Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-07-12 17:41 -0400 (Fri, 12 Jul 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4741 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4483 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4512 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4461 |
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 742/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
flowGraph 1.12.0 (landing page) Alice Yue
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | 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. |
Package: flowGraph |
Version: 1.12.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:flowGraph.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings flowGraph_1.12.0.tar.gz |
StartedAt: 2024-07-11 04:36:51 -0400 (Thu, 11 Jul 2024) |
EndedAt: 2024-07-11 04:46:41 -0400 (Thu, 11 Jul 2024) |
EllapsedTime: 590.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: flowGraph.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:flowGraph.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings flowGraph_1.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/flowGraph.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 12.7.5 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘flowGraph/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘flowGraph’ version ‘1.12.0’ * 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 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_load 86.901 1.077 105.919 fg_save_plots 86.923 1.053 105.033 fg_save 86.677 0.706 102.650 fg_get_summary_index 4.895 0.054 6.384 fg_get_summary 4.641 0.037 5.620 * 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 ‘/Users/biocbuild/bbs-3.19-bioc/meat/flowGraph.Rcheck/00check.log’ for details.
flowGraph.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL flowGraph ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘flowGraph’ ... ** 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 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(flowGraph) > > test_check("flowGraph") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 34 ] > > proc.time() user system elapsed 12.248 0.586 14.848
flowGraph.Rcheck/flowGraph-Ex.timings
name | user | system | elapsed | |
cell_type_layers | 0.006 | 0.002 | 0.009 | |
fg_add_feature | 0.832 | 0.020 | 0.996 | |
fg_add_summary | 2.308 | 0.029 | 2.724 | |
fg_clean_phen | 0.001 | 0.000 | 0.001 | |
fg_clear_features | 2.182 | 0.020 | 2.545 | |
fg_clear_summary | 0.875 | 0.013 | 1.045 | |
fg_extract_phenotypes | 0.700 | 0.012 | 0.847 | |
fg_extract_raw | 2.139 | 0.024 | 2.595 | |
fg_extract_samples | 0.665 | 0.010 | 0.833 | |
fg_feat_cumsum | 0.663 | 0.009 | 0.878 | |
fg_feat_edge_specenr | 1.047 | 0.010 | 1.283 | |
fg_feat_mean_class | 0.670 | 0.012 | 0.818 | |
fg_feat_node_prop | 0.667 | 0.008 | 0.800 | |
fg_feat_node_specenr | 1.026 | 0.014 | 1.253 | |
fg_feat_prop_edge | 0.686 | 0.009 | 0.806 | |
fg_get_feature | 0.652 | 0.009 | 0.782 | |
fg_get_feature_desc | 2.138 | 0.020 | 2.521 | |
fg_get_feature_means | 3.273 | 0.031 | 4.011 | |
fg_get_graph | 0.667 | 0.011 | 0.809 | |
fg_get_markers | 0.663 | 0.008 | 0.788 | |
fg_get_meta | 0.657 | 0.008 | 0.775 | |
fg_get_summary | 4.641 | 0.037 | 5.620 | |
fg_get_summary_desc | 2.161 | 0.021 | 2.528 | |
fg_get_summary_index | 4.895 | 0.054 | 6.384 | |
fg_get_summary_tables | 3.259 | 0.058 | 4.399 | |
fg_gsub_ids | 0.660 | 0.014 | 0.946 | |
fg_gsub_markers | 0.799 | 0.009 | 0.939 | |
fg_load | 86.901 | 1.077 | 105.919 | |
fg_merge | 0.686 | 0.014 | 1.009 | |
fg_merge_samples | 0.711 | 0.035 | 1.303 | |
fg_plot | 1.001 | 0.022 | 1.465 | |
fg_plot_box | 1.534 | 0.015 | 1.790 | |
fg_plot_pVSdiff | 0.904 | 0.010 | 1.029 | |
fg_plot_qq | 2.584 | 0.392 | 3.663 | |
fg_replace_meta | 0.644 | 0.009 | 0.720 | |
fg_rm_feature | 2.150 | 0.022 | 2.461 | |
fg_rm_summary | 0.897 | 0.011 | 1.133 | |
fg_save | 86.677 | 0.706 | 102.650 | |
fg_save_plots | 86.923 | 1.053 | 105.033 | |
fg_set_layout | 0.681 | 0.014 | 0.808 | |
fg_summary | 0.911 | 0.015 | 1.062 | |
flowGraph-class | 0.002 | 0.002 | 0.005 | |
flowGraph | 3.195 | 0.034 | 3.791 | |
flowGraphSubset | 0.001 | 0.000 | 0.001 | |
flowGraphSubset_summary_adjust | 0.000 | 0.001 | 0.003 | |
flowGraphSubset_summary_pars | 0.000 | 0.002 | 0.001 | |
get_phen_list | 0.029 | 0.002 | 0.035 | |
get_phen_meta | 0.005 | 0.002 | 0.008 | |
ggdf | 0.686 | 0.015 | 0.811 | |
loop_ind_f | 0.001 | 0.001 | 0.003 | |
meandiff | 0.001 | 0.001 | 0.002 | |
plot_gr | 3.183 | 0.067 | 3.820 | |
set_layout_graph | 0.726 | 0.108 | 0.949 | |
summary_table | 0.008 | 0.001 | 0.010 | |
time_output | 0.001 | 0.000 | 0.001 | |
tstr | 0.000 | 0.001 | 0.001 | |