Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:05 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 1407/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
nethet 1.38.0 (landing page) Nicolas Staedler
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino8 | 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: 1.38.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:nethet.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings nethet_1.38.0.tar.gz |
StartedAt: 2024-12-20 04:05:15 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 04:09:13 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 237.5 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: nethet.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:nethet.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings nethet_1.38.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/nethet.Rcheck' * using R version 4.4.2 (2024-10-31 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.3.0 GNU Fortran (GCC) 13.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'nethet/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'nethet' version '1.38.0' * 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 '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 'F:/biocbuild/bbs-3.20-bioc/meat/nethet.Rcheck/00install.out' for details. * used C compiler: 'gcc.exe (GCC) 13.3.0' * 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 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 for x64 is not available File 'F:/biocbuild/bbs-3.20-bioc/R/library/nethet/libs/x64/nethet.dll': Found '_exit', possibly from '_exit' (C) 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 nor [v]sprintf. 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 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 36.92 0.00 36.95 ggmgsa_multisplit 21.84 0.00 21.84 mixglasso 17.78 0.64 18.43 diffregr_multisplit 7.98 0.36 8.34 diffnet_multisplit 6.53 0.00 6.54 * 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 'F:/biocbuild/bbs-3.20-bioc/meat/nethet.Rcheck/00check.log' for details.
nethet.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL nethet ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'nethet' ... ** using staged installation ** libs using C compiler: 'gcc.exe (GCC) 13.3.0' gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c betamat_diffnet.c -o betamat_diffnet.o gcc -shared -s -static-libgcc -o nethet.dll tmp.def betamat_diffnet.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-nethet/00new/nethet/libs/x64 ** 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' ** 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 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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 10.87 0.73 11.60
nethet.Rcheck/nethet-Ex.timings
name | user | system | elapsed | |
aggpval | 0 | 0 | 0 | |
bwprun_mixglasso | 2.41 | 0.06 | 2.47 | |
diffnet_multisplit | 6.53 | 0.00 | 6.54 | |
diffnet_singlesplit | 3.33 | 0.00 | 3.33 | |
diffregr_multisplit | 7.98 | 0.36 | 8.34 | |
diffregr_singlesplit | 0.55 | 0.01 | 0.56 | |
dot_plot | 0.87 | 0.08 | 0.96 | |
export_network | 0.15 | 0.00 | 0.14 | |
generate_2networks | 0.05 | 0.00 | 0.05 | |
generate_inv_cov | 0.08 | 0.14 | 0.22 | |
ggmgsa_multisplit | 21.84 | 0.00 | 21.84 | |
gsea.iriz | 0 | 0 | 0 | |
het_cv_glasso | 36.92 | 0.00 | 36.95 | |
invcov2parcor | 0 | 0 | 0 | |
invcov2parcor_array | 0 | 0 | 0 | |
logratio | 0.01 | 0.00 | 0.02 | |
mixglasso | 17.78 | 0.64 | 18.43 | |
plot_2networks | 0.07 | 0.00 | 0.07 | |
scatter_plot | 1.59 | 0.00 | 1.65 | |
screen_aic.glasso | 1.27 | 0.00 | 1.27 | |
screen_bic.glasso | 1.31 | 0.02 | 1.33 | |
screen_cv.glasso | 2.59 | 0.00 | 2.59 | |
screen_cv1se.lasso | 0.11 | 0.00 | 0.11 | |
screen_cvfix.lasso | 0.13 | 0.00 | 0.12 | |
screen_cvmin.lasso | 0.17 | 0.00 | 0.17 | |
screen_cvsqrt.lasso | 0.14 | 0.00 | 0.14 | |
screen_cvtrunc.lasso | 0.16 | 0.00 | 0.16 | |
sim_mix | 0 | 0 | 0 | |
sim_mix_networks | 0.01 | 0.00 | 0.01 | |