BioC 2.13: CHECK report for netresponse on perceval

Package: netresponse

Version: 1.14.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch netresponse_1.14.0.tar.gz

StartedAt: 2014-04-05 03:01:13 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 03:08:04 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 411.5 seconds

RetCode: 0

Status:  OK

CheckDir: netresponse.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/netresponse.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.14.0’
* 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 ... [19s/20s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 dependencies in R code ... NOTE
‘library’ or ‘require’ calls to packages already attached by Depends:
  ‘ggplot2’ ‘graph’ ‘mclust’ ‘minet’ ‘reshape’ ‘Rgraphviz’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘dmt’ ‘ggplot2’ ‘graph’ ‘igraph’ ‘infotheo’ ‘mclust’ ‘methods’
  ‘minet’ ‘qvalue’ ‘RColorBrewer’ ‘reshape’ ‘Rgraphviz’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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 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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘netresponse.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [103s/107s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
ICMg.combined.sampler 67.556  0.306  69.768
detect.responses      11.592  1.082  13.192
netresponse-package    6.892  0.556   7.712
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘bicmixture.R’ [8s/8s]
  Running ‘ICMg.test.R’ [21s/22s]
  Running ‘mixture.model.test.multimodal.R’ [11s/11s]
  Running ‘mixture.model.test.R’ [8s/9s]
  Running ‘mixture.model.test.singlemode.R’ [8s/9s]
  Running ‘timing.R’ [0s/0s]
  Running ‘toydata2.R’ [0s/0s]
  Running ‘validate.netresponse.R’ [20s/21s]
  Running ‘validate.pca.basis.R’ [30s/31s]
  Running ‘vdpmixture.R’ [8s/9s]
 [117s/121s] 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 4 notes.
See
  ‘/Users/biocbuild/bbs-2.13-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 -Wall  -c netresponse.c -o netresponse.o
netresponse.c: In function ‘mHPpost’:
netresponse.c:264: warning: unused variable ‘prior_fields’
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-2.13-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	67.556	0.306	69.768
ICMg.links.sampler	3.939	0.107	4.333
NetResponseModel-class	0.009	0.006	0.015
PlotMixture	0.006	0.004	0.011
PlotMixtureBivariate	0.007	0.002	0.010
PlotMixtureMultivariate	0.002	0.003	0.006
PlotMixtureMultivariate.deprecated	0.007	0.003	0.010
PlotMixtureUnivariate	0.003	0.002	0.005
add.ellipse	0.006	0.004	0.009
centerData	0.006	0.003	0.009
check.matrix	0.003	0.004	0.007
check.network	0.002	0.003	0.004
detect.responses	11.592	1.082	13.192
dna	0.034	0.012	0.047
enrichment.list.factor	0.002	0.002	0.005
enrichment.list.factor.minimal	0.002	0.003	0.005
filter.netw	0.011	0.005	0.017
filter.network	0.009	0.003	0.012
find.similar.features	0.749	0.085	1.179
generate.toydata	0.002	0.002	0.004
get.dat	0.006	0.006	0.013
get.mis	0.007	0.005	0.012
get.model.parameters	0.013	0.010	0.022
get.subnets	0.007	0.006	0.011
getqofz	0.001	0.002	0.003
independent.models	0.001	0.003	0.004
list.significant.responses	0.007	0.005	0.012
listify.groupings	0.002	0.002	0.004
model.stats	0.012	0.007	0.020
netresponse-package	6.892	0.556	7.712
order.responses	0.002	0.003	0.127
osmo	0.052	0.016	0.069
pick.model.pairs	0.006	0.003	0.009
pick.model.parameters	0.005	0.003	0.008
plot.data	0.002	0.002	0.005
plot.expression	0.007	0.005	0.013
plot.response	0.009	0.003	0.012
plot.responses	0.002	0.002	0.004
plot.scale	0.005	0.005	0.009
plot.subnet	0.007	0.004	0.011
plotAssociations	0.002	0.002	0.005
plotPCA	0.002	0.003	0.005
read.sif	0.002	0.002	0.005
remove.negative.edges	0.001	0.003	0.006
response.enrichment	0.002	0.002	0.004
response2sample	0.015	0.008	0.023
sample2response	0.006	0.005	0.010
set.breaks	0.003	0.004	0.006
toydata	0.009	0.006	0.015
update.model.pair	0.004	0.003	0.007
vdp.mixt	0.104	0.018	0.131
vectorize.groupings	0.002	0.002	0.005
write.netresponse.results	0.002	0.003	0.005