Package: nethet

Version: 1.15.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:nethet.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings nethet_1.15.0.tar.gz

StartedAt: 2019-04-09 02:30:41 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 02:34:04 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 203.0 seconds

RetCode: 0

Status:  OK

CheckDir: nethet.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:nethet.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings nethet_1.15.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/nethet.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.15.0’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
het_cv_glasso       26.823  0.055  27.148
mixglasso           20.674  0.240  22.136
ggmgsa_multisplit   16.605  0.027  16.794
diffregr_multisplit 11.407  0.083  12.072
* 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
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/nethet.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL nethet
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘nethet’ ...
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c betamat_diffnet.c -o betamat_diffnet.o
clang -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 -o nethet.so betamat_diffnet.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/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	3.815	0.135	3.978
diffnet_multisplit	4.662	0.010	4.726
diffnet_singlesplit	2.314	0.005	2.328
diffregr_multisplit	11.407	0.083	12.072
diffregr_singlesplit	0.719	0.005	0.735
dot_plot	1.481	0.008	1.507
export_network	0.611	0.003	0.622
generate_2networks	0.051	0.001	0.053
generate_inv_cov	0.112	0.104	0.221
ggmgsa_multisplit	16.605	0.027	16.794
gsea.iriz	0.023	0.000	0.024
het_cv_glasso	26.823	0.055	27.148
invcov2parcor	0.001	0.000	0.001
invcov2parcor_array	0.004	0.000	0.005
logratio	0.002	0.000	0.001
mixglasso	20.674	0.240	22.136
plot_2networks	0.060	0.001	0.066
scatter_plot	2.397	0.011	2.529
screen_aic.glasso	1.000	0.004	1.058
screen_bic.glasso	1.000	0.002	1.062
screen_cv.glasso	1.966	0.004	2.062
screen_cv1se.lasso	0.173	0.001	0.181
screen_cvfix.lasso	0.171	0.000	0.174
screen_cvmin.lasso	0.195	0.001	0.198
screen_cvsqrt.lasso	0.182	0.001	0.183
screen_cvtrunc.lasso	0.188	0.001	0.191
screen_mb	0.009	0.000	0.008
sim_mix	0.004	0.002	0.006
sim_mix_networks	0.007	0.000	0.007