Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-10-15 15:06:35 -0400 (Fri, 15 Oct 2021).

CHECK results for flowGraph on machv2

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? here 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 652/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowGraph 1.0.0  (landing page)
Alice Yue
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/flowGraph
git_branch: RELEASE_3_13
git_last_commit: 00d2dcb
git_last_commit_date: 2021-05-19 12:58:24 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: flowGraph
Version: 1.0.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:flowGraph.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings flowGraph_1.0.0.tar.gz
StartedAt: 2021-10-14 19:07:09 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 19:12:26 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 316.6 seconds
RetCode: 0
Status:   OK  
CheckDir: flowGraph.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:flowGraph.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings flowGraph_1.0.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/flowGraph.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.0.0’
* 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 54.270  0.240  54.696
fg_load       53.092  0.304  53.442
fg_save       51.010  0.198  51.310
* 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-3.13-bioc/meat/flowGraph.Rcheck/00check.log’
for details.



Installation output

flowGraph.Rcheck/00install.out

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##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL flowGraph
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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 
  7.240   0.281   7.503 

Example timings

flowGraph.Rcheck/flowGraph-Ex.timings

nameusersystemelapsed
cell_type_layers0.0030.0000.003
fg_add_feature0.4450.0090.456
fg_add_summary0.9580.0070.965
fg_clean_phen000
fg_clear_features1.1310.0051.136
fg_clear_summary0.4530.0030.457
fg_extract_phenotypes0.3480.0050.352
fg_extract_raw1.2540.0071.262
fg_extract_samples0.3820.0050.387
fg_feat_cumsum0.3320.0050.337
fg_feat_edge_specenr0.3870.0050.393
fg_feat_mean_class0.3940.0050.398
fg_feat_node_prop0.3730.0040.376
fg_feat_node_specenr0.4490.0050.454
fg_feat_prop_edge0.3350.0020.338
fg_get_feature0.3820.0030.384
fg_get_feature_desc1.1970.0051.202
fg_get_feature_means1.9570.0071.965
fg_get_graph0.3980.0030.402
fg_get_markers0.3540.0020.356
fg_get_meta0.4370.0030.441
fg_get_summary2.6110.0072.618
fg_get_summary_desc1.2350.0321.268
fg_get_summary_index2.6320.0082.680
fg_get_summary_tables1.7810.0071.791
fg_gsub_ids0.4280.0040.431
fg_gsub_markers0.4660.0040.470
fg_load53.092 0.30453.442
fg_merge0.3220.0040.326
fg_merge_samples0.4280.0060.435
fg_plot0.6070.0050.612
fg_plot_box1.0040.0061.010
fg_plot_pVSdiff0.5480.0040.552
fg_plot_qq2.3330.1462.753
fg_replace_meta0.4470.0040.452
fg_rm_feature1.3710.0071.378
fg_rm_summary0.5950.0050.600
fg_save51.010 0.19851.310
fg_save_plots54.270 0.24054.696
fg_set_layout0.3400.0040.344
fg_summary0.5520.0040.556
flowGraph-class0.0010.0010.001
flowGraph1.5280.0081.537
flowGraphSubset0.0000.0010.000
flowGraphSubset_summary_adjust0.0010.0010.001
flowGraphSubset_summary_pars0.0010.0000.001
get_phen_list0.0160.0010.017
get_phen_meta0.0030.0010.003
ggdf0.4020.0050.406
loop_ind_f0.0010.0010.001
meandiff0.0010.0010.001
plot_gr1.5030.0261.532
set_layout_graph0.4900.0730.563
summary_table0.0060.0010.008
time_output0.0010.0000.001
tstr0.0010.0000.000