Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-10-19 13:22:57 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
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 merida1


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 683/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowGraph 1.4.0  (landing page)
Alice Yue
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/flowGraph
git_branch: RELEASE_3_15
git_last_commit: fadfcc1
git_last_commit_date: 2022-04-26 12:11:24 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: flowGraph
Version: 1.4.0
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_1.4.0.tar.gz
StartedAt: 2022-10-19 02:31:29 -0400 (Wed, 19 Oct 2022)
EndedAt: 2022-10-19 02:38:45 -0400 (Wed, 19 Oct 2022)
EllapsedTime: 436.0 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_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/flowGraph.Rcheck’
* using R version 4.2.1 (2022-06-23)
* 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 ‘1.4.0’
* 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       75.970  0.307  77.232
fg_load       74.412  0.451  75.587
fg_save_plots 73.888  0.288  74.383
* 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-3.15-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 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 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 
 10.788   0.355  11.138 

Example timings

flowGraph.Rcheck/flowGraph-Ex.timings

nameusersystemelapsed
cell_type_layers0.0040.0010.005
fg_add_feature0.6670.0100.677
fg_add_summary1.9520.0141.971
fg_clean_phen000
fg_clear_features1.8460.0091.857
fg_clear_summary0.7260.0050.733
fg_extract_phenotypes0.5200.0050.525
fg_extract_raw1.7110.0081.720
fg_extract_samples0.5190.0030.523
fg_feat_cumsum0.5090.0040.515
fg_feat_edge_specenr0.8530.0050.860
fg_feat_mean_class0.5190.0060.526
fg_feat_node_prop0.5420.0030.547
fg_feat_node_specenr0.8920.0090.906
fg_feat_prop_edge0.5260.0030.530
fg_get_feature0.4950.0050.499
fg_get_feature_desc1.8440.0121.866
fg_get_feature_means2.8750.0132.965
fg_get_graph0.5500.0050.565
fg_get_markers0.5360.0040.544
fg_get_meta0.5500.0040.563
fg_get_summary4.0170.0144.059
fg_get_summary_desc1.8450.0081.858
fg_get_summary_index4.2170.0154.243
fg_get_summary_tables2.7190.0132.745
fg_gsub_ids0.5250.0040.530
fg_gsub_markers0.6370.0040.642
fg_load74.412 0.45175.587
fg_merge0.5320.0050.539
fg_merge_samples0.5700.0070.580
fg_plot0.8040.0050.813
fg_plot_box1.2910.0071.302
fg_plot_pVSdiff0.7750.0040.781
fg_plot_qq3.2410.3043.942
fg_replace_meta0.5220.0060.530
fg_rm_feature1.8670.0081.880
fg_rm_summary0.7070.0040.712
fg_save75.970 0.30777.232
fg_save_plots73.888 0.28874.383
fg_set_layout0.5810.0040.586
fg_summary0.7520.0050.759
flowGraph-class0.0010.0000.002
flowGraph2.7440.0112.775
flowGraphSubset0.0000.0000.001
flowGraphSubset_summary_adjust000
flowGraphSubset_summary_pars0.0000.0000.001
get_phen_list0.0220.0010.022
get_phen_meta0.0030.0000.003
ggdf0.5600.0030.565
loop_ind_f0.0010.0000.000
meandiff000
plot_gr2.6720.0242.712
set_layout_graph0.5830.0250.611
summary_table0.0080.0000.008
time_output0.0010.0000.002
tstr0.0000.0000.001