Package: nethet

Version: 1.12.0

Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:nethet.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings nethet_1.12.0.tar.gz

StartedAt: 2018-10-17 03:38:18 -0400 (Wed, 17 Oct 2018)

EndedAt: 2018-10-17 03:43:54 -0400 (Wed, 17 Oct 2018)

EllapsedTime: 335.8 seconds

RetCode: 0

Status:  OK

CheckDir: nethet.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:nethet.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings nethet_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/nethet.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'nethet/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'nethet' version '1.12.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.7-bioc/R/library/nethet/libs/i386/nethet.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
het_cv_glasso       32.03   0.00   32.03
mixglasso           19.88   0.02   19.89
ggmgsa_multisplit   16.91   0.02   16.94
diffregr_multisplit  8.40   0.04    8.43
diffnet_multisplit   6.47   0.01    6.50
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
het_cv_glasso       35.22   0.00   35.24
ggmgsa_multisplit   20.72   0.00   20.74
mixglasso           13.35   0.02   13.36
diffregr_multisplit  9.53   0.00    9.53
diffnet_multisplit   6.47   0.00    6.47
* 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
  'C:/Users/biocbuild/bbs-3.7-bioc/meat/nethet.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/nethet_1.12.0.tar.gz && rm -rf nethet.buildbin-libdir && mkdir nethet.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=nethet.buildbin-libdir nethet_1.12.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL nethet_1.12.0.zip && rm nethet_1.12.0.tar.gz nethet_1.12.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 89526  100 89526    0     0  1564k      0 --:--:-- --:--:-- --:--:-- 1784k

install for i386

* installing *source* package 'nethet' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c betamat_diffnet.c -o betamat_diffnet.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o nethet.dll tmp.def betamat_diffnet.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/nethet.buildbin-libdir/nethet/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'nethet'
    finding HTML links ... done
    EXPStep.mix                             html  
    MStepGlasso                             html  
    NetHet-package                          html  
    agg.pval                                html  
    agg.score.iriz.scale                    html  
    agg.score.iriz.shift                    html  
    aggpval                                 html  
    aic.glasso                              html  
    beta.mat                                html  
    beta.mat.diffregr                       html  
    bic.glasso                              html  
    buildDotPlotDataFrame                   html  
    bwprun_mixglasso                        html  
    cv.fold                                 html  
    cv.glasso                               html  
    diffnet_multisplit                      html  
    diffnet_pval                            html  
    diffnet_singlesplit                     html  
    diffregr_multisplit                     html  
    diffregr_pval                           html  
    diffregr_singlesplit                    html  
    dot_plot                                html  
    error.bars                              html  
    est2.my.ev2                             html  
    est2.my.ev2.diffregr                    html  
    est2.my.ev3                             html  
    est2.my.ev3.diffregr                    html  
    est2.ww.mat.diffregr                    html  
    est2.ww.mat2                            html  
    est2.ww.mat2.diffregr                   html  
    export_network                          html  
    func.uinit                              html  
    generate_2networks                      html  
    generate_inv_cov                        html  
    getinvcov                               html  
    ggmgsa_multisplit                       html  
    ggmgsa_singlesplit                      html  
    glasso.invcor                           html  
    glasso.invcov                           html  
    glasso.parcor                           html  
    gsea.highdimT2                          html  
    gsea.iriz                               html  
    gsea.iriz.scale                         html  
    gsea.iriz.shift                         html  
    gsea.t2cov                              html  
    het_cv_glasso                           html  
    hugepath                                html  
    inf.mat                                 html  
    invcov2parcor                           html  
    invcov2parcor_array                     html  
    lambda.max                              html  
    lambdagrid_lin                          html  
    lambdagrid_mult                         html  
    loglik_mix                              html  
    logratio                                html  
    logratio.diffregr                       html  
    make_grid                               html  
    mcov                                    html  
    mixglasso                               html  
    mixglasso_init                          html  
    mixglasso_ncomp_fixed                   html  
    mle.ggm                                 html  
    my.ev2.diffregr                         html  
    my.p.adjust                             html  
    my.ttest                                html  
    my.ttest2                               html  
    mytrunc.method                          html  
    perm.diffregr_pval                      html  
    perm.diffregr_teststat                  html  
    plot.diffnet                            html  
    plot.diffregr                           html  
    plot.ggmgsa                             html  
    plot.nethetclustering                   html  
    plotCV                                  html  
    plot_2networks                          html  
    print.nethetsummary                     html  
    q.matrix.diffregr                       html  
    q.matrix.diffregr3                      html  
    q.matrix.diffregr4                      html  
    q.matrix3                               html  
    q.matrix4                               html  
    scatter_plot                            html  
    screen_aic.glasso                       html  
    screen_bic.glasso                       html  
    screen_cv.glasso                        html  
    screen_cv1se.lasso                      html  
    screen_cvfix.lasso                      html  
    screen_cvmin.lasso                      html  
    screen_cvsqrt.lasso                     html  
    screen_cvtrunc.lasso                    html  
    screen_full                             html  
    screen_lasso                            html  
    screen_mb                               html  
    screen_mb2                              html  
    screen_shrink                           html  
    shapiro_screen                          html  
    sim_mix                                 html  
    sim_mix_networks                        html  
    sparse_conc                             html  
    summary.diffnet                         html  
    summary.diffregr                        html  
    summary.ggmgsa                          html  
    summary.nethetclustering                html  
    sumoffdiag                              html  
    symmkldist                              html  
    t2cov.lr                                html  
    t2diagcov.lr                            html  
    test.sd                                 html  
    test.t2                                 html  
    tr                                      html  
    twosample_single_regr                   html  
    w.kldist                                html  
    ww.mat                                  html  
    ww.mat.diffregr                         html  
    ww.mat2                                 html  
    ww.mat2.diffregr                        html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'nethet' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c betamat_diffnet.c -o betamat_diffnet.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o nethet.dll tmp.def betamat_diffnet.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/nethet.buildbin-libdir/nethet/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'nethet' as nethet_1.12.0.zip
* DONE (nethet)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'nethet' successfully unpacked and MD5 sums checked
In R CMD INSTALL