| Back to Build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-06-06 11:00:31 -0000 (Tue, 06 Jun 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.0 (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 | ||||
|
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. |
| Package 710/2199 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| flowGraph 1.9.0 (landing page) Alice Yue
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | |||||||||
| 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 |
##############################################################################
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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
###
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##############################################################################
* 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.
flowGraph.Rcheck/00install.out
############################################################################## ############################################################################## ### ### 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)
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
flowGraph.Rcheck/flowGraph-Ex.timings
| name | user | system | elapsed | |
| cell_type_layers | 0.004 | 0.000 | 0.004 | |
| fg_add_feature | 0.535 | 0.004 | 0.676 | |
| fg_add_summary | 1.305 | 0.028 | 1.339 | |
| fg_clean_phen | 0 | 0 | 0 | |
| fg_clear_features | 1.250 | 0.020 | 1.274 | |
| fg_clear_summary | 0.507 | 0.004 | 0.512 | |
| fg_extract_phenotypes | 0.390 | 0.000 | 0.391 | |
| fg_extract_raw | 1.213 | 0.000 | 1.218 | |
| fg_extract_samples | 0.423 | 0.000 | 0.722 | |
| fg_feat_cumsum | 0.429 | 0.000 | 0.542 | |
| fg_feat_edge_specenr | 0.574 | 0.032 | 0.671 | |
| fg_feat_mean_class | 0.422 | 0.000 | 0.844 | |
| fg_feat_node_prop | 0.431 | 0.004 | 0.519 | |
| fg_feat_node_specenr | 0.586 | 0.000 | 0.587 | |
| fg_feat_prop_edge | 0.430 | 0.000 | 0.713 | |
| fg_get_feature | 0.425 | 0.004 | 0.461 | |
| fg_get_feature_desc | 1.261 | 0.000 | 1.587 | |
| fg_get_feature_means | 1.867 | 0.004 | 1.877 | |
| fg_get_graph | 0.418 | 0.036 | 0.455 | |
| fg_get_markers | 0.405 | 0.000 | 0.407 | |
| fg_get_meta | 0.408 | 0.000 | 0.409 | |
| fg_get_summary | 2.614 | 0.004 | 2.623 | |
| fg_get_summary_desc | 1.177 | 0.000 | 1.180 | |
| fg_get_summary_index | 2.668 | 0.068 | 2.742 | |
| fg_get_summary_tables | 1.765 | 0.008 | 1.776 | |
| fg_gsub_ids | 0.364 | 0.004 | 0.370 | |
| fg_gsub_markers | 0.452 | 0.004 | 0.458 | |
| fg_load | 52.431 | 0.359 | 52.867 | |
| fg_merge | 0.442 | 0.004 | 0.447 | |
| fg_merge_samples | 0.455 | 0.000 | 0.456 | |
| fg_plot | 0.608 | 0.004 | 0.614 | |
| fg_plot_box | 0.951 | 0.000 | 0.953 | |
| fg_plot_pVSdiff | 0.614 | 0.000 | 0.615 | |
| fg_plot_qq | 1.748 | 0.000 | 1.751 | |
| fg_replace_meta | 0.431 | 0.004 | 0.436 | |
| fg_rm_feature | 1.284 | 0.024 | 1.310 | |
| fg_rm_summary | 0.557 | 0.000 | 0.559 | |
| fg_save | 53.252 | 0.379 | 53.736 | |
| fg_save_plots | 53.481 | 0.304 | 53.894 | |
| fg_set_layout | 0.401 | 0.000 | 0.402 | |
| fg_summary | 0.547 | 0.000 | 0.549 | |
| flowGraph-class | 0.001 | 0.000 | 0.001 | |
| flowGraph | 1.755 | 0.004 | 1.762 | |
| flowGraphSubset | 0 | 0 | 0 | |
| flowGraphSubset_summary_adjust | 0 | 0 | 0 | |
| flowGraphSubset_summary_pars | 0 | 0 | 0 | |
| get_phen_list | 0.02 | 0.00 | 0.02 | |
| get_phen_meta | 0.002 | 0.000 | 0.002 | |
| ggdf | 0.411 | 0.000 | 0.413 | |
| loop_ind_f | 0.000 | 0.000 | 0.001 | |
| meandiff | 0.000 | 0.000 | 0.001 | |
| plot_gr | 2.029 | 0.008 | 2.040 | |
| set_layout_graph | 0.420 | 0.012 | 0.433 | |
| summary_table | 0.004 | 0.000 | 0.005 | |
| time_output | 0.000 | 0.000 | 0.001 | |
| tstr | 0.000 | 0.000 | 0.001 | |