Package: netresponse

Version: 1.11.15

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings netresponse_1.11.15.tar.gz

StartedAt: 2013-01-16 04:46:27 -0800 (Wed, 16 Jan 2013)

EndedAt: 2013-01-16 04:51:40 -0800 (Wed, 16 Jan 2013)

EllapsedTime: 313.7 seconds

RetCode: 0

Status:  OK

CheckDir: netresponse.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/netresponse.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* 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 ‘1.11.15’
* 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 ... 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 ... OK
* 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 ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
ICMg.combined.sampler 54.223  0.024  54.272
detect.responses      10.112  0.068  10.182
netresponse-package    6.093  0.040   6.134
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘ICMg.test.R’
  Running ‘bicmixture.R’
  Running ‘mixture.model.test.R’
  Running ‘mixture.model.test.multimodal.R’
  Running ‘mixture.model.test.singlemode.R’
  Running ‘timing.R’
  Running ‘toydata2.R’
  Running ‘validate.netresponse.R’
  Running ‘validate.pca.basis.R’
  Running ‘vdpmixture.R’
 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

* 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  -c netresponse.c -o netresponse.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o netresponse.so netresponse.o -L/home/biocbuild/bbs-2.12-bioc/R/lib -lR
installing to /loc/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
   ‘netresponse.Rnw’ 
** testing if installed package can be loaded

* DONE (netresponse)

name	user	system	elapsed
ICMg.combined.sampler	54.223	0.024	54.272
ICMg.links.sampler	4.385	0.028	4.411
NetResponseModel-class	0.008	0.000	0.007
PlotMixtureBivariate	0.000	0.000	0.002
PlotMixtureMultivariate	0.004	0.000	0.005
PlotMixtureUnivariate	0.004	0.000	0.005
add.ellipse	0.004	0.000	0.003
centerData	0.008	0.000	0.005
check.matrix	0.008	0.000	0.004
check.network	0.004	0.000	0.002
detect.responses	10.112	0.068	10.182
dna	0.032	0.000	0.033
filter.netw	0.004	0.000	0.003
filter.network	0.004	0.000	0.003
find.similar.features	0.608	0.008	0.615
generate.toydata	0.008	0.000	0.009
get.dat	0.008	0.000	0.008
get.mis	0.004	0.000	0.002
get.model.parameters	0.008	0.008	0.015
get.subnets	0.000	0.000	0.003
getqofz	0.008	0.000	0.008
independent.models	0.008	0.000	0.007
list.significant.responses	0.008	0.000	0.007
model.stats	0.008	0.000	0.013
netresponse-package	6.093	0.040	6.134
order.responses	0.000	0.004	0.004
osmo	0.044	0.004	0.049
pick.model.pairs	0.004	0.000	0.005
pick.model.parameters	0.004	0.000	0.004
plot.data	0.000	0.000	0.002
plot.expression	0.008	0.000	0.006
plot.response	0.008	0.000	0.007
plot.responses	0.008	0.000	0.005
plot.scale	0.008	0.000	0.012
plot.subnet	0.000	0.000	0.003
plotAssociations	0.000	0.004	0.003
plotPCA	0.000	0.000	0.003
read.sif	0.000	0.000	0.003
remove.negative.edges	0.004	0.000	0.005
response.enrichment	0.004	0.000	0.005
response2sample	0.016	0.000	0.015
sample2response	0.008	0.000	0.006
set.breaks	0.004	0.000	0.003
toydata	0.004	0.004	0.010
update.model.pair	0.004	0.000	0.005
vdp.mixt	0.088	0.004	0.091
write.netresponse.results	0.004	0.000	0.003