Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-27 11:43 -0400 (Tue, 27 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4421 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4415 |
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 1390/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
nethet 1.37.0 (landing page) Nicolas Staedler
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
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: 1.37.0 |
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_1.37.0.tar.gz |
StartedAt: 2024-08-26 22:08:55 -0400 (Mon, 26 Aug 2024) |
EndedAt: 2024-08-26 22:12:22 -0400 (Mon, 26 Aug 2024) |
EllapsedTime: 207.4 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_1.37.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/nethet.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-apple-darwin20 * 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 ‘1.37.0’ * 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-3.20-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 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 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 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 32.981 0.136 33.258 ggmgsa_multisplit 20.655 0.103 20.858 mixglasso 13.680 0.574 14.318 diffregr_multisplit 6.753 0.137 6.926 diffnet_multisplit 5.954 0.040 6.033 * 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 running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 4 NOTEs See ‘/Users/biocbuild/bbs-3.20-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/4.4-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/4.4-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 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 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)= 4.91167 [ FAIL 0 | WARN 0 | SKIP 0 | PASS 18 ] > > proc.time() user system elapsed 8.735 0.503 9.296
nethet.Rcheck/nethet-Ex.timings
name | user | system | elapsed | |
aggpval | 0.004 | 0.001 | 0.004 | |
bwprun_mixglasso | 2.032 | 0.110 | 2.155 | |
diffnet_multisplit | 5.954 | 0.040 | 6.033 | |
diffnet_singlesplit | 2.901 | 0.017 | 2.935 | |
diffregr_multisplit | 6.753 | 0.137 | 6.926 | |
diffregr_singlesplit | 0.465 | 0.009 | 0.476 | |
dot_plot | 0.837 | 0.019 | 0.861 | |
export_network | 0.133 | 0.004 | 0.137 | |
generate_2networks | 0.026 | 0.002 | 0.028 | |
generate_inv_cov | 0.049 | 0.110 | 0.160 | |
ggmgsa_multisplit | 20.655 | 0.103 | 20.858 | |
gsea.iriz | 0.006 | 0.000 | 0.006 | |
het_cv_glasso | 32.981 | 0.136 | 33.258 | |
invcov2parcor | 0.001 | 0.000 | 0.002 | |
invcov2parcor_array | 0.005 | 0.000 | 0.006 | |
logratio | 0.001 | 0.001 | 0.001 | |
mixglasso | 13.680 | 0.574 | 14.318 | |
plot_2networks | 0.031 | 0.001 | 0.032 | |
scatter_plot | 1.307 | 0.024 | 1.335 | |
screen_aic.glasso | 1.092 | 0.013 | 1.112 | |
screen_bic.glasso | 1.104 | 0.004 | 1.111 | |
screen_cv.glasso | 2.144 | 0.006 | 2.154 | |
screen_cv1se.lasso | 0.119 | 0.002 | 0.122 | |
screen_cvfix.lasso | 0.100 | 0.001 | 0.102 | |
screen_cvmin.lasso | 0.107 | 0.005 | 0.113 | |
screen_cvsqrt.lasso | 0.113 | 0.002 | 0.117 | |
screen_cvtrunc.lasso | 0.116 | 0.003 | 0.119 | |
sim_mix | 0.003 | 0.004 | 0.008 | |
sim_mix_networks | 0.007 | 0.000 | 0.006 | |