Package: nethet

Version: 1.10.0

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings nethet_1.10.0.tar.gz

StartedAt: 2018-04-12 01:27:33 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 01:30:15 -0400 (Thu, 12 Apr 2018)

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-3.6-bioc/R/bin/R CMD check --no-vignettes --timings nethet_1.10.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/nethet.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.10.0’
* 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 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 ... 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 ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
het_cv_glasso       26.120  0.000  26.155
ggmgsa_multisplit   15.704  0.004  15.718
mixglasso           14.128  0.032  14.173
diffregr_multisplit  8.264  0.000   8.268
diffnet_multisplit   6.412  0.000   6.418
* 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 NOTE
See
  ‘/home/biocbuild/bbs-3.6-bioc/meat/nethet.Rcheck/00check.log’
for details.

* installing *source* package ‘nethet’ ...
** libs
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c betamat_diffnet.c -o betamat_diffnet.o
g++ -shared -L/home/biocbuild/bbs-3.6-bioc/R/lib -L/usr/local/lib -o nethet.so betamat_diffnet.o -L/home/biocbuild/bbs-3.6-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.6-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	0.004	0.000	0.007
bwprun_mixglasso	3.320	0.016	3.340
diffnet_multisplit	6.412	0.000	6.418
diffnet_singlesplit	2.440	0.004	2.446
diffregr_multisplit	8.264	0.000	8.268
diffregr_singlesplit	0.436	0.004	0.440
dot_plot	1.932	0.004	1.935
export_network	0.272	0.000	0.274
generate_2networks	0.040	0.000	0.038
generate_inv_cov	0.048	0.032	0.079
ggmgsa_multisplit	15.704	0.004	15.718
gsea.iriz	0.044	0.000	0.046
het_cv_glasso	26.120	0.000	26.155
invcov2parcor	0.004	0.000	0.001
invcov2parcor_array	0.004	0.000	0.004
logratio	0.000	0.000	0.001
mixglasso	14.128	0.032	14.173
plot_2networks	0.040	0.000	0.038
scatter_plot	1.864	0.004	1.870
screen_aic.glasso	0.736	0.000	0.738
screen_bic.glasso	0.732	0.000	0.732
screen_cv.glasso	1.784	0.000	1.785
screen_cv1se.lasso	0.128	0.000	0.128
screen_cvfix.lasso	0.136	0.000	0.134
screen_cvmin.lasso	0.136	0.000	0.137
screen_cvsqrt.lasso	0.128	0.000	0.126
screen_cvtrunc.lasso	0.128	0.000	0.129
screen_mb	0.032	0.000	0.029
sim_mix	0.004	0.000	0.004
sim_mix_networks	0.012	0.000	0.012