Back to Multiple platform build/check report for BioC 3.16: simplified long |
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This page was generated on 2023-04-12 11:06:17 -0400 (Wed, 12 Apr 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
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 |
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. |
Package 1343/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
nethet 1.30.0 (landing page) Nicolas Staedler
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
Package: nethet |
Version: 1.30.0 |
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_1.30.0.tar.gz |
StartedAt: 2023-04-10 21:31:36 -0400 (Mon, 10 Apr 2023) |
EndedAt: 2023-04-10 21:34:30 -0400 (Mon, 10 Apr 2023) |
EllapsedTime: 173.8 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_1.30.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/nethet.Rcheck’ * using R version 4.2.3 (2023-03-15) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘nethet/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘nethet’ version ‘1.30.0’ * 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 ‘mclust::dmvnorm’ by ‘mvtnorm::dmvnorm’ when loading ‘nethet’ Warning: replacing previous import ‘multtest::update’ by ‘stats::update’ when loading ‘nethet’ See ‘/Users/biocbuild/bbs-3.16-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 * 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 29.524 0.059 29.623 ggmgsa_multisplit 17.863 0.054 17.943 mixglasso 12.543 0.835 13.426 diffregr_multisplit 5.907 0.157 6.075 diffnet_multisplit 5.162 0.019 5.192 * 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-3.16-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/4.2/Resources/library’ * installing *source* package ‘nethet’ ... ** using staged installation ** libs clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c betamat_diffnet.c -o betamat_diffnet.o clang -mmacosx-version-min=10.13 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/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/4.2/Resources/library/00LOCK-nethet/00new/nethet/libs ** 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 ** 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’ ** checking absolute paths in shared objects and dynamic libraries ** 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 * DONE (nethet)
nethet.Rcheck/tests/testthat.Rout
R version 4.2.3 (2023-03-15) -- "Shortstop Beagle" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin17.0 (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") -mixglasso: comp too small; min(n_k)= 3.850067 [ FAIL 0 | WARN 0 | SKIP 0 | PASS 18 ] > > proc.time() user system elapsed 5.451 0.333 5.796
nethet.Rcheck/nethet-Ex.timings
name | user | system | elapsed | |
aggpval | 0.003 | 0.001 | 0.004 | |
bwprun_mixglasso | 1.724 | 0.147 | 1.876 | |
diffnet_multisplit | 5.162 | 0.019 | 5.192 | |
diffnet_singlesplit | 2.615 | 0.007 | 2.626 | |
diffregr_multisplit | 5.907 | 0.157 | 6.075 | |
diffregr_singlesplit | 0.411 | 0.014 | 0.425 | |
dot_plot | 0.624 | 0.023 | 0.648 | |
export_network | 0.123 | 0.003 | 0.125 | |
generate_2networks | 0.029 | 0.002 | 0.030 | |
generate_inv_cov | 0.042 | 0.102 | 0.143 | |
ggmgsa_multisplit | 17.863 | 0.054 | 17.943 | |
gsea.iriz | 0.006 | 0.001 | 0.007 | |
het_cv_glasso | 29.524 | 0.059 | 29.623 | |
invcov2parcor | 0.001 | 0.000 | 0.001 | |
invcov2parcor_array | 0.004 | 0.001 | 0.004 | |
logratio | 0.001 | 0.000 | 0.001 | |
mixglasso | 12.543 | 0.835 | 13.426 | |
plot_2networks | 0.026 | 0.002 | 0.027 | |
scatter_plot | 1.067 | 0.026 | 1.095 | |
screen_aic.glasso | 1.056 | 0.018 | 1.076 | |
screen_bic.glasso | 0.988 | 0.001 | 0.990 | |
screen_cv.glasso | 2.039 | 0.006 | 2.052 | |
screen_cv1se.lasso | 0.105 | 0.001 | 0.106 | |
screen_cvfix.lasso | 0.101 | 0.000 | 0.101 | |
screen_cvmin.lasso | 0.110 | 0.011 | 0.123 | |
screen_cvsqrt.lasso | 0.089 | 0.001 | 0.090 | |
screen_cvtrunc.lasso | 0.102 | 0.006 | 0.108 | |
sim_mix | 0.002 | 0.005 | 0.007 | |
sim_mix_networks | 0.006 | 0.000 | 0.007 | |