Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-08-06 17:38 -0400 (Tue, 06 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4756 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4490 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4519 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4468 |
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 1419/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
nethet 1.36.0 (landing page) Nicolas Staedler
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
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: 1.36.0 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:nethet.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings nethet_1.36.0.tar.gz |
StartedAt: 2024-08-05 02:11:09 -0400 (Mon, 05 Aug 2024) |
EndedAt: 2024-08-05 02:17:17 -0400 (Mon, 05 Aug 2024) |
EllapsedTime: 367.7 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: nethet.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:nethet.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings nethet_1.36.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/nethet.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘nethet/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘nethet’ version ‘1.36.0’ * 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 ‘/home/biocbuild/bbs-3.19-bioc/meat/nethet.Rcheck/00install.out’ for details. * used C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ * 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 code 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 screen_shrink: no visible global function definition for ‘performance.pcor’ Undefined global functions or variables: performance.pcor * checking Rd files ... NOTE checkRd: (-1) NetHet-package.Rd:19: Lost braces 19 | St{\"a}dler, N. and Mukherjee, S. (2013). Two-Sample Testing in High-Dimensional Models. | ^ checkRd: (-1) bwprun_mixglasso.Rd:32: Lost braces; missing escapes or markup? 32 | init={'cl.init','r.means','random','kmeans','kmeans.hc','hc'}. Default='kmeans.hc'} | ^ checkRd: (-1) func.uinit.Rd:16: Lost braces; missing escapes or markup? 16 | init={'cl.init','r.means','random','kmeans','kmeans.hc','hc'}} | ^ checkRd: (-1) mixglasso.Rd:31: Lost braces; missing escapes or markup? 31 | init={'cl.init','r.means','random','kmeans','kmeans.hc','hc'}. Default='kmeans'} | ^ checkRd: (-1) mixglasso_ncomp_fixed.Rd:22: Lost braces; missing escapes or markup? 22 | init={'cl.init','r.means','random','kmeans','kmeans.hc','hc'}. Default='kmeans'} | ^ * checking Rd metadata ... NOTE Invalid package aliases in Rd file 'NetHet-package.Rd': ‘NetHet-package’ * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed het_cv_glasso 31.462 0.184 31.645 ggmgsa_multisplit 19.013 0.149 19.163 mixglasso 13.100 0.031 13.132 diffnet_multisplit 6.148 0.305 6.453 diffregr_multisplit 5.777 0.160 5.936 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 4 NOTEs See ‘/home/biocbuild/bbs-3.19-bioc/meat/nethet.Rcheck/00check.log’ for details.
nethet.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL nethet ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’ * installing *source* package ‘nethet’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c betamat_diffnet.c -o betamat_diffnet.o gcc -shared -L/home/biocbuild/bbs-3.19-bioc/R/lib -L/usr/local/lib -o nethet.so betamat_diffnet.o -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.19-bioc/R/site-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 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu 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") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 18 ] > > proc.time() user system elapsed 6.314 0.295 6.598
nethet.Rcheck/nethet-Ex.timings
name | user | system | elapsed | |
aggpval | 0.003 | 0.003 | 0.006 | |
bwprun_mixglasso | 1.782 | 0.024 | 1.806 | |
diffnet_multisplit | 6.148 | 0.305 | 6.453 | |
diffnet_singlesplit | 2.974 | 0.084 | 3.058 | |
diffregr_multisplit | 5.777 | 0.160 | 5.936 | |
diffregr_singlesplit | 0.425 | 0.000 | 0.425 | |
dot_plot | 0.744 | 0.008 | 0.752 | |
export_network | 0.140 | 0.004 | 0.144 | |
generate_2networks | 0.033 | 0.000 | 0.032 | |
generate_inv_cov | 0.053 | 0.148 | 0.201 | |
ggmgsa_multisplit | 19.013 | 0.149 | 19.163 | |
gsea.iriz | 0.004 | 0.002 | 0.005 | |
het_cv_glasso | 31.462 | 0.184 | 31.645 | |
invcov2parcor | 0.001 | 0.000 | 0.001 | |
invcov2parcor_array | 0.002 | 0.003 | 0.006 | |
logratio | 0.001 | 0.000 | 0.001 | |
mixglasso | 13.100 | 0.031 | 13.132 | |
plot_2networks | 0.032 | 0.000 | 0.032 | |
scatter_plot | 1.132 | 0.020 | 1.152 | |
screen_aic.glasso | 1.071 | 0.000 | 1.071 | |
screen_bic.glasso | 0.992 | 0.000 | 0.991 | |
screen_cv.glasso | 1.998 | 0.032 | 2.030 | |
screen_cv1se.lasso | 0.102 | 0.000 | 0.102 | |
screen_cvfix.lasso | 0.099 | 0.000 | 0.099 | |
screen_cvmin.lasso | 0.106 | 0.000 | 0.106 | |
screen_cvsqrt.lasso | 0.097 | 0.000 | 0.098 | |
screen_cvtrunc.lasso | 0.103 | 0.003 | 0.107 | |
sim_mix | 0.000 | 0.007 | 0.006 | |
sim_mix_networks | 0.005 | 0.001 | 0.007 | |