Package: nethet

Version: 1.15.0

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_1.15.0.tar.gz

StartedAt: 2019-03-18 03:11:22 -0400 (Mon, 18 Mar 2019)

EndedAt: 2019-03-18 03:15:02 -0400 (Mon, 18 Mar 2019)

EllapsedTime: 219.4 seconds

RetCode: 0

Status:  OK

CheckDir: nethet.Rcheck

Warnings: 0

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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_1.15.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/nethet.Rcheck’
* using R Under development (unstable) (2019-01-21 r75999)
* 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 ‘1.15.0’
* 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 ‘nethet’ can be installed ... 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 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 : <anonymous>: 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’
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 : <anonymous>: 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 : <anonymous>: no visible global function definition for
  ‘lines’
screen_mb2 : <anonymous>: no visible global function definition for
  ‘coef’
shapiro_screen : <anonymous>: no visible global function definition for
  ‘shapiro.test’
shapiro_screen: no visible global function definition for ‘p.adjust’
sim_mix_networks : <anonymous>: 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 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", "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       30.376  0.000  31.877
mixglasso           19.331  0.047  19.970
ggmgsa_multisplit   17.975  0.005  18.640
diffregr_multisplit 10.685  0.051  11.286
diffnet_multisplit   5.089  0.008   5.558
* 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: 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’ ...
** 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/nethet/libs
** R
** inst
** byte-compile and prepare 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	0.006	0.000	0.007
bwprun_mixglasso	3.887	0.044	3.982
diffnet_multisplit	5.089	0.008	5.558
diffnet_singlesplit	2.546	0.008	2.935
diffregr_multisplit	10.685	0.051	11.286
diffregr_singlesplit	0.710	0.000	0.724
dot_plot	1.70	0.00	1.72
export_network	0.360	0.000	0.408
generate_2networks	0.066	0.000	0.091
generate_inv_cov	0.069	0.063	0.171
ggmgsa_multisplit	17.975	0.005	18.640
gsea.iriz	0.018	0.000	0.024
het_cv_glasso	30.376	0.000	31.877
invcov2parcor	0.001	0.000	0.001
invcov2parcor_array	0.007	0.000	0.007
logratio	0.001	0.000	0.001
mixglasso	19.331	0.047	19.970
plot_2networks	0.056	0.000	0.056
scatter_plot	2.342	0.000	2.436
screen_aic.glasso	1.061	0.000	1.230
screen_bic.glasso	1.061	0.000	1.133
screen_cv.glasso	2.051	0.000	2.055
screen_cv1se.lasso	0.191	0.000	0.191
screen_cvfix.lasso	0.194	0.000	0.195
screen_cvmin.lasso	0.205	0.000	0.208
screen_cvsqrt.lasso	0.197	0.000	0.223
screen_cvtrunc.lasso	0.205	0.000	0.210
screen_mb	0.014	0.000	0.014
sim_mix	0.006	0.000	0.006
sim_mix_networks	0.011	0.000	0.011