Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-08-28 11:42 -0400 (Thu, 28 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4824 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4604 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4545 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4579 |
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 749/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
flowGraph 1.16.0 (landing page) Alice Yue
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the flowGraph package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/flowGraph.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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: flowGraph |
Version: 1.16.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:flowGraph.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings flowGraph_1.16.0.tar.gz |
StartedAt: 2025-08-26 09:41:31 -0000 (Tue, 26 Aug 2025) |
EndedAt: 2025-08-26 09:46:17 -0000 (Tue, 26 Aug 2025) |
EllapsedTime: 285.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: flowGraph.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:flowGraph.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings flowGraph_1.16.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/flowGraph.Rcheck’ * using R Under development (unstable) (2025-02-19 r87757) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘flowGraph/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘flowGraph’ version ‘1.16.0’ * 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 ‘flowGraph’ can be installed ... OK * 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 get_child: no visible binding for global variable ‘no_cores’ get_paren: no visible binding for global variable ‘no_cores’ ms_psig: no visible binding for global variable ‘meta’ Undefined global functions or variables: meta no_cores * checking Rd files ... NOTE checkRd: (-1) fg_get_graph.Rd:13: Lost braces 13 | A list containing two data frames (\code{v} and ]code{e}) | ^ checkRd: (-1) ggdf.Rd:22: Lost braces 22 | code{ggdf} adds to the data frames \code{v} and \code{e} in slot | ^ * 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 data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed fg_save_plots 52.406 0.331 52.861 fg_save 52.110 0.348 52.580 fg_load 50.841 0.355 51.316 * 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: 2 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/flowGraph.Rcheck/00check.log’ for details.
flowGraph.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL flowGraph ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’ * installing *source* package ‘flowGraph’ ... ** this is package ‘flowGraph’ version ‘1.16.0’ ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help Loading required namespace: flowGraph *** 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 (flowGraph)
flowGraph.Rcheck/tests/testthat.Rout
R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: aarch64-unknown-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(flowGraph) > > test_check("flowGraph") [ FAIL 0 | WARN 1 | SKIP 0 | PASS 34 ] [ FAIL 0 | WARN 1 | SKIP 0 | PASS 34 ] > > proc.time() user system elapsed 6.660 0.242 6.901
flowGraph.Rcheck/flowGraph-Ex.timings
name | user | system | elapsed | |
cell_type_layers | 0.004 | 0.000 | 0.004 | |
fg_add_feature | 0.484 | 0.004 | 0.489 | |
fg_add_summary | 1.170 | 0.000 | 1.172 | |
fg_clean_phen | 0 | 0 | 0 | |
fg_clear_features | 1.178 | 0.004 | 1.183 | |
fg_clear_summary | 0.492 | 0.032 | 0.525 | |
fg_extract_phenotypes | 0.393 | 0.004 | 0.396 | |
fg_extract_raw | 1.126 | 0.000 | 1.128 | |
fg_extract_samples | 0.371 | 0.004 | 0.375 | |
fg_feat_cumsum | 0.384 | 0.004 | 0.388 | |
fg_feat_edge_specenr | 0.557 | 0.032 | 0.589 | |
fg_feat_mean_class | 0.387 | 0.000 | 0.388 | |
fg_feat_node_prop | 0.374 | 0.000 | 0.374 | |
fg_feat_node_specenr | 0.548 | 0.004 | 0.552 | |
fg_feat_prop_edge | 0.399 | 0.000 | 0.399 | |
fg_get_feature | 0.383 | 0.000 | 0.384 | |
fg_get_feature_desc | 1.151 | 0.008 | 1.161 | |
fg_get_feature_means | 1.739 | 0.016 | 1.758 | |
fg_get_graph | 0.372 | 0.004 | 0.376 | |
fg_get_markers | 0.38 | 0.00 | 0.38 | |
fg_get_meta | 0.388 | 0.000 | 0.388 | |
fg_get_summary | 2.468 | 0.020 | 2.493 | |
fg_get_summary_desc | 1.143 | 0.000 | 1.146 | |
fg_get_summary_index | 2.607 | 0.036 | 2.649 | |
fg_get_summary_tables | 1.664 | 0.052 | 1.719 | |
fg_gsub_ids | 0.367 | 0.000 | 0.368 | |
fg_gsub_markers | 0.438 | 0.000 | 0.439 | |
fg_load | 50.841 | 0.355 | 51.316 | |
fg_merge | 0.389 | 0.008 | 0.397 | |
fg_merge_samples | 0.444 | 0.012 | 0.457 | |
fg_plot | 0.577 | 0.008 | 0.586 | |
fg_plot_box | 0.883 | 0.004 | 0.889 | |
fg_plot_pVSdiff | 0.586 | 0.000 | 0.588 | |
fg_plot_qq | 1.362 | 0.007 | 1.390 | |
fg_replace_meta | 0.406 | 0.004 | 0.411 | |
fg_rm_feature | 1.202 | 0.008 | 1.214 | |
fg_rm_summary | 0.550 | 0.000 | 0.552 | |
fg_save | 52.110 | 0.348 | 52.580 | |
fg_save_plots | 52.406 | 0.331 | 52.861 | |
fg_set_layout | 0.393 | 0.000 | 0.395 | |
fg_summary | 0.512 | 0.000 | 0.514 | |
flowGraph-class | 0.001 | 0.000 | 0.001 | |
flowGraph | 1.689 | 0.000 | 1.694 | |
flowGraphSubset | 0 | 0 | 0 | |
flowGraphSubset_summary_adjust | 0 | 0 | 0 | |
flowGraphSubset_summary_pars | 0.000 | 0.000 | 0.001 | |
get_phen_list | 0.017 | 0.000 | 0.016 | |
get_phen_meta | 0.002 | 0.000 | 0.002 | |
ggdf | 0.422 | 0.000 | 0.422 | |
loop_ind_f | 0.001 | 0.000 | 0.000 | |
meandiff | 0.001 | 0.000 | 0.001 | |
plot_gr | 1.980 | 0.044 | 2.046 | |
set_layout_graph | 0.399 | 0.011 | 0.412 | |
summary_table | 0.004 | 0.000 | 0.004 | |
time_output | 0.001 | 0.000 | 0.000 | |
tstr | 0 | 0 | 0 | |