BioC 2.12: CHECK report for netresponse on george2

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/netresponse.Rcheck’
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* 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/21s] 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 ... [106s/126s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
ICMg.combined.sampler 65.240  0.144  76.302
detect.responses      13.553  0.508  14.362
netresponse-package    9.537  0.268  17.846
ICMg.links.sampler     5.444  0.052   5.687
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘ICMg.test.R’ [20s/21s]
  Running ‘bicmixture.R’ [9s/9s]
  Running ‘mixture.model.test.R’ [9s/9s]
  Running ‘mixture.model.test.multimodal.R’ [12s/13s]
  Running ‘mixture.model.test.singlemode.R’ [10s/10s]
  Running ‘timing.R’ [0s/0s]
  Running ‘toydata2.R’ [0s/0s]
  Running ‘validate.netresponse.R’ [23s/23s]
  Running ‘validate.pca.basis.R’ [36s/37s]
  Running ‘vdpmixture.R’ [9s/10s]
 [130s/134s] 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
  ‘/home/biocbuild/bbs-2.12-bioc/meat/netresponse.Rcheck/00check.log’
for details.

* installing *source* package ‘netresponse’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c netresponse.c -o netresponse.o
netresponse.c: In function ‘mHPpost’:
netresponse.c:264:15: warning: unused variable ‘prior_fields’ [-Wunused-variable]
netresponse.c: In function ‘mLogLambda’:
netresponse.c:713:20: warning: ‘U_p’ may be used uninitialized in this function [-Wuninitialized]
netresponse.c:713:20: warning: ‘KsiBeta’ may be used uninitialized in this function [-Wuninitialized]
netresponse.c:713:20: warning: ‘KsiAlpha’ may be used uninitialized in this function [-Wuninitialized]
netresponse.c:713:20: warning: ‘BetaKsi’ may be used uninitialized in this function [-Wuninitialized]
netresponse.c:713:20: warning: ‘AlphaKsi’ may be used uninitialized in this function [-Wuninitialized]
netresponse.c:713:20: warning: ‘Mutilde’ may be used uninitialized in this function [-Wuninitialized]
netresponse.c:713:20: warning: ‘Mubar’ may be used uninitialized in this function [-Wuninitialized]
netresponse.c:713:20: warning: ‘S2mu’ may be used uninitialized in this function [-Wuninitialized]
netresponse.c:713:20: warning: ‘Mumu’ may be used uninitialized in this function [-Wuninitialized]
gcc -std=gnu99 -shared -L/usr/local/lib -o netresponse.so netresponse.o -L/home/biocbuild/bbs-2.12-bioc/R/lib -lR
installing to /home/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	65.240	0.144	76.302
ICMg.links.sampler	5.444	0.052	5.687
NetResponseModel-class	0.012	0.000	0.014
PlotMixture	0.008	0.000	0.004
PlotMixtureBivariate	0.012	0.000	0.008
PlotMixtureMultivariate	0.008	0.004	0.011
PlotMixtureMultivariate.deprecated	0.000	0.000	0.003
PlotMixtureUnivariate	0.004	0.000	0.005
add.ellipse	0.004	0.004	0.011
centerData	0.012	0.000	0.011
check.matrix	0.004	0.004	0.005
check.network	0.012	0.004	0.014
detect.responses	13.553	0.508	14.362
dna	0.040	0.012	0.051
enrichment.list.factor	0.000	0.008	0.007
filter.netw	0.008	0.000	0.007
filter.network	0.004	0.000	0.005
find.similar.features	0.960	0.036	1.089
generate.toydata	0.004	0.000	0.004
get.dat	0.016	0.000	0.030
get.mis	0.012	0.000	0.012
get.model.parameters	0.024	0.000	0.053
get.subnets	0.012	0.000	0.029
getqofz	0.016	0.000	0.030
independent.models	0.004	0.000	0.005
list.significant.responses	0.028	0.004	0.065
model.stats	0.012	0.016	0.057
netresponse-package	9.537	0.268	17.846
order.responses	0.000	0.004	0.017
osmo	0.052	0.004	0.081
pick.model.pairs	0.004	0.004	0.008
pick.model.parameters	0.008	0.000	0.007
plot.data	0.004	0.000	0.004
plot.expression	0.004	0.000	0.005
plot.response	0.000	0.004	0.005
plot.responses	0.008	0.000	0.008
plot.scale	0.008	0.000	0.008
plot.subnet	0.008	0.000	0.008
plotAssociations	0.004	0.000	0.003
plotPCA	0.004	0.000	0.004
read.sif	0.004	0.000	0.003
remove.negative.edges	0.008	0.000	0.024
response.enrichment	0.008	0.000	0.006
response2sample	0.024	0.000	0.023
sample2response	0.012	0.000	0.013
set.breaks	0.004	0.008	0.011
toydata	0.012	0.000	0.014
update.model.pair	0.004	0.000	0.007
vdp.mixt	0.108	0.012	0.151
write.netresponse.results	0.000	0.004	0.005

BioC 2.12: CHECK report for netresponse on george2

Summary

Command output