Package: nethet

Version: 1.16.1

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:nethet.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings nethet_1.16.1.tar.gz

StartedAt: 2019-10-16 03:32:49 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 03:36:01 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 192.1 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: nethet.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:nethet.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings nethet_1.16.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/nethet.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.16.1’
* 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 ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘mclust::dmvnorm’ by ‘mvtnorm::dmvnorm’ when loading ‘nethet’
See ‘/home/biocbuild/bbs-3.9-bioc/meat/nethet.Rcheck/00install.out’ for details.
* 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 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
MStepGlasso: no visible global function definition for ‘cov.wt’
agg.pval: no visible global function definition for ‘quantile’
aggpval: no visible global function definition for ‘optimize’
aggpval : : no visible global function definition for
  ‘quantile’
aic.glasso: no visible global function definition for ‘var’
bic.glasso: no visible global function definition for ‘var’
cv.glasso: no visible global function definition for ‘var’
cv.glasso: no visible binding for global variable ‘var’
diffnet_multisplit: no visible global function definition for
  ‘optimize’
diffnet_multisplit: no visible binding for global variable ‘median’
diffnet_multisplit: no visible global function definition for ‘median’
diffregr_multisplit: no visible global function definition for
  ‘optimize’
diffregr_multisplit: no visible global function definition for ‘median’
diffregr_singlesplit: no visible global function definition for ‘coef’
diffregr_singlesplit: no visible global function definition for ‘lm’
error.bars: no visible global function definition for ‘segments’
est2.my.ev2.diffregr: no visible global function definition for ‘var’
est2.my.ev3.diffregr: no visible global function definition for ‘var’
est2.ww.mat.diffregr: no visible global function definition for ‘var’
est2.ww.mat2.diffregr: no visible global function definition for ‘var’
export_network: no visible global function definition for ‘write.csv’
func.uinit: no visible global function definition for ‘kmeans’
getinvcov: no visible global function definition for ‘rbeta’
ggmgsa_multisplit: no visible binding for global variable ‘median’
glasso.parcor: no visible global function definition for ‘sd’
gsea.iriz.scale: no visible global function definition for ‘pnorm’
gsea.iriz.shift: no visible global function definition for ‘pnorm’
lambda.max: no visible global function definition for ‘var’
logratio.diffregr: no visible global function definition for ‘dnorm’
mcov: no visible global function definition for ‘cov.wt’
mcov: no visible global function definition for ‘var’
mixglasso_init: no visible global function definition for ‘cov.wt’
my.p.adjust: no visible global function definition for ‘p.adjust’
my.ttest: no visible global function definition for ‘var’
my.ttest2: no visible global function definition for ‘var’
perm.diffregr_teststat: no visible global function definition for
  ‘coef’
perm.diffregr_teststat: no visible global function definition for ‘lm’
plot.diffnet: no visible global function definition for ‘hist’
plot.diffnet: no visible global function definition for ‘abline’
plot.diffnet: no visible global function definition for ‘legend’
plot.diffregr: no visible global function definition for ‘hist’
plot.diffregr: no visible global function definition for ‘abline’
plot.diffregr: no visible global function definition for ‘legend’
plot.ggmgsa: no visible global function definition for ‘boxplot’
plot.nethetclustering: no visible global function definition for ‘pdf’
plot.nethetclustering: no visible global function definition for ‘grey’
plot.nethetclustering: no visible global function definition for
  ‘legend’
plot.nethetclustering: no visible global function definition for
  ‘dev.off’
plot_2networks: no visible global function definition for ‘par’
scatter_plot : : no visible global function definition for
  ‘cor’
screen_cv.glasso: no visible global function definition for ‘var’
screen_cv.glasso: no visible binding for global variable ‘var’
screen_cv1se.lasso: no visible global function definition for ‘coef’
screen_cvfix.lasso: no visible global function definition for ‘coef’
screen_cvmin.lasso: no visible global function definition for ‘coef’
screen_cvsqrt.lasso: no visible global function definition for ‘coef’
screen_cvtrunc.lasso: no visible global function definition for ‘coef’
screen_mb: no visible global function definition for ‘var’
screen_mb: no visible binding for global variable ‘var’
screen_mb2 : : no visible global function definition for
  ‘lines’
screen_mb2 : : no visible global function definition for
  ‘coef’
shapiro_screen : : no visible global function definition for
  ‘shapiro.test’
shapiro_screen: no visible global function definition for ‘p.adjust’
sim_mix_networks : : no visible global function definition
  for ‘rnorm’
t2cov.lr: no visible global function definition for ‘var’
t2cov.lr: no visible global function definition for ‘pchisq’
t2diagcov.lr: no visible global function definition for ‘var’
t2diagcov.lr: no visible global function definition for ‘pchisq’
test.sd: no visible global function definition for ‘var’
test.sd: no visible global function definition for ‘pnorm’
twosample_single_regr: no visible global function definition for ‘coef’
twosample_single_regr: no visible global function definition for ‘lm’
Undefined global functions or variables:
  abline boxplot coef cor cov.wt dev.off dnorm grey hist kmeans legend
  lines lm median optimize p.adjust par pchisq pdf pnorm quantile rbeta
  rnorm sd segments shapiro.test var write.csv
Consider adding
  importFrom("grDevices", "dev.off", "grey", "pdf")
  importFrom("graphics", "abline", "boxplot", "hist", "legend", "lines",
             "par", "segments")
  importFrom("stats", "coef", "cor", "cov.wt", "dnorm", "kmeans", "lm",
             "median", "optimize", "p.adjust", "pchisq", "pnorm",
             "quantile", "rbeta", "rnorm", "sd", "shapiro.test", "var")
  importFrom("utils", "write.csv")
to your NAMESPACE file.
* 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 ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
het_cv_glasso       30.265  0.003  30.270
ggmgsa_multisplit   16.924  0.000  16.949
mixglasso           12.380  0.008  12.404
diffregr_multisplit  9.086  0.043   9.139
diffnet_multisplit   5.396  0.000   5.396
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/nethet.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL nethet
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘nethet’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c betamat_diffnet.c -o betamat_diffnet.o
gcc -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o nethet.so betamat_diffnet.o -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-nethet/00new/nethet/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘mclust::dmvnorm’ by ‘mvtnorm::dmvnorm’ when loading ‘nethet’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘mclust::dmvnorm’ by ‘mvtnorm::dmvnorm’ when loading ‘nethet’
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘mclust::dmvnorm’ by ‘mvtnorm::dmvnorm’ when loading ‘nethet’
** testing if installed package keeps a record of temporary installation path
* DONE (nethet)

R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(nethet)
Warning message:
replacing previous import 'mclust::dmvnorm' by 'mvtnorm::dmvnorm' when loading 'nethet' 
> 
> test_check("nethet")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 18 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  9.487   0.192   9.667 

name	user	system	elapsed
aggpval	0.007	0.000	0.007
bwprun_mixglasso	1.726	0.020	1.746
diffnet_multisplit	5.396	0.000	5.396
diffnet_singlesplit	2.603	0.000	2.602
diffregr_multisplit	9.086	0.043	9.139
diffregr_singlesplit	0.748	0.000	0.748
dot_plot	1.132	0.000	1.133
export_network	0.135	0.000	0.135
generate_2networks	0.033	0.000	0.032
generate_inv_cov	0.054	0.036	0.090
ggmgsa_multisplit	16.924	0.000	16.949
gsea.iriz	0.011	0.000	0.011
het_cv_glasso	30.265	0.003	30.270
invcov2parcor	0.001	0.000	0.001
invcov2parcor_array	0.008	0.000	0.007
logratio	0.002	0.000	0.002
mixglasso	12.380	0.008	12.404
plot_2networks	0.054	0.000	0.054
scatter_plot	1.895	0.004	1.898
screen_aic.glasso	1.087	0.000	1.087
screen_bic.glasso	1.063	0.000	1.063
screen_cv.glasso	2.213	0.000	2.213
screen_cv1se.lasso	0.200	0.000	0.201
screen_cvfix.lasso	0.200	0.000	0.199
screen_cvmin.lasso	0.21	0.00	0.21
screen_cvsqrt.lasso	0.204	0.000	0.205
screen_cvtrunc.lasso	0.202	0.000	0.202
screen_mb	0.01	0.00	0.01
sim_mix	0.006	0.000	0.005
sim_mix_networks	0.010	0.000	0.011