Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-06-11 15:40 -0400 (Tue, 11 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4679 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4414 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4441 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4394 |
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 719/2239 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
flowGraph 1.13.0 (landing page) Alice Yue
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino4 | 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: 1.13.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:flowGraph.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings flowGraph_1.13.0.tar.gz |
StartedAt: 2024-06-10 02:48:49 -0400 (Mon, 10 Jun 2024) |
EndedAt: 2024-06-10 02:54:19 -0400 (Mon, 10 Jun 2024) |
EllapsedTime: 330.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: flowGraph.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:flowGraph.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings flowGraph_1.13.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/flowGraph.Rcheck' * using R version 4.4.0 RC (2024-04-16 r86468 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'flowGraph/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'flowGraph' version '1.13.0' * 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 '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_save_plots 42.42 1.31 43.73 fg_save 41.51 1.30 42.83 fg_load 40.09 1.25 41.47 * 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 'F:/biocbuild/bbs-3.20-bioc/meat/flowGraph.Rcheck/00check.log' for details.
flowGraph.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL flowGraph ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/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 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 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(flowGraph) > > test_check("flowGraph") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 34 ] > > proc.time() user system elapsed 5.12 3.37 8.43
flowGraph.Rcheck/flowGraph-Ex.timings
name | user | system | elapsed | |
cell_type_layers | 0 | 0 | 0 | |
fg_add_feature | 0.38 | 0.02 | 0.39 | |
fg_add_summary | 0.89 | 0.00 | 0.89 | |
fg_clean_phen | 0 | 0 | 0 | |
fg_clear_features | 1.00 | 0.03 | 1.03 | |
fg_clear_summary | 0.39 | 0.00 | 0.39 | |
fg_extract_phenotypes | 0.20 | 0.04 | 0.25 | |
fg_extract_raw | 0.72 | 0.04 | 0.75 | |
fg_extract_samples | 0.25 | 0.01 | 0.27 | |
fg_feat_cumsum | 0.30 | 0.02 | 0.31 | |
fg_feat_edge_specenr | 0.43 | 0.01 | 0.45 | |
fg_feat_mean_class | 0.29 | 0.00 | 0.29 | |
fg_feat_node_prop | 0.23 | 0.00 | 0.23 | |
fg_feat_node_specenr | 0.34 | 0.02 | 0.36 | |
fg_feat_prop_edge | 0.24 | 0.00 | 0.23 | |
fg_get_feature | 0.22 | 0.00 | 0.22 | |
fg_get_feature_desc | 0.68 | 0.01 | 0.71 | |
fg_get_feature_means | 1.13 | 0.07 | 1.18 | |
fg_get_graph | 0.22 | 0.01 | 0.24 | |
fg_get_markers | 0.37 | 0.00 | 0.37 | |
fg_get_meta | 0.28 | 0.00 | 0.28 | |
fg_get_summary | 1.77 | 0.03 | 1.80 | |
fg_get_summary_desc | 0.95 | 0.03 | 0.98 | |
fg_get_summary_index | 1.94 | 0.04 | 1.97 | |
fg_get_summary_tables | 1.25 | 0.03 | 1.28 | |
fg_gsub_ids | 0.36 | 0.00 | 0.36 | |
fg_gsub_markers | 0.44 | 0.03 | 0.47 | |
fg_load | 40.09 | 1.25 | 41.47 | |
fg_merge | 0.33 | 0.00 | 0.33 | |
fg_merge_samples | 0.26 | 0.00 | 0.26 | |
fg_plot | 0.38 | 0.03 | 0.41 | |
fg_plot_box | 0.53 | 0.02 | 0.54 | |
fg_plot_pVSdiff | 0.38 | 0.05 | 0.43 | |
fg_plot_qq | 1.06 | 0.03 | 1.51 | |
fg_replace_meta | 0.26 | 0.01 | 0.28 | |
fg_rm_feature | 0.77 | 0.04 | 0.80 | |
fg_rm_summary | 0.30 | 0.01 | 0.31 | |
fg_save | 41.51 | 1.30 | 42.83 | |
fg_save_plots | 42.42 | 1.31 | 43.73 | |
fg_set_layout | 0.27 | 0.00 | 0.27 | |
fg_summary | 0.54 | 0.00 | 0.54 | |
flowGraph-class | 0.02 | 0.00 | 0.02 | |
flowGraph | 1.28 | 0.02 | 1.30 | |
flowGraphSubset | 0 | 0 | 0 | |
flowGraphSubset_summary_adjust | 0 | 0 | 0 | |
flowGraphSubset_summary_pars | 0 | 0 | 0 | |
get_phen_list | 0.01 | 0.01 | 0.03 | |
get_phen_meta | 0 | 0 | 0 | |
ggdf | 0.38 | 0.02 | 0.39 | |
loop_ind_f | 0 | 0 | 0 | |
meandiff | 0 | 0 | 0 | |
plot_gr | 1.59 | 0.09 | 2.09 | |
set_layout_graph | 0.36 | 0.02 | 0.38 | |
summary_table | 0 | 0 | 0 | |
time_output | 0 | 0 | 0 | |
tstr | 0 | 0 | 0 | |