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This page was generated on 2022-04-13 12:06:59 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for nethet on tokay2


To the developers/maintainers of the nethet package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/nethet.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1285/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
nethet 1.26.0  (landing page)
Nicolas Staedler
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/nethet
git_branch: RELEASE_3_14
git_last_commit: b1233b3
git_last_commit_date: 2021-10-26 12:18:03 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: nethet
Version: 1.26.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:nethet.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings nethet_1.26.0.tar.gz
StartedAt: 2022-04-12 23:43:46 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 23:49:04 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 317.5 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: nethet.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:nethet.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings nethet_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/nethet.Rcheck'
* using R version 4.1.3 (2022-03-10)
* 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 '1.26.0'
* 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 ... WARNING
Found the following significant warnings:
  Warning: replacing previous import 'mclust::dmvnorm' by 'mvtnorm::dmvnorm' when loading 'nethet'
  Warning: replacing previous import 'multtest::update' by 'stats::update' when loading 'nethet'
See 'C:/Users/biocbuild/bbs-3.14-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
* 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
screen_shrink: no visible global function definition for
  'performance.pcor'
Undefined global functions or variables:
  performance.pcor
* 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-3.14-bioc/R/library/nethet/libs/i386/nethet.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/nethet/libs/x64/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 (user + system) or elapsed time > 5s
                     user system elapsed
het_cv_glasso       24.31   0.00   24.38
ggmgsa_multisplit   15.97   0.00   15.97
mixglasso           12.05   0.04   12.08
diffregr_multisplit  7.06   0.06    7.13
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
het_cv_glasso       31.67   0.00   31.68
ggmgsa_multisplit   19.09   0.00   19.09
mixglasso           13.36   0.03   13.39
diffregr_multisplit  8.50   0.01    8.52
diffnet_multisplit   5.57   0.00    5.63
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/nethet.Rcheck/00check.log'
for details.

Installation output

nethet.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/nethet_1.26.0.tar.gz && rm -rf nethet.buildbin-libdir && mkdir nethet.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=nethet.buildbin-libdir nethet_1.26.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL nethet_1.26.0.zip && rm nethet_1.26.0.tar.gz nethet_1.26.0.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 88701  100 88701    0     0   383k      0 --:--:-- --:--:-- --:--:--  384k

install for i386

* installing *source* package 'nethet' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c betamat_diffnet.c -o betamat_diffnet.o
C:/rtools40/mingw32/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-3~1.14-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/nethet.buildbin-libdir/00LOCK-nethet/00new/nethet/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'mclust::dmvnorm' by 'mvtnorm::dmvnorm' when loading 'nethet'
Warning: replacing previous import 'multtest::update' by 'stats::update' when loading 'nethet'
** 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_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 from temporary location
Warning: replacing previous import 'mclust::dmvnorm' by 'mvtnorm::dmvnorm' when loading 'nethet'
Warning: replacing previous import 'multtest::update' by 'stats::update' when loading 'nethet'
** testing if installed package can be loaded from final location
Warning: replacing previous import 'mclust::dmvnorm' by 'mvtnorm::dmvnorm' when loading 'nethet'
Warning: replacing previous import 'multtest::update' by 'stats::update' when loading 'nethet'
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'nethet' ...
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c betamat_diffnet.c -o betamat_diffnet.o
C:/rtools40/mingw64/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-3~1.14-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/nethet.buildbin-libdir/nethet/libs/x64
** testing if installed package can be loaded
Warning: replacing previous import 'mclust::dmvnorm' by 'mvtnorm::dmvnorm' when loading 'nethet'
Warning: replacing previous import 'multtest::update' by 'stats::update' when loading 'nethet'
* MD5 sums
packaged installation of 'nethet' as nethet_1.26.0.zip
* DONE (nethet)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'nethet' successfully unpacked and MD5 sums checked

Tests output

nethet.Rcheck/tests_i386/testthat.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 messages:
1: replacing previous import 'mclust::dmvnorm' by 'mvtnorm::dmvnorm' when loading 'nethet' 
2: replacing previous import 'multtest::update' by 'stats::update' when loading 'nethet' 
> 
> test_check("nethet")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 18 ]
> 
> proc.time()
   user  system elapsed 
  10.64    0.32   10.93

nethet.Rcheck/tests_x64/testthat.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 messages:
1: replacing previous import 'mclust::dmvnorm' by 'mvtnorm::dmvnorm' when loading 'nethet' 
2: replacing previous import 'multtest::update' by 'stats::update' when loading 'nethet' 
> 
> test_check("nethet")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 18 ]
> 
> proc.time()
   user  system elapsed 
   8.76    0.32    9.07

Example timings

nethet.Rcheck/examples_i386/nethet-Ex.timings

nameusersystemelapsed
aggpval0.020.000.02
bwprun_mixglasso2.310.032.34
diffnet_multisplit4.690.004.73
diffnet_singlesplit2.330.002.32
diffregr_multisplit7.060.067.13
diffregr_singlesplit0.530.000.53
dot_plot0.660.000.66
export_network0.140.000.14
generate_2networks0.030.020.04
generate_inv_cov0.050.070.13
ggmgsa_multisplit15.97 0.0015.97
gsea.iriz0.010.000.01
het_cv_glasso24.31 0.0024.38
invcov2parcor000
invcov2parcor_array000
logratio000
mixglasso12.05 0.0412.08
plot_2networks0.050.000.04
scatter_plot1.090.001.10
screen_aic.glasso0.830.000.82
screen_bic.glasso0.770.000.77
screen_cv.glasso1.590.001.59
screen_cv1se.lasso0.110.000.11
screen_cvfix.lasso0.110.000.11
screen_cvmin.lasso0.120.000.13
screen_cvsqrt.lasso0.110.000.11
screen_cvtrunc.lasso0.130.000.12
sim_mix000
sim_mix_networks0.010.000.02

nethet.Rcheck/examples_x64/nethet-Ex.timings

nameusersystemelapsed
aggpval000
bwprun_mixglasso2.270.002.27
diffnet_multisplit5.570.005.63
diffnet_singlesplit2.710.002.72
diffregr_multisplit8.500.018.52
diffregr_singlesplit0.940.000.94
dot_plot0.670.000.67
export_network0.180.000.17
generate_2networks0.030.000.03
generate_inv_cov0.090.030.13
ggmgsa_multisplit19.09 0.0019.09
gsea.iriz0.020.000.02
het_cv_glasso31.67 0.0031.68
invcov2parcor000
invcov2parcor_array0.020.000.02
logratio000
mixglasso13.36 0.0313.39
plot_2networks0.030.000.04
scatter_plot1.470.001.46
screen_aic.glasso0.990.000.99
screen_bic.glasso0.980.000.98
screen_cv.glasso1.990.001.99
screen_cv1se.lasso0.120.000.12
screen_cvfix.lasso0.130.000.13
screen_cvmin.lasso0.120.000.12
screen_cvsqrt.lasso0.110.000.11
screen_cvtrunc.lasso0.130.000.13
sim_mix000
sim_mix_networks0.010.000.01