Nicolas Staedler
| Snapshot Date: 2024-04-15 14:05:01 -0400 (Mon, 15 Apr 2024) |
| git_url: https://git.bioconductor.org/packages/nethet |
| git_branch: RELEASE_3_18 |
| git_last_commit: e771f90 |
| git_last_commit_date: 2023-10-24 10:40:40 -0400 (Tue, 24 Oct 2023) |
| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2024-04-17 11:38:00 -0400 (Wed, 17 Apr 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4676 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4414 |
| merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4437 |
| 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 | ||||
| Package 1403/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| nethet 1.34.0 (landing page) Nicolas Staedler
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
|
To the developers/maintainers of the nethet package: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: nethet |
| Version: 1.34.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:nethet.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings nethet_1.34.0.tar.gz |
| StartedAt: 2024-04-16 06:11:28 -0400 (Tue, 16 Apr 2024) |
| EndedAt: 2024-04-16 06:17:13 -0400 (Tue, 16 Apr 2024) |
| EllapsedTime: 344.6 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: nethet.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:nethet.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings nethet_1.34.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/nethet.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘nethet/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘nethet’ version ‘1.34.0’
* 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 ... WARNING
Found the following significant warnings:
Warning: replacing previous import ‘limma::logsumexp’ by ‘mclust::logsumexp’ when loading ‘nethet’
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 ‘/Users/biocbuild/bbs-3.18-bioc/meat/nethet.Rcheck/00install.out’ for details.
* used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* 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
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 is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
het_cv_glasso 34.994 0.159 36.872
mixglasso 24.409 0.485 26.140
ggmgsa_multisplit 21.447 0.113 22.894
diffregr_multisplit 13.481 0.190 14.527
diffnet_multisplit 6.409 0.028 6.556
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
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
‘/Users/biocbuild/bbs-3.18-bioc/meat/nethet.Rcheck/00check.log’
for details.
nethet.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL nethet ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’ * installing *source* package ‘nethet’ ... ** using staged installation ** libs using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.sdk’ clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c betamat_diffnet.c -o betamat_diffnet.o clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/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/4.3-x86_64/Resources/library/00LOCK-nethet/00new/nethet/libs ** R ** inst ** byte-compile and prepare package for lazy loading Warning: replacing previous import ‘limma::logsumexp’ by ‘mclust::logsumexp’ when loading ‘nethet’ 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 ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: replacing previous import ‘limma::logsumexp’ by ‘mclust::logsumexp’ when loading ‘nethet’ Warning: replacing previous import ‘mclust::dmvnorm’ by ‘mvtnorm::dmvnorm’ when loading ‘nethet’ Warning: replacing previous import ‘multtest::update’ by ‘stats::update’ when loading ‘nethet’ ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location Warning: replacing previous import ‘limma::logsumexp’ by ‘mclust::logsumexp’ when loading ‘nethet’ 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 * DONE (nethet)
nethet.Rcheck/tests/testthat.Rout
R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (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 'limma::logsumexp' by 'mclust::logsumexp' when loading 'nethet'
2: replacing previous import 'mclust::dmvnorm' by 'mvtnorm::dmvnorm' when loading 'nethet'
3: replacing previous import 'multtest::update' by 'stats::update' when loading 'nethet'
>
> test_check("nethet")
-mixglasso: comp too small; min(n_k)= 4.952774
-mixglasso: comp too small; min(n_k)= 4.949353
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 18 ]
>
> proc.time()
user system elapsed
13.523 0.683 14.886
nethet.Rcheck/nethet-Ex.timings
| name | user | system | elapsed | |
| aggpval | 0.012 | 0.003 | 0.016 | |
| bwprun_mixglasso | 3.877 | 0.167 | 4.088 | |
| diffnet_multisplit | 6.409 | 0.028 | 6.556 | |
| diffnet_singlesplit | 3.366 | 0.013 | 3.431 | |
| diffregr_multisplit | 13.481 | 0.190 | 14.527 | |
| diffregr_singlesplit | 0.886 | 0.015 | 0.967 | |
| dot_plot | 1.597 | 0.030 | 1.672 | |
| export_network | 0.304 | 0.010 | 0.316 | |
| generate_2networks | 0.066 | 0.003 | 0.070 | |
| generate_inv_cov | 0.136 | 0.381 | 0.519 | |
| ggmgsa_multisplit | 21.447 | 0.113 | 22.894 | |
| gsea.iriz | 0.016 | 0.002 | 0.017 | |
| het_cv_glasso | 34.994 | 0.159 | 36.872 | |
| invcov2parcor | 0.002 | 0.000 | 0.002 | |
| invcov2parcor_array | 0.010 | 0.000 | 0.011 | |
| logratio | 0.002 | 0.001 | 0.003 | |
| mixglasso | 24.409 | 0.485 | 26.140 | |
| plot_2networks | 0.065 | 0.004 | 0.073 | |
| scatter_plot | 2.966 | 0.041 | 3.076 | |
| screen_aic.glasso | 1.118 | 0.004 | 1.172 | |
| screen_bic.glasso | 1.159 | 0.005 | 1.213 | |
| screen_cv.glasso | 2.221 | 0.008 | 2.325 | |
| screen_cv1se.lasso | 0.231 | 0.005 | 0.357 | |
| screen_cvfix.lasso | 0.227 | 0.002 | 0.303 | |
| screen_cvmin.lasso | 0.241 | 0.007 | 0.311 | |
| screen_cvsqrt.lasso | 0.230 | 0.003 | 0.251 | |
| screen_cvtrunc.lasso | 0.238 | 0.009 | 0.287 | |
| sim_mix | 0.007 | 0.016 | 0.024 | |
| sim_mix_networks | 0.013 | 0.000 | 0.015 | |