BioC 3.1: CHECK report for nethet on zin2

Package: nethet

Version: 1.0.1

Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings nethet_1.0.1.tar.gz

StartedAt: 2015-10-09 03:56:13 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 03:58:55 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 162.0 seconds

RetCode: 0

Status:  OK

CheckDir: nethet.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings nethet_1.0.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/nethet.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘nethet/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘nethet’ version ‘1.0.1’
* 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 ‘nethet’ can be installed ... [8s/8s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 loading without being on the library search path ... OK
* checking 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [86s/86s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
het_cv_glasso       24.448  0.008  24.453
mixglasso           16.605  0.005  16.609
ggmgsa_multisplit   14.181  0.000  14.176
diffregr_multisplit  9.258  0.000   9.297
* 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
* DONE

Status: OK

* installing *source* package ‘nethet’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c betamat_diffnet.c -o betamat_diffnet.o
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.1-bioc/R/lib -L/usr/local/lib -o nethet.so betamat_diffnet.o -L/home/biocbuild/bbs-3.1-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.1-bioc/meat/nethet.Rcheck/nethet/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (nethet)

name	user	system	elapsed
aggpval	0.005	0.000	0.005
bwprun_mixglasso	3.702	0.003	3.748
diffnet_multisplit	4.851	0.008	4.866
diffnet_singlesplit	2.390	0.000	2.387
diffregr_multisplit	9.258	0.000	9.297
diffregr_singlesplit	0.634	0.000	0.651
dot_plot	0.835	0.004	0.839
export_network	0.363	0.000	0.363
generate_2networks	0.063	0.000	0.063
generate_inv_cov	0.072	0.052	0.124
ggmgsa_multisplit	14.181	0.000	14.176
gsea.iriz	0.009	0.000	0.009
het_cv_glasso	24.448	0.008	24.453
invcov2parcor	0.001	0.000	0.001
invcov2parcor_array	0.004	0.000	0.004
logratio	0.002	0.000	0.001
mixglasso	16.605	0.005	16.609
plot_2networks	0.068	0.000	0.069
scatter_plot	1.524	0.004	1.539
screen_aic.glasso	0.652	0.000	0.651
screen_bic.glasso	0.624	0.000	0.624
screen_cv.glasso	1.521	0.000	1.520
screen_cv1se.lasso	0.164	0.000	0.164
screen_cvfix.lasso	0.172	0.000	0.172
screen_cvmin.lasso	0.161	0.000	0.160
screen_cvsqrt.lasso	0.147	0.000	0.147
screen_cvtrunc.lasso	0.151	0.000	0.151
screen_mb	0.008	0.000	0.008
sim_mix	0.004	0.000	0.004
sim_mix_networks	0.009	0.000	0.009