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This page was generated on 2023-06-06 11:00:31 -0000 (Tue, 06 Jun 2023).

HostnameOSArch (*)R versionInstalled pkgs
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.3.0 (2023-04-21) -- "Already Tomorrow" 4366
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 kunpeng2


To the developers/maintainers of the flowGraph package:
- 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 Troubleshooting Build Report for more information.

- Use the following Renviron settings to reproduce errors and warnings.

Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details.

raw results

Package 710/2199HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowGraph 1.9.0  (landing page)
Alice Yue
Snapshot Date: 2023-06-05 06:35:06 -0000 (Mon, 05 Jun 2023)
git_url: https://git.bioconductor.org/packages/flowGraph
git_branch: devel
git_last_commit: 16aaa2b
git_last_commit_date: 2023-04-25 15:25:24 -0000 (Tue, 25 Apr 2023)
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

Summary

Package: flowGraph
Version: 1.9.0
Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:flowGraph.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings flowGraph_1.9.0.tar.gz
StartedAt: 2023-06-05 22:31:54 -0000 (Mon, 05 Jun 2023)
EndedAt: 2023-06-05 22:37:19 -0000 (Mon, 05 Jun 2023)
EllapsedTime: 324.6 seconds
RetCode: 0
Status:   OK  
CheckDir: flowGraph.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:flowGraph.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings flowGraph_1.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/flowGraph.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘flowGraph/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowGraph’ version ‘1.9.0’
* 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 loading without being on the library search path ... 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 53.481  0.304  53.894
fg_save       53.252  0.379  53.736
fg_load       52.431  0.359  52.867
* 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 ...
  ‘flowGraph.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/flowGraph.Rcheck/00check.log’
for details.



Installation output

flowGraph.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL flowGraph
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.3.0/site-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 4.3.0 (2023-04-21) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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 
  6.885   0.200   7.086 

Example timings

flowGraph.Rcheck/flowGraph-Ex.timings

nameusersystemelapsed
cell_type_layers0.0040.0000.004
fg_add_feature0.5350.0040.676
fg_add_summary1.3050.0281.339
fg_clean_phen000
fg_clear_features1.2500.0201.274
fg_clear_summary0.5070.0040.512
fg_extract_phenotypes0.3900.0000.391
fg_extract_raw1.2130.0001.218
fg_extract_samples0.4230.0000.722
fg_feat_cumsum0.4290.0000.542
fg_feat_edge_specenr0.5740.0320.671
fg_feat_mean_class0.4220.0000.844
fg_feat_node_prop0.4310.0040.519
fg_feat_node_specenr0.5860.0000.587
fg_feat_prop_edge0.4300.0000.713
fg_get_feature0.4250.0040.461
fg_get_feature_desc1.2610.0001.587
fg_get_feature_means1.8670.0041.877
fg_get_graph0.4180.0360.455
fg_get_markers0.4050.0000.407
fg_get_meta0.4080.0000.409
fg_get_summary2.6140.0042.623
fg_get_summary_desc1.1770.0001.180
fg_get_summary_index2.6680.0682.742
fg_get_summary_tables1.7650.0081.776
fg_gsub_ids0.3640.0040.370
fg_gsub_markers0.4520.0040.458
fg_load52.431 0.35952.867
fg_merge0.4420.0040.447
fg_merge_samples0.4550.0000.456
fg_plot0.6080.0040.614
fg_plot_box0.9510.0000.953
fg_plot_pVSdiff0.6140.0000.615
fg_plot_qq1.7480.0001.751
fg_replace_meta0.4310.0040.436
fg_rm_feature1.2840.0241.310
fg_rm_summary0.5570.0000.559
fg_save53.252 0.37953.736
fg_save_plots53.481 0.30453.894
fg_set_layout0.4010.0000.402
fg_summary0.5470.0000.549
flowGraph-class0.0010.0000.001
flowGraph1.7550.0041.762
flowGraphSubset000
flowGraphSubset_summary_adjust000
flowGraphSubset_summary_pars000
get_phen_list0.020.000.02
get_phen_meta0.0020.0000.002
ggdf0.4110.0000.413
loop_ind_f0.0000.0000.001
meandiff0.0000.0000.001
plot_gr2.0290.0082.040
set_layout_graph0.4200.0120.433
summary_table0.0040.0000.005
time_output0.0000.0000.001
tstr0.0000.0000.001