BioC 2.12: CHECK report for netresponse on petty

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/netresponse.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* using platform: i386-apple-darwin9.8.0 (32-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 ... [16s/16s] 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 '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 ... [135s/135s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
ICMg.combined.sampler 94.290  0.162  94.465
detect.responses      15.791  0.269  16.062
netresponse-package   10.287  0.177  10.465
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'ICMg.test.R' [26s/26s]
  Running 'bicmixture.R' [7s/7s]
  Running 'mixture.model.test.R' [8s/8s]
  Running 'mixture.model.test.multimodal.R' [9s/9s]
  Running 'mixture.model.test.singlemode.R' [7s/7s]
  Running 'timing.R' [0s/1s]
  Running 'toydata2.R' [0s/0s]
  Running 'validate.netresponse.R' [18s/18s]
  Running 'validate.pca.basis.R' [28s/28s]
  Running 'vdpmixture.R' [6s/6s]
 [110s/110s] 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 was 1 note.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/netresponse.Rcheck/00check.log'
for details.

* installing *source* package 'netresponse' ...
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c netresponse.c -o netresponse.o
netresponse.c: In function 'mHPpost':
netresponse.c:264: warning: unused variable 'prior_fields'
netresponse.c: In function 'mLogLambda':
netresponse.c:656: warning: 'KsiBeta' may be used uninitialized in this function
netresponse.c:656: warning: 'KsiAlpha' may be used uninitialized in this function
netresponse.c:656: warning: 'BetaKsi' may be used uninitialized in this function
netresponse.c:656: warning: 'AlphaKsi' may be used uninitialized in this function
netresponse.c:655: warning: 'Mutilde' may be used uninitialized in this function
netresponse.c:655: warning: 'Mubar' may be used uninitialized in this function
netresponse.c:655: warning: 'S2mu' may be used uninitialized in this function
netresponse.c:655: warning: 'Mumu' may be used uninitialized in this function
netresponse.c:656: warning: 'U_p' may be used uninitialized in this function
gcc -arch i386 -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/i386
** 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	94.290	0.162	94.465
ICMg.links.sampler	4.257	0.061	4.319
NetResponseModel-class	0.007	0.007	0.013
PlotMixture	0.002	0.004	0.007
PlotMixtureBivariate	0.005	0.006	0.012
PlotMixtureMultivariate	0.005	0.006	0.012
PlotMixtureMultivariate.deprecated	0.003	0.005	0.007
PlotMixtureUnivariate	0.005	0.006	0.011
add.ellipse	0.005	0.005	0.011
centerData	0.002	0.004	0.007
check.matrix	0.003	0.004	0.007
check.network	0.003	0.004	0.006
detect.responses	15.791	0.269	16.062
dna	0.041	0.010	0.051
enrichment.list.factor	0.002	0.003	0.006
filter.netw	0.002	0.004	0.007
filter.network	0.002	0.005	0.007
find.similar.features	0.774	0.026	0.801
generate.toydata	0.007	0.007	0.014
get.dat	0.006	0.008	0.014
get.mis	0.002	0.003	0.006
get.model.parameters	0.011	0.011	0.023
get.subnets	0.006	0.006	0.012
getqofz	0.003	0.005	0.008
independent.models	0.003	0.005	0.007
list.significant.responses	0.008	0.007	0.014
model.stats	0.014	0.012	0.026
netresponse-package	10.287	0.177	10.465
order.responses	0.003	0.006	0.009
osmo	0.092	0.012	0.106
pick.model.pairs	0.005	0.007	0.013
pick.model.parameters	0.006	0.007	0.014
plot.data	0.006	0.007	0.013
plot.expression	0.002	0.006	0.009
plot.response	0.003	0.006	0.009
plot.responses	0.004	0.008	0.013
plot.scale	0.005	0.009	0.015
plot.subnet	0.002	0.004	0.007
plotAssociations	0.002	0.004	0.006
plotPCA	0.002	0.004	0.006
read.sif	0.003	0.005	0.008
remove.negative.edges	0.002	0.004	0.006
response.enrichment	0.005	0.006	0.012
response2sample	0.016	0.014	0.032
sample2response	0.004	0.007	0.011
set.breaks	0.004	0.006	0.010
toydata	0.008	0.009	0.017
update.model.pair	0.005	0.008	0.014
vdp.mixt	0.106	0.014	0.121
write.netresponse.results	0.002	0.004	0.006

Summary

Command output