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This page was generated on 2024-04-18 11:32:10 -0400 (Thu, 18 Apr 2024).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson1macOS 13.6.1 Venturaarm644.3.3 (2024-02-29) -- "Angel Food Cake" 4388
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 730/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowGraph 1.10.0  (landing page)
Alice Yue
Snapshot Date: 2024-04-16 09:00:03 -0400 (Tue, 16 Apr 2024)
git_url: https://git.bioconductor.org/packages/flowGraph
git_branch: RELEASE_3_18
git_last_commit: 9b8a39e
git_last_commit_date: 2023-10-24 11:28:28 -0400 (Tue, 24 Oct 2023)
kjohnson1macOS 13.6.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for flowGraph on kjohnson1


To the developers/maintainers of the flowGraph package:
- 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: 1.10.0
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_1.10.0.tar.gz
StartedAt: 2024-04-17 13:55:42 -0400 (Wed, 17 Apr 2024)
EndedAt: 2024-04-17 14:00:10 -0400 (Wed, 17 Apr 2024)
EllapsedTime: 267.9 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_1.10.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/flowGraph.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flowGraph/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowGraph’ version ‘1.10.0’
* 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_plots 49.689  0.374  52.885
fg_save       48.116  0.313  49.029
fg_load       46.711  0.382  47.468
* 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-3.18-bioc-mac-arm64/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/4.3-arm64/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 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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 
   5.42    0.29    5.79 

Example timings

flowGraph.Rcheck/flowGraph-Ex.timings

nameusersystemelapsed
cell_type_layers0.0050.0010.009
fg_add_feature0.3140.0090.331
fg_add_summary0.7890.0100.800
fg_clean_phen0.0010.0010.000
fg_clear_features0.7590.0080.767
fg_clear_summary0.2800.0040.284
fg_extract_phenotypes0.2380.0050.245
fg_extract_raw0.7520.0060.763
fg_extract_samples0.2280.0040.234
fg_feat_cumsum0.2250.0030.228
fg_feat_edge_specenr0.3980.0060.411
fg_feat_mean_class0.2390.0050.252
fg_feat_node_prop0.2220.0040.227
fg_feat_node_specenr0.3970.0070.406
fg_feat_prop_edge0.2200.0050.230
fg_get_feature0.2220.0040.227
fg_get_feature_desc0.7800.0070.790
fg_get_feature_means1.1440.0081.161
fg_get_graph0.2200.0030.223
fg_get_markers0.2100.0040.215
fg_get_meta0.2230.0030.226
fg_get_summary1.5550.0101.569
fg_get_summary_desc0.7590.0060.766
fg_get_summary_index1.7590.0211.780
fg_get_summary_tables0.9990.0091.008
fg_gsub_ids0.2020.0050.206
fg_gsub_markers0.2550.0050.260
fg_load46.711 0.38247.468
fg_merge0.2670.0050.275
fg_merge_samples0.2940.0040.300
fg_plot0.3940.0050.402
fg_plot_box0.5780.0070.589
fg_plot_pVSdiff0.3360.0040.340
fg_plot_qq1.1070.0571.186
fg_replace_meta0.2420.0040.245
fg_rm_feature0.9980.0091.018
fg_rm_summary0.3650.0040.371
fg_save48.116 0.31349.029
fg_save_plots49.689 0.37452.885
fg_set_layout0.2770.0050.282
fg_summary0.3210.0050.349
flowGraph-class0.0010.0010.001
flowGraph1.2560.0131.498
flowGraphSubset0.0000.0000.001
flowGraphSubset_summary_adjust0.0000.0010.001
flowGraphSubset_summary_pars0.0000.0010.001
get_phen_list0.0130.0010.014
get_phen_meta0.0020.0000.001
ggdf0.2750.0070.355
loop_ind_f0.0010.0000.001
meandiff0.0010.0000.001
plot_gr1.4820.0291.894
set_layout_graph0.2950.0400.410
summary_table0.0040.0000.005
time_output0.0010.0010.000
tstr000