Back to Multiple platform build/check report for BioC 3.19:   simplified   long
ABCDE[F]GHIJKLMNOPQRSTUVWXYZ

This page was generated on 2024-05-04 11:36:34 -0400 (Sat, 04 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4753
palomino3Windows Server 2022 Datacenterx644.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" 4486
lconwaymacOS 12.7.1 Montereyx86_644.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" 4519
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4479
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 742/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowGraph 1.12.0  (landing page)
Alice Yue
Snapshot Date: 2024-05-03 14:00:19 -0400 (Fri, 03 May 2024)
git_url: https://git.bioconductor.org/packages/flowGraph
git_branch: RELEASE_3_19
git_last_commit: 60893ac
git_last_commit_date: 2024-04-30 11:29:54 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 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
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for flowGraph on nebbiolo1


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.
- 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: 1.12.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:flowGraph.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings flowGraph_1.12.0.tar.gz
StartedAt: 2024-05-03 23:20:52 -0400 (Fri, 03 May 2024)
EndedAt: 2024-05-03 23:24:51 -0400 (Fri, 03 May 2024)
EllapsedTime: 239.0 seconds
RetCode: 0
Status:   OK  
CheckDir: flowGraph.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:flowGraph.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings flowGraph_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/flowGraph.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘flowGraph/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowGraph’ version ‘1.12.0’
* 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 code 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 ... NOTE
checkRd: (-1) fg_get_graph.Rd:13: Lost braces
    13 | A list containing two data frames (\code{v} and ]code{e})
       |                                                      ^
checkRd: (-1) ggdf.Rd:22: Lost braces
    22 | code{ggdf} adds to the data frames \code{v} and \code{e} in slot
       |     ^
* 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 40.211  0.812  41.024
fg_load       39.429  0.924  40.260
fg_save       39.262  0.764  40.026
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/flowGraph.Rcheck/00check.log’
for details.


Installation output

flowGraph.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL flowGraph
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/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 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 
  4.859   0.245   5.091 

Example timings

flowGraph.Rcheck/flowGraph-Ex.timings

nameusersystemelapsed
cell_type_layers0.0040.0000.004
fg_add_feature0.3020.0090.312
fg_add_summary0.7800.0050.784
fg_clean_phen000
fg_clear_features0.8050.0080.812
fg_clear_summary0.30.00.3
fg_extract_phenotypes0.2350.0000.236
fg_extract_raw0.6940.0040.698
fg_extract_samples0.2450.0080.253
fg_feat_cumsum0.2280.0280.255
fg_feat_edge_specenr0.3550.0000.355
fg_feat_mean_class0.2270.0040.231
fg_feat_node_prop0.2340.0000.233
fg_feat_node_specenr0.3500.0000.349
fg_feat_prop_edge0.2590.0000.259
fg_get_feature0.2240.0040.228
fg_get_feature_desc0.7370.0030.741
fg_get_feature_means1.1310.0201.151
fg_get_graph0.2450.0000.245
fg_get_markers0.2360.0000.236
fg_get_meta0.2190.0040.223
fg_get_summary1.5340.0281.562
fg_get_summary_desc0.7230.0040.727
fg_get_summary_index1.7930.0401.833
fg_get_summary_tables0.9850.0080.992
fg_gsub_ids0.2180.0000.218
fg_gsub_markers0.260.000.26
fg_load39.429 0.92440.260
fg_merge0.2510.0040.255
fg_merge_samples0.2850.0000.285
fg_plot0.3770.0000.378
fg_plot_box0.6310.0000.631
fg_plot_pVSdiff0.3670.0080.376
fg_plot_qq1.0680.0161.085
fg_replace_meta0.2920.0000.292
fg_rm_feature0.8690.0040.874
fg_rm_summary0.4170.0000.417
fg_save39.262 0.76440.026
fg_save_plots40.211 0.81241.024
fg_set_layout0.2490.0040.253
fg_summary0.3220.0080.329
flowGraph-class0.0010.0000.001
flowGraph1.1500.0081.158
flowGraphSubset000
flowGraphSubset_summary_adjust000
flowGraphSubset_summary_pars000
get_phen_list0.0130.0010.014
get_phen_meta0.0020.0010.002
ggdf0.2660.0040.270
loop_ind_f0.0010.0000.000
meandiff000
plot_gr1.4370.0031.447
set_layout_graph0.2770.0230.301
summary_table0.0000.0030.003
time_output0.0010.0000.001
tstr000