| 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).
| Hostname | OS | Arch (*) | R version | Installed pkgs | 
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 | 
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 | 
| lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (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 | ||||
| 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. | 
| Package 696/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| flowGraph 1.6.0  (landing page) Alice Yue 
 | nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK |  | ||||||||
| lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK |  | ||||||||
| 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 | 
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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
###
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* 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.
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)
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 
flowGraph.Rcheck/flowGraph-Ex.timings
| name | user | system | elapsed | |
| cell_type_layers | 0.003 | 0.001 | 0.004 | |
| fg_add_feature | 0.360 | 0.016 | 0.385 | |
| fg_add_summary | 0.787 | 0.009 | 0.796 | |
| fg_clean_phen | 0.001 | 0.000 | 0.000 | |
| fg_clear_features | 0.677 | 0.005 | 0.682 | |
| fg_clear_summary | 0.267 | 0.002 | 0.269 | |
| fg_extract_phenotypes | 0.210 | 0.003 | 0.213 | |
| fg_extract_raw | 0.744 | 0.008 | 0.753 | |
| fg_extract_samples | 0.247 | 0.003 | 0.251 | |
| fg_feat_cumsum | 0.219 | 0.003 | 0.222 | |
| fg_feat_edge_specenr | 0.330 | 0.003 | 0.333 | |
| fg_feat_mean_class | 0.231 | 0.004 | 0.235 | |
| fg_feat_node_prop | 0.257 | 0.003 | 0.261 | |
| fg_feat_node_specenr | 0.408 | 0.005 | 0.414 | |
| fg_feat_prop_edge | 0.212 | 0.005 | 0.217 | |
| fg_get_feature | 0.213 | 0.001 | 0.215 | |
| fg_get_feature_desc | 0.630 | 0.003 | 0.633 | |
| fg_get_feature_means | 0.924 | 0.005 | 0.929 | |
| fg_get_graph | 0.220 | 0.003 | 0.224 | |
| fg_get_markers | 0.205 | 0.002 | 0.208 | |
| fg_get_meta | 0.217 | 0.002 | 0.219 | |
| fg_get_summary | 1.424 | 0.008 | 1.433 | |
| fg_get_summary_desc | 0.790 | 0.006 | 0.798 | |
| fg_get_summary_index | 1.777 | 0.012 | 1.791 | |
| fg_get_summary_tables | 1.152 | 0.008 | 1.162 | |
| fg_gsub_ids | 0.216 | 0.003 | 0.220 | |
| fg_gsub_markers | 0.322 | 0.004 | 0.326 | |
| fg_load | 34.670 | 0.326 | 35.068 | |
| fg_merge | 0.251 | 0.003 | 0.256 | |
| fg_merge_samples | 0.248 | 0.003 | 0.251 | |
| fg_plot | 0.315 | 0.003 | 0.318 | |
| fg_plot_box | 0.572 | 0.005 | 0.577 | |
| fg_plot_pVSdiff | 0.312 | 0.003 | 0.316 | |
| fg_plot_qq | 1.256 | 0.261 | 1.669 | |
| fg_replace_meta | 0.273 | 0.005 | 0.280 | |
| fg_rm_feature | 0.697 | 0.007 | 0.705 | |
| fg_rm_summary | 0.357 | 0.005 | 0.364 | |
| fg_save | 35.515 | 0.214 | 35.817 | |
| fg_save_plots | 34.557 | 0.242 | 34.892 | |
| fg_set_layout | 0.264 | 0.005 | 0.268 | |
| fg_summary | 0.364 | 0.003 | 0.369 | |
| flowGraph-class | 0.001 | 0.001 | 0.002 | |
| flowGraph | 1.238 | 0.010 | 1.256 | |
| flowGraphSubset | 0 | 0 | 0 | |
| flowGraphSubset_summary_adjust | 0.001 | 0.001 | 0.000 | |
| flowGraphSubset_summary_pars | 0.000 | 0.000 | 0.001 | |
| get_phen_list | 0.013 | 0.000 | 0.014 | |
| get_phen_meta | 0.002 | 0.001 | 0.003 | |
| ggdf | 0.252 | 0.005 | 0.259 | |
| loop_ind_f | 0.000 | 0.001 | 0.001 | |
| meandiff | 0.001 | 0.000 | 0.001 | |
| plot_gr | 1.200 | 0.023 | 1.237 | |
| set_layout_graph | 0.276 | 0.043 | 0.320 | |
| summary_table | 0.004 | 0.001 | 0.004 | |
| time_output | 0.001 | 0.001 | 0.000 | |
| tstr | 0.001 | 0.000 | 0.000 | |