Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2024-07-16 11:40 -0400 (Tue, 16 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4677
palomino6Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4416
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4444
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4393
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4373
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 720/2243HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowGraph 1.13.0  (landing page)
Alice Yue
Snapshot Date: 2024-07-15 14:00 -0400 (Mon, 15 Jul 2024)
git_url: https://git.bioconductor.org/packages/flowGraph
git_branch: devel
git_last_commit: 4f830fb
git_last_commit_date: 2024-04-30 11:29:54 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino6Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  


CHECK results for flowGraph on palomino6

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: 1.13.0
Command: C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:flowGraph.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings flowGraph_1.13.0.tar.gz
StartedAt: 2024-07-16 00:06:44 -0400 (Tue, 16 Jul 2024)
EndedAt: 2024-07-16 00:10:13 -0400 (Tue, 16 Jul 2024)
EllapsedTime: 209.1 seconds
RetCode: 0
Status:   OK  
CheckDir: flowGraph.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:flowGraph.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings flowGraph_1.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.20-bioc/meat/flowGraph.Rcheck'
* using R version 4.4.1 (2024-06-14 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       33.59   1.39   35.31
fg_save_plots 33.19   1.29   34.52
fg_load       32.95   1.50   34.55
* 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
  'C:/Users/biocbuild/bbs-3.20-bioc/meat/flowGraph.Rcheck/00check.log'
for details.


Installation output

flowGraph.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL flowGraph
###
##############################################################################
##############################################################################


* installing to library 'C:/Users/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)

Tests output

flowGraph.Rcheck/tests/testthat.Rout


R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
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 
   4.17    0.35    4.51 

Example timings

flowGraph.Rcheck/flowGraph-Ex.timings

nameusersystemelapsed
cell_type_layers000
fg_add_feature0.220.040.27
fg_add_summary0.700.050.75
fg_clean_phen000
fg_clear_features0.640.060.70
fg_clear_summary0.270.030.30
fg_extract_phenotypes0.170.050.25
fg_extract_raw0.670.000.67
fg_extract_samples0.190.030.22
fg_feat_cumsum0.220.000.22
fg_feat_edge_specenr0.310.010.35
fg_feat_mean_class0.210.000.22
fg_feat_node_prop0.210.020.22
fg_feat_node_specenr0.330.000.33
fg_feat_prop_edge0.230.000.23
fg_get_feature0.200.010.22
fg_get_feature_desc0.690.020.70
fg_get_feature_means1.030.021.05
fg_get_graph0.220.010.24
fg_get_markers0.230.000.23
fg_get_meta0.220.000.22
fg_get_summary1.460.061.53
fg_get_summary_desc0.680.000.72
fg_get_summary_index1.680.021.69
fg_get_summary_tables0.930.010.95
fg_gsub_ids0.210.000.20
fg_gsub_markers0.250.000.25
fg_load32.95 1.5034.55
fg_merge0.230.000.23
fg_merge_samples0.220.020.24
fg_plot0.380.050.42
fg_plot_box0.510.030.55
fg_plot_pVSdiff0.360.000.36
fg_plot_qq0.800.010.82
fg_replace_meta0.230.000.24
fg_rm_feature0.740.000.73
fg_rm_summary0.30.00.3
fg_save33.59 1.3935.31
fg_save_plots33.19 1.2934.52
fg_set_layout0.220.010.23
fg_summary0.320.020.35
flowGraph-class0.020.000.01
flowGraph0.950.041.00
flowGraphSubset000
flowGraphSubset_summary_adjust000
flowGraphSubset_summary_pars000
get_phen_list0.020.000.01
get_phen_meta000
ggdf0.220.020.24
loop_ind_f000
meandiff000
plot_gr1.060.071.14
set_layout_graph0.250.030.28
summary_table000
time_output000
tstr000