Back to Multiple platform build/check report for BioC 3.16:   simplified   long
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This page was generated on 2023-04-12 11:06:07 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
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

CHECK results for flowGraph on lconway


To the developers/maintainers of the flowGraph package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 696/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowGraph 1.6.0  (landing page)
Alice Yue
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/flowGraph
git_branch: RELEASE_3_16
git_last_commit: d0d96a7
git_last_commit_date: 2022-11-01 11:23:33 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: flowGraph
Version: 1.6.0
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_1.6.0.tar.gz
StartedAt: 2023-04-10 20:15:17 -0400 (Mon, 10 Apr 2023)
EndedAt: 2023-04-10 20:18:49 -0400 (Mon, 10 Apr 2023)
EllapsedTime: 212.3 seconds
RetCode: 0
Status:   OK  
CheckDir: flowGraph.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### 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_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/flowGraph.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flowGraph/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowGraph’ version ‘1.6.0’
* 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 R 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 ... OK
* 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       35.515  0.214  35.817
fg_load       34.670  0.326  35.068
fg_save_plots 34.557  0.242  34.892
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.16-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/4.2/Resources/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 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

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 
  5.102   0.281   5.401 

Example timings

flowGraph.Rcheck/flowGraph-Ex.timings

nameusersystemelapsed
cell_type_layers0.0030.0010.004
fg_add_feature0.3600.0160.385
fg_add_summary0.7870.0090.796
fg_clean_phen0.0010.0000.000
fg_clear_features0.6770.0050.682
fg_clear_summary0.2670.0020.269
fg_extract_phenotypes0.2100.0030.213
fg_extract_raw0.7440.0080.753
fg_extract_samples0.2470.0030.251
fg_feat_cumsum0.2190.0030.222
fg_feat_edge_specenr0.3300.0030.333
fg_feat_mean_class0.2310.0040.235
fg_feat_node_prop0.2570.0030.261
fg_feat_node_specenr0.4080.0050.414
fg_feat_prop_edge0.2120.0050.217
fg_get_feature0.2130.0010.215
fg_get_feature_desc0.6300.0030.633
fg_get_feature_means0.9240.0050.929
fg_get_graph0.2200.0030.224
fg_get_markers0.2050.0020.208
fg_get_meta0.2170.0020.219
fg_get_summary1.4240.0081.433
fg_get_summary_desc0.7900.0060.798
fg_get_summary_index1.7770.0121.791
fg_get_summary_tables1.1520.0081.162
fg_gsub_ids0.2160.0030.220
fg_gsub_markers0.3220.0040.326
fg_load34.670 0.32635.068
fg_merge0.2510.0030.256
fg_merge_samples0.2480.0030.251
fg_plot0.3150.0030.318
fg_plot_box0.5720.0050.577
fg_plot_pVSdiff0.3120.0030.316
fg_plot_qq1.2560.2611.669
fg_replace_meta0.2730.0050.280
fg_rm_feature0.6970.0070.705
fg_rm_summary0.3570.0050.364
fg_save35.515 0.21435.817
fg_save_plots34.557 0.24234.892
fg_set_layout0.2640.0050.268
fg_summary0.3640.0030.369
flowGraph-class0.0010.0010.002
flowGraph1.2380.0101.256
flowGraphSubset000
flowGraphSubset_summary_adjust0.0010.0010.000
flowGraphSubset_summary_pars0.0000.0000.001
get_phen_list0.0130.0000.014
get_phen_meta0.0020.0010.003
ggdf0.2520.0050.259
loop_ind_f0.0000.0010.001
meandiff0.0010.0000.001
plot_gr1.2000.0231.237
set_layout_graph0.2760.0430.320
summary_table0.0040.0010.004
time_output0.0010.0010.000
tstr0.0010.0000.000