Back to Multiple platform build/check report for BioC 3.22:   simplified   long
ABCDE[F]GHIJKLMNOPQRSTUVWXYZ

This page was generated on 2025-08-01 12:08 -0400 (Fri, 01 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4796
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4534
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4578
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4519
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4517
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 742/2313HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowGraph 1.17.0  (landing page)
Alice Yue
Snapshot Date: 2025-07-31 13:25 -0400 (Thu, 31 Jul 2025)
git_url: https://git.bioconductor.org/packages/flowGraph
git_branch: devel
git_last_commit: 16b2487
git_last_commit_date: 2025-04-15 12:15:54 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for flowGraph on lconway

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: 1.17.0
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_1.17.0.tar.gz
StartedAt: 2025-07-31 21:06:00 -0400 (Thu, 31 Jul 2025)
EndedAt: 2025-07-31 21:10:28 -0400 (Thu, 31 Jul 2025)
EllapsedTime: 267.4 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_1.17.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/flowGraph.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flowGraph/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowGraph’ version ‘1.17.0’
* 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       45.782  0.383  46.499
fg_load       45.463  0.512  46.332
fg_save_plots 44.410  0.375  45.034
* 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-3.22-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-x86_64/Resources/library’
* installing *source* package ‘flowGraph’ ...
** this is package ‘flowGraph’ version ‘1.17.0’
** 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 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 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 1 | SKIP 0 | PASS 34 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 34 ]
> 
> proc.time()
   user  system elapsed 
  5.968   0.312   6.326 

Example timings

flowGraph.Rcheck/flowGraph-Ex.timings

nameusersystemelapsed
cell_type_layers0.0030.0010.004
fg_add_feature0.4230.0110.435
fg_add_summary1.0590.0161.083
fg_clean_phen000
fg_clear_features1.0130.0101.029
fg_clear_summary0.3940.0060.401
fg_extract_phenotypes0.3180.0050.324
fg_extract_raw1.0000.0101.015
fg_extract_samples0.3280.0050.335
fg_feat_cumsum0.3430.0060.350
fg_feat_edge_specenr0.5300.0070.541
fg_feat_mean_class0.3200.0060.328
fg_feat_node_prop0.3320.0050.341
fg_feat_node_specenr0.5090.0070.519
fg_feat_prop_edge0.3340.0050.341
fg_get_feature0.3310.0040.337
fg_get_feature_desc1.0320.0121.052
fg_get_feature_means1.5470.0141.573
fg_get_graph0.3290.0050.336
fg_get_markers0.3570.0060.367
fg_get_meta0.3300.0050.336
fg_get_summary2.1030.0162.131
fg_get_summary_desc1.0410.0091.055
fg_get_summary_index2.1690.0182.198
fg_get_summary_tables1.3770.0121.395
fg_gsub_ids0.3150.0050.323
fg_gsub_markers0.3620.0040.368
fg_load45.463 0.51246.332
fg_merge0.2970.0060.307
fg_merge_samples0.3270.0060.336
fg_plot0.4250.0070.440
fg_plot_box0.6770.0080.691
fg_plot_pVSdiff0.4400.0050.447
fg_plot_qq1.0460.0851.157
fg_replace_meta0.2640.0040.269
fg_rm_feature0.8840.0090.900
fg_rm_summary0.3700.0040.377
fg_save45.782 0.38346.499
fg_save_plots44.410 0.37545.034
fg_set_layout0.3480.0050.356
fg_summary0.4190.0050.426
flowGraph-class0.0010.0010.002
flowGraph1.4220.0121.439
flowGraphSubset0.0000.0010.000
flowGraphSubset_summary_adjust0.0000.0000.001
flowGraphSubset_summary_pars000
get_phen_list0.0160.0000.016
get_phen_meta0.0020.0000.002
ggdf0.3160.0060.324
loop_ind_f0.0010.0000.000
meandiff0.0010.0000.001
plot_gr1.4670.0311.511
set_layout_graph0.3380.0350.374
summary_table0.0030.0000.003
time_output0.0010.0010.001
tstr000