BioC 3.2: CHECK report for nethet on perceval

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings nethet_1.1.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/nethet.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.1.1’
* 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 ... [12s/14s] 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 ... [134s/134s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
het_cv_glasso       41.027  0.029  41.058
ggmgsa_multisplit   24.685  0.019  24.705
mixglasso           23.313  0.040  23.353
diffregr_multisplit 11.591  0.072  11.665
diffnet_multisplit   8.401  0.028   8.459
* 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
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 betamat_diffnet.c -o betamat_diffnet.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -L/usr/local/lib -o nethet.so betamat_diffnet.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.2-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	0.001	0.007
bwprun_mixglasso	4.804	0.032	4.850
diffnet_multisplit	8.401	0.028	8.459
diffnet_singlesplit	4.007	0.011	4.021
diffregr_multisplit	11.591	0.072	11.665
diffregr_singlesplit	0.750	0.005	0.756
dot_plot	1.011	0.008	1.020
export_network	0.463	0.007	0.470
generate_2networks	0.066	0.002	0.067
generate_inv_cov	0.080	0.097	0.177
ggmgsa_multisplit	24.685	0.019	24.705
gsea.iriz	0.011	0.000	0.012
het_cv_glasso	41.027	0.029	41.058
invcov2parcor	0.001	0.000	0.002
invcov2parcor_array	0.004	0.000	0.004
logratio	0.002	0.000	0.002
mixglasso	23.313	0.040	23.353
plot_2networks	0.077	0.002	0.078
scatter_plot	1.889	0.010	1.900
screen_aic.glasso	1.113	0.003	1.116
screen_bic.glasso	1.179	0.002	1.181
screen_cv.glasso	2.504	0.005	2.508
screen_cv1se.lasso	0.491	0.002	0.493
screen_cvfix.lasso	0.209	0.001	0.209
screen_cvmin.lasso	0.203	0.001	0.205
screen_cvsqrt.lasso	0.217	0.001	0.218
screen_cvtrunc.lasso	0.203	0.001	0.204
screen_mb	0.010	0.001	0.010
sim_mix	0.004	0.002	0.006
sim_mix_networks	0.013	0.000	0.013

BioC 3.2: CHECK report for nethet on perceval

Summary

Command output