Back to Multiple platform build/check report for BioC 3.22:   simplified   long
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This page was generated on 2025-07-18 12:05 -0400 (Fri, 18 Jul 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4787
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4525
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4568
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4509
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4510
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 741/2311HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowGraph 1.17.0  (landing page)
Alice Yue
Snapshot Date: 2025-07-17 13:25 -0400 (Thu, 17 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 nebbiolo2

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: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:flowGraph.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings flowGraph_1.17.0.tar.gz
StartedAt: 2025-07-17 22:23:36 -0400 (Thu, 17 Jul 2025)
EndedAt: 2025-07-17 22:27:32 -0400 (Thu, 17 Jul 2025)
EllapsedTime: 235.4 seconds
RetCode: 0
Status:   OK  
CheckDir: flowGraph.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:flowGraph.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings flowGraph_1.17.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/flowGraph.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* 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 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       39.007  0.853  39.863
fg_load       38.995  0.850  39.807
fg_save_plots 39.000  0.788  39.791
* 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-3.22-bioc/meat/flowGraph.Rcheck/00check.log’
for details.


Installation output

flowGraph.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL flowGraph
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-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-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 1 | SKIP 0 | PASS 34 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 34 ]
> 
> proc.time()
   user  system elapsed 
   4.76    0.19    4.94 

Example timings

flowGraph.Rcheck/flowGraph-Ex.timings

nameusersystemelapsed
cell_type_layers0.0020.0010.003
fg_add_feature0.3310.0100.341
fg_add_summary0.7780.0020.780
fg_clean_phen0.0010.0000.000
fg_clear_features0.7950.0040.799
fg_clear_summary0.3410.0000.340
fg_extract_phenotypes0.2560.0010.257
fg_extract_raw0.7300.0030.733
fg_extract_samples0.2540.0000.255
fg_feat_cumsum0.2670.0240.291
fg_feat_edge_specenr0.4050.0190.423
fg_feat_mean_class0.2760.0040.280
fg_feat_node_prop0.2560.0000.256
fg_feat_node_specenr0.3790.0020.383
fg_feat_prop_edge0.2560.0020.259
fg_get_feature0.2490.0020.251
fg_get_feature_desc0.7670.0300.797
fg_get_feature_means1.1220.0021.123
fg_get_graph0.2570.0010.259
fg_get_markers0.2510.0010.252
fg_get_meta0.2580.0040.262
fg_get_summary1.5740.0301.603
fg_get_summary_desc0.7640.0000.763
fg_get_summary_index1.7030.0521.756
fg_get_summary_tables1.0610.0051.066
fg_gsub_ids0.2430.0000.243
fg_gsub_markers0.2910.0010.292
fg_load38.995 0.85039.807
fg_merge0.2490.0020.250
fg_merge_samples0.2610.0010.262
fg_plot0.3470.0030.350
fg_plot_box0.5420.0010.543
fg_plot_pVSdiff0.3670.0010.368
fg_plot_qq0.8730.0040.878
fg_replace_meta0.2510.0010.252
fg_rm_feature0.7340.0000.734
fg_rm_summary0.3290.0010.331
fg_save39.007 0.85339.863
fg_save_plots39.000 0.78839.791
fg_set_layout0.2650.0080.273
fg_summary0.3380.0090.347
flowGraph-class0.0010.0000.001
flowGraph1.1000.0051.105
flowGraphSubset000
flowGraphSubset_summary_adjust000
flowGraphSubset_summary_pars000
get_phen_list0.0120.0000.013
get_phen_meta0.0020.0000.002
ggdf0.2610.0010.262
loop_ind_f000
meandiff0.0000.0010.001
plot_gr1.3350.0081.347
set_layout_graph0.2680.0050.274
summary_table0.0030.0000.003
time_output0.0000.0000.001
tstr0.0010.0000.000