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This page was generated on 2025-10-16 11:40 -0400 (Thu, 16 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4833
merida1macOS 12.7.6 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4614
kjohnson1macOS 13.7.5 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4555
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4586
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 749/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowGraph 1.16.0  (landing page)
Alice Yue
Snapshot Date: 2025-10-13 13:40 -0400 (Mon, 13 Oct 2025)
git_url: https://git.bioconductor.org/packages/flowGraph
git_branch: RELEASE_3_21
git_last_commit: faf5530
git_last_commit_date: 2025-04-15 12:15:54 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.6 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.7.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for flowGraph on kjohnson1

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.

raw results


Summary

Package: flowGraph
Version: 1.16.0
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_1.16.0.tar.gz
StartedAt: 2025-10-14 21:50:13 -0400 (Tue, 14 Oct 2025)
EndedAt: 2025-10-14 21:55:43 -0400 (Tue, 14 Oct 2025)
EllapsedTime: 329.6 seconds
RetCode: 0
Status:   OK  
CheckDir: flowGraph.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/flowGraph.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flowGraph/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowGraph’ version ‘1.16.0’
* 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 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 66.885  0.905  68.489
fg_load       64.437  0.893  67.777
fg_save       64.193  0.950  67.436
* 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-3.21-bioc/meat/flowGraph.Rcheck/00check.log’
for details.


Installation output

flowGraph.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL flowGraph
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/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)

Tests output

flowGraph.Rcheck/tests/testthat.Rout


R version 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-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 1 | SKIP 0 | PASS 34 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 34 ]
> 
> proc.time()
   user  system elapsed 
  5.371   0.335   5.722 

Example timings

flowGraph.Rcheck/flowGraph-Ex.timings

nameusersystemelapsed
cell_type_layers0.0040.0010.005
fg_add_feature0.3430.0110.354
fg_add_summary0.9030.0140.920
fg_clean_phen0.0000.0000.001
fg_clear_features0.7910.0090.812
fg_clear_summary0.3080.0050.316
fg_extract_phenotypes0.2590.0050.264
fg_extract_raw0.7840.0080.806
fg_extract_samples0.2810.0040.293
fg_feat_cumsum0.2590.0050.268
fg_feat_edge_specenr0.4390.0060.453
fg_feat_mean_class0.2420.0040.246
fg_feat_node_prop0.2390.0040.243
fg_feat_node_specenr0.4170.0070.425
fg_feat_prop_edge0.2640.0050.269
fg_get_feature0.2410.0040.246
fg_get_feature_desc0.8030.0080.812
fg_get_feature_means1.1550.0101.168
fg_get_graph0.2700.0060.278
fg_get_markers0.2490.0030.251
fg_get_meta0.2750.0040.278
fg_get_summary1.6980.0461.745
fg_get_summary_desc0.7100.0070.717
fg_get_summary_index1.3540.0091.364
fg_get_summary_tables1.0530.0101.066
fg_gsub_ids0.2220.0030.227
fg_gsub_markers0.2790.0040.284
fg_load64.437 0.89367.777
fg_merge0.3030.0050.372
fg_merge_samples0.3200.0060.380
fg_plot0.4860.0100.543
fg_plot_box0.8320.0151.049
fg_plot_pVSdiff0.4100.0090.462
fg_plot_qq1.7670.2052.160
fg_replace_meta0.2700.0040.273
fg_rm_feature0.8440.0080.887
fg_rm_summary0.7570.0060.765
fg_save64.193 0.95067.436
fg_save_plots66.885 0.90568.489
fg_set_layout0.2600.0060.265
fg_summary0.3420.0050.346
flowGraph-class0.0010.0010.001
flowGraph1.1800.0131.199
flowGraphSubset0.0000.0000.001
flowGraphSubset_summary_adjust0.0000.0010.001
flowGraphSubset_summary_pars0.0000.0010.001
get_phen_list0.0210.0010.021
get_phen_meta0.0020.0010.002
ggdf0.2640.0060.272
loop_ind_f0.0010.0000.001
meandiff0.0010.0010.001
plot_gr1.5740.0281.612
set_layout_graph0.2930.0360.330
summary_table0.0030.0000.004
time_output0.0010.0000.001
tstr000