Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-05-17 11:36:04 -0400 (Fri, 17 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4751 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4485 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4515 |
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 | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
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: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:flowGraph.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings flowGraph_1.12.0.tar.gz |
StartedAt: 2024-05-16 22:47:05 -0400 (Thu, 16 May 2024) |
EndedAt: 2024-05-16 22:51:04 -0400 (Thu, 16 May 2024) |
EllapsedTime: 238.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: flowGraph.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:flowGraph.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings flowGraph_1.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/flowGraph.Rcheck’ * using R version 4.4.0 (2024-04-24) * 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 ‘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 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 39.939 0.816 40.755 fg_load 39.261 0.891 40.057 fg_save 38.797 0.812 39.610 * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/home/biocbuild/bbs-3.19-bioc/meat/flowGraph.Rcheck/00check.log’ for details.
flowGraph.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL flowGraph ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-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 4.4.0 (2024-04-24) -- "Puppy Cup" 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(flowGraph) > > test_check("flowGraph") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 34 ] > > proc.time() user system elapsed 4.707 0.192 4.887
flowGraph.Rcheck/flowGraph-Ex.timings
name | user | system | elapsed | |
cell_type_layers | 0.004 | 0.000 | 0.004 | |
fg_add_feature | 0.295 | 0.008 | 0.303 | |
fg_add_summary | 0.760 | 0.004 | 0.764 | |
fg_clean_phen | 0.000 | 0.000 | 0.001 | |
fg_clear_features | 0.794 | 0.008 | 0.802 | |
fg_clear_summary | 0.3 | 0.0 | 0.3 | |
fg_extract_phenotypes | 0.23 | 0.00 | 0.23 | |
fg_extract_raw | 0.79 | 0.02 | 0.81 | |
fg_extract_samples | 0.234 | 0.004 | 0.239 | |
fg_feat_cumsum | 0.239 | 0.000 | 0.240 | |
fg_feat_edge_specenr | 0.351 | 0.004 | 0.356 | |
fg_feat_mean_class | 0.243 | 0.000 | 0.243 | |
fg_feat_node_prop | 0.235 | 0.000 | 0.236 | |
fg_feat_node_specenr | 0.357 | 0.008 | 0.365 | |
fg_feat_prop_edge | 0.263 | 0.000 | 0.263 | |
fg_get_feature | 0.244 | 0.004 | 0.247 | |
fg_get_feature_desc | 0.757 | 0.024 | 0.781 | |
fg_get_feature_means | 1.122 | 0.004 | 1.126 | |
fg_get_graph | 0.230 | 0.004 | 0.233 | |
fg_get_markers | 0.238 | 0.004 | 0.242 | |
fg_get_meta | 0.236 | 0.000 | 0.237 | |
fg_get_summary | 1.586 | 0.004 | 1.591 | |
fg_get_summary_desc | 0.782 | 0.020 | 0.801 | |
fg_get_summary_index | 1.733 | 0.068 | 1.801 | |
fg_get_summary_tables | 1.014 | 0.020 | 1.034 | |
fg_gsub_ids | 0.218 | 0.024 | 0.242 | |
fg_gsub_markers | 0.262 | 0.000 | 0.262 | |
fg_load | 39.261 | 0.891 | 40.057 | |
fg_merge | 0.264 | 0.008 | 0.272 | |
fg_merge_samples | 0.287 | 0.043 | 0.330 | |
fg_plot | 0.368 | 0.004 | 0.372 | |
fg_plot_box | 0.598 | 0.000 | 0.599 | |
fg_plot_pVSdiff | 0.344 | 0.000 | 0.345 | |
fg_plot_qq | 0.979 | 0.012 | 0.992 | |
fg_replace_meta | 0.274 | 0.000 | 0.274 | |
fg_rm_feature | 0.793 | 0.004 | 0.798 | |
fg_rm_summary | 0.356 | 0.000 | 0.356 | |
fg_save | 38.797 | 0.812 | 39.610 | |
fg_save_plots | 39.939 | 0.816 | 40.755 | |
fg_set_layout | 0.257 | 0.004 | 0.262 | |
fg_summary | 0.324 | 0.004 | 0.328 | |
flowGraph-class | 0.001 | 0.000 | 0.001 | |
flowGraph | 1.066 | 0.008 | 1.074 | |
flowGraphSubset | 0.001 | 0.000 | 0.000 | |
flowGraphSubset_summary_adjust | 0.001 | 0.000 | 0.000 | |
flowGraphSubset_summary_pars | 0.001 | 0.000 | 0.000 | |
get_phen_list | 0.014 | 0.000 | 0.013 | |
get_phen_meta | 0.002 | 0.000 | 0.002 | |
ggdf | 0.253 | 0.004 | 0.256 | |
loop_ind_f | 0.000 | 0.000 | 0.001 | |
meandiff | 0.000 | 0.000 | 0.001 | |
plot_gr | 1.349 | 0.012 | 1.367 | |
set_layout_graph | 0.253 | 0.032 | 0.285 | |
summary_table | 0.003 | 0.000 | 0.003 | |
time_output | 0.001 | 0.000 | 0.001 | |
tstr | 0 | 0 | 0 | |