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 11:39 -0400 (Tue, 27 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
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 627/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
EGAD 1.33.0 (landing page) Sara Ballouz
| 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 EGAD package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/EGAD.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: EGAD |
Version: 1.33.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:EGAD.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings EGAD_1.33.0.tar.gz |
StartedAt: 2024-08-26 22:35:10 -0400 (Mon, 26 Aug 2024) |
EndedAt: 2024-08-26 22:38:25 -0400 (Mon, 26 Aug 2024) |
EllapsedTime: 195.4 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: EGAD.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:EGAD.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings EGAD_1.33.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/EGAD.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 ‘EGAD/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘EGAD’ version ‘1.33.0’ * package encoding: UTF-8 * 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 ‘EGAD’ can be installed ... OK * checking installed package size ... NOTE installed size is 37.3Mb sub-directories of 1Mb or more: data 37.0Mb * checking package 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 ... OK * 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... WARNING Files in the 'vignettes' directory but no files in 'inst/doc': ‘EGAD.Rmd’ ‘EGAD.bib’ ‘figures/figure_GO_comb.png’ ‘figures/figure_aurocs_comparisons.png’ ‘figures/figure_benchmark.png’ ‘figures/figure_degree_corr.png’ ‘figures/figure_indirect.png’ ‘figures/figure_mf.png’ ‘figures/figure_mf_yeast_human.png’ ‘figures/figure_nd_yeast_human.png’ ‘figures/figure_nv.png’ ‘figures/figure_nv_yeast_human.png’ ‘figures/figure_overlay.png’ ‘figures/figure_pheno_comb.png’ ‘figures/figure_pheno_degree_corr.png’ ‘figures/figure_pheno_mf.png’ ‘figures/figure_pheno_nv.png’ ‘figures/figure_smoother.png’ ‘figures/gba_schematic_resized.png’ ‘figures/labels_resized.png’ ‘figures/mf_schematic.png’ ‘figures/network_resized.png’ ‘figures/overview_resized.png’ * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking package vignettes ... NOTE Package has ‘vignettes’ subdirectory but apparently no vignettes. Perhaps the ‘VignetteBuilder’ information is missing from the DESCRIPTION file? * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 2 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/EGAD.Rcheck/00check.log’ for details.
EGAD.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL EGAD ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘EGAD’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (EGAD)
EGAD.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(EGAD) Setting options('download.file.method.GEOquery'='auto') Setting options('GEOquery.inmemory.gpl'=FALSE) > > test_check("EGAD") [ FAIL 0 | WARN 0 | SKIP 2 | PASS 9 ] ══ Skipped tests (2) ═══════════════════════════════════════════════════════════ • empty test (2): 'test.mf.r:3:1', 'test.nv.r:3:1' [ FAIL 0 | WARN 0 | SKIP 2 | PASS 9 ] > > proc.time() user system elapsed 8.736 0.423 9.147
EGAD.Rcheck/EGAD-Ex.timings
name | user | system | elapsed | |
assortativity | 0.001 | 0.000 | 0.001 | |
auc_multifunc | 0.000 | 0.000 | 0.001 | |
auprc | 0.005 | 0.000 | 0.004 | |
auroc_analytic | 0 | 0 | 0 | |
build_binary_network | 0.000 | 0.001 | 0.001 | |
build_coexp_expressionSet | 0.001 | 0.002 | 0.003 | |
build_coexp_network | 0.005 | 0.000 | 0.004 | |
build_semantic_similarity_network | 0.001 | 0.000 | 0.000 | |
build_weighted_network | 0 | 0 | 0 | |
calculate_multifunc | 0.002 | 0.000 | 0.002 | |
conv_smoother | 0.011 | 0.000 | 0.011 | |
extend_network | 0.011 | 0.008 | 0.019 | |
filter_network | 0.001 | 0.000 | 0.001 | |
filter_network_cols | 0.001 | 0.000 | 0.002 | |
filter_network_rows | 0.001 | 0.000 | 0.002 | |
filter_orthologs | 0.000 | 0.000 | 0.001 | |
fmeasure | 0.001 | 0.000 | 0.000 | |
get_auc | 0.001 | 0.000 | 0.001 | |
get_counts | 0.003 | 0.000 | 0.003 | |
get_density | 0.001 | 0.000 | 0.000 | |
get_prc | 0 | 0 | 0 | |
get_roc | 0.000 | 0.000 | 0.001 | |
make_annotations | 0.001 | 0.000 | 0.001 | |
make_gene_network | 0.001 | 0.000 | 0.001 | |
make_genelist | 0.001 | 0.000 | 0.000 | |
neighbor_voting | 0.021 | 0.000 | 0.021 | |
node_degree | 0.001 | 0.000 | 0.000 | |
plot_densities | 0.022 | 0.000 | 0.022 | |
plot_density_compare | 0.003 | 0.003 | 0.007 | |
plot_distribution | 0.005 | 0.000 | 0.005 | |
plot_network_heatmap | 0.032 | 0.000 | 0.032 | |
plot_prc | 0.011 | 0.000 | 0.011 | |
plot_roc | 0.001 | 0.000 | 0.002 | |
plot_roc_overlay | 0.072 | 0.004 | 0.076 | |
predictions | 0.005 | 0.002 | 0.007 | |
repmat | 0.000 | 0.001 | 0.001 | |
run_GBA | 0.022 | 0.009 | 0.032 | |