12.534
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'ICMg.test.R' [30s/30s]
  Running 'bicmixture.R' [9s/9s]
  Running 'mixture.model.test.R' [9s/9s]
  Running 'mixture.model.test.multimodal.R' [11s/13s]
  Running 'mixture.model.test.singlemode.R' [9s/10s]
  Running 'timing.R' [1s/1s]
  Running 'toydata2.R' [1s/1s]
  Running 'validate.netresponse.R' [23s/24s]
  Running 'validate.pca.basis.R' [37s/41s]
  Running 'vdpmixture.R' [9s/9s]
 [139s/146s] 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 -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
** testing if installed package can be loaded
* DONE (netresponse)

name	user	system	elapsed
ICMg.combined.sampler	111.561	0.346	126.648
ICMg.links.sampler	4.807	0.106	4.975
NetResponseModel-class	0.007	0.005	0.013
PlotMixture	0.002	0.002	0.004
PlotMixtureBivariate	0.006	0.004	0.012
PlotMixtureMultivariate	0.005	0.003	0.008
PlotMixtureMultivariate.deprecated	0.002	0.002	0.003
PlotMixtureUnivariate	0.003	0.003	0.005
add.ellipse	0.005	0.004	0.008
centerData	0.005	0.002	0.007
check.matrix	0.001	0.002	0.004
check.network	0.005	0.004	0.010
detect.responses	18.229	1.374	20.631
dna	0.052	0.015	0.068
enrichment.list.factor	0.002	0.002	0.004
filter.netw	0.002	0.003	0.005
filter.network	0.002	0.003	0.006
find.similar.features	1.217	0.105	1.354
generate.toydata	0.001	0.001	0.003
get.dat	0.003	0.004	0.008
get.mis	0.008	0.005	0.012
get.model.parameters	0.015	0.009	0.024
get.subnets	0.003	0.004	0.008
getqofz	0.008	0.004	0.011
independent.models	0.007	0.003	0.010
list.significant.responses	0.008	0.003	0.011
model.stats	0.014	0.007	0.020
netresponse-package	11.102	0.843	12.534
order.responses	0.002	0.003	0.007
osmo	0.085	0.015	0.100
pick.model.pairs	0.006	0.003	0.008
pick.model.parameters	0.006	0.002	0.011
plot.data	0.002	0.002	0.003
plot.expression	0.006	0.004	0.010
plot.response	0.009	0.004	0.013
plot.responses	0.004	0.003	0.007
plot.scale	0.002	0.003	0.005
plot.subnet	0.003	0.004	0.007
plotAssociations	0.002	0.004	0.006
plotPCA	0.006	0.004	0.011
read.sif	0.006	0.003	0.009
remove.negative.edges	0.005	0.004	0.009
response.enrichment	0.006	0.004	0.009
response2sample	0.016	0.008	0.024
sample2response	0.007	0.005	0.012
set.breaks	0.004	0.003	0.007
toydata	0.012	0.007	0.019
update.model.pair	0.006	0.003	0.008
vdp.mixt	0.155	0.020	0.176
write.netresponse.results	0.002	0.003	0.004

BioC 2.12: CHECK report for netresponse on petty

Summary

Command output