Back to Multiple platform build/check report for BioC 3.15
ABCDE[F]GHIJKLMNOPQRSTUVWXYZ

This page was generated on 2022-10-19 13:20:16 -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 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? 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: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:flowGraph.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings flowGraph_1.4.0.tar.gz
StartedAt: 2022-10-18 19:46:38 -0400 (Tue, 18 Oct 2022)
EndedAt: 2022-10-18 19:50:09 -0400 (Tue, 18 Oct 2022)
EllapsedTime: 211.6 seconds
RetCode: 0
Status:   OK  
CheckDir: flowGraph.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:flowGraph.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings flowGraph_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/flowGraph.Rcheck’
* using R version 4.2.1 (2022-06-23)
* 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 ‘1.4.0’
* 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_plots 37.890  0.592  38.482
fg_save       36.733  0.624  37.357
fg_load       35.360  0.664  36.025
* 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-3.15-bioc/meat/flowGraph.Rcheck/00check.log’
for details.



Installation output

flowGraph.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL flowGraph
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-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 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 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 
  4.771   0.206   4.961 

Example timings

flowGraph.Rcheck/flowGraph-Ex.timings

nameusersystemelapsed
cell_type_layers0.0030.0000.003
fg_add_feature0.3200.0040.323
fg_add_summary0.7680.0000.767
fg_clean_phen0.0000.0010.000
fg_clear_features0.7330.0190.752
fg_clear_summary0.2870.0000.287
fg_extract_phenotypes0.2160.0000.216
fg_extract_raw0.6820.0120.694
fg_extract_samples0.2160.0000.216
fg_feat_cumsum0.2220.0040.225
fg_feat_edge_specenr0.3280.0040.332
fg_feat_mean_class0.2180.0000.219
fg_feat_node_prop0.2110.0040.215
fg_feat_node_specenr0.3440.0320.375
fg_feat_prop_edge0.2790.0080.287
fg_get_feature0.2280.0000.228
fg_get_feature_desc0.6860.0080.694
fg_get_feature_means1.1090.0041.112
fg_get_graph0.2300.0000.231
fg_get_markers0.2270.0000.227
fg_get_meta0.2280.0040.233
fg_get_summary1.5470.0001.547
fg_get_summary_desc0.7290.0000.730
fg_get_summary_index1.7180.0801.799
fg_get_summary_tables0.9730.0080.980
fg_gsub_ids0.1980.0010.201
fg_gsub_markers0.2310.0060.237
fg_load35.360 0.66436.025
fg_merge0.2330.0040.237
fg_merge_samples0.3380.0040.342
fg_plot0.3610.0000.360
fg_plot_box0.6300.0000.631
fg_plot_pVSdiff0.3880.0000.388
fg_plot_qq1.1930.0121.204
fg_replace_meta0.2430.0030.247
fg_rm_feature0.7730.0030.777
fg_rm_summary0.3290.0000.328
fg_save36.733 0.62437.357
fg_save_plots37.890 0.59238.482
fg_set_layout0.2240.0000.223
fg_summary0.3190.0000.319
flowGraph-class0.0000.0020.002
flowGraph1.0640.0101.075
flowGraphSubset0.0000.0010.001
flowGraphSubset_summary_adjust0.0000.0010.001
flowGraphSubset_summary_pars000
get_phen_list0.0100.0000.011
get_phen_meta0.0020.0000.002
ggdf0.2250.0000.225
loop_ind_f0.0010.0000.001
meandiff0.0000.0000.001
plot_gr1.3440.0041.348
set_layout_graph0.2620.0320.294
summary_table0.0040.0000.003
time_output0.0010.0000.001
tstr000