Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-10-15 15:05:40 -0400 (Fri, 15 Oct 2021).

CHECK results for flowGraph on nebbiolo1

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: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:flowGraph.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings flowGraph_1.0.0.tar.gz
StartedAt: 2021-10-14 09:52:33 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 09:55:43 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 190.6 seconds
RetCode: 0
Status:   OK  
CheckDir: flowGraph.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:flowGraph.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings flowGraph_1.0.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/flowGraph.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (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 35.851  0.588  36.442
fg_save       34.822  0.624  35.449
fg_load       32.972  0.812  33.792
* 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
  ‘/home/biocbuild/bbs-3.13-bioc/meat/flowGraph.Rcheck/00check.log’
for details.



Installation output

flowGraph.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL flowGraph
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/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-pc-linux-gnu (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 
  4.093   0.182   4.259 

Example timings

flowGraph.Rcheck/flowGraph-Ex.timings

nameusersystemelapsed
cell_type_layers0.0000.0030.003
fg_add_feature0.2450.0050.249
fg_add_summary0.6320.0040.635
fg_clean_phen000
fg_clear_features0.6710.0000.671
fg_clear_summary0.2600.0080.268
fg_extract_phenotypes0.2080.0000.209
fg_extract_raw0.6110.0000.611
fg_extract_samples0.2020.0000.203
fg_feat_cumsum0.2030.0030.206
fg_feat_edge_specenr0.2430.0040.246
fg_feat_mean_class0.2080.0000.208
fg_feat_node_prop0.1990.0000.200
fg_feat_node_specenr0.2410.0010.241
fg_feat_prop_edge0.2060.0030.210
fg_get_feature0.1980.0000.198
fg_get_feature_desc0.6010.0000.601
fg_get_feature_means0.980.000.98
fg_get_graph0.1910.0080.198
fg_get_markers0.210.000.21
fg_get_meta0.2130.0000.214
fg_get_summary1.4250.0071.432
fg_get_summary_desc0.7740.0240.798
fg_get_summary_index1.2530.0081.261
fg_get_summary_tables0.8740.0040.878
fg_gsub_ids0.1820.0000.181
fg_gsub_markers0.2150.0000.215
fg_load32.972 0.81233.792
fg_merge0.2150.0000.214
fg_merge_samples0.2280.0080.236
fg_plot0.3130.0000.314
fg_plot_box0.6660.0280.694
fg_plot_pVSdiff0.4440.0000.444
fg_plot_qq0.9960.0121.009
fg_replace_meta0.2410.0000.241
fg_rm_feature0.6950.0080.702
fg_rm_summary0.3120.0000.312
fg_save34.822 0.62435.449
fg_save_plots35.851 0.58836.442
fg_set_layout0.2020.0000.202
fg_summary0.270.000.27
flowGraph-class0.0000.0010.001
flowGraph0.8070.0060.813
flowGraphSubset0.0000.0010.000
flowGraphSubset_summary_adjust0.0000.0010.000
flowGraphSubset_summary_pars0.0000.0010.000
get_phen_list0.0100.0010.011
get_phen_meta0.0020.0000.002
ggdf0.1960.0040.201
loop_ind_f0.0000.0000.001
meandiff000
plot_gr1.0900.0041.094
set_layout_graph0.1950.0360.230
summary_table0.0020.0000.003
time_output0.0010.0000.001
tstr0.0000.0000.001