Back to Build/check report for BioC 3.17
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This page was generated on 2023-01-02 09:00:29 -0500 (Mon, 02 Jan 2023).

HostnameOSArch (*)R versionInstalled pkgs
palomino5Windows Server 2022 Datacenterx64R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" 4165
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 palomino5


To the developers/maintainers of the flowGraph package:
Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 685/2158HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowGraph 1.7.0  (landing page)
Alice Yue
Snapshot Date: 2022-12-28 11:00:06 -0500 (Wed, 28 Dec 2022)
git_url: https://git.bioconductor.org/packages/flowGraph
git_branch: master
git_last_commit: 6701384
git_last_commit_date: 2022-11-01 11:23:33 -0500 (Tue, 01 Nov 2022)
palomino5Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  

Summary

Package: flowGraph
Version: 1.7.0
Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:flowGraph.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings flowGraph_1.7.0.tar.gz
StartedAt: 2022-12-28 23:51:13 -0500 (Wed, 28 Dec 2022)
EndedAt: 2022-12-28 23:54:52 -0500 (Wed, 28 Dec 2022)
EllapsedTime: 218.4 seconds
RetCode: 0
Status:   OK  
CheckDir: flowGraph.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:flowGraph.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings flowGraph_1.7.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/flowGraph.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 10.4.0
    GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'flowGraph/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'flowGraph' version '1.7.0'
* 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 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 39.72   0.75   40.49
fg_save       38.25   0.82   39.10
fg_load       35.83   0.92   36.77
* 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
  'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/flowGraph.Rcheck/00check.log'
for details.



Installation output

flowGraph.Rcheck/00install.out

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###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL flowGraph
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.17-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 Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 
   4.04    0.34    4.76 

Example timings

flowGraph.Rcheck/flowGraph-Ex.timings

nameusersystemelapsed
cell_type_layers0.010.000.01
fg_add_feature0.240.020.25
fg_add_summary0.670.010.69
fg_clean_phen000
fg_clear_features0.620.020.64
fg_clear_summary0.250.000.25
fg_extract_phenotypes0.210.000.20
fg_extract_raw0.610.030.65
fg_extract_samples0.180.010.20
fg_feat_cumsum0.210.000.20
fg_feat_edge_specenr0.360.000.36
fg_feat_mean_class0.290.040.33
fg_feat_node_prop0.160.030.19
fg_feat_node_specenr0.280.010.29
fg_feat_prop_edge0.30.00.3
fg_get_feature0.190.000.19
fg_get_feature_desc0.670.050.72
fg_get_feature_means0.900.050.95
fg_get_graph0.210.000.20
fg_get_markers0.200.000.21
fg_get_meta0.20.00.2
fg_get_summary1.800.031.83
fg_get_summary_desc0.590.010.61
fg_get_summary_index1.600.031.62
fg_get_summary_tables1.170.041.20
fg_gsub_ids0.190.000.19
fg_gsub_markers0.200.010.22
fg_load35.83 0.9236.77
fg_merge0.250.000.25
fg_merge_samples0.330.020.34
fg_plot0.360.030.39
fg_plot_box0.570.030.61
fg_plot_pVSdiff0.310.000.31
fg_plot_qq0.970.031.23
fg_replace_meta0.220.000.22
fg_rm_feature0.780.010.79
fg_rm_summary0.280.000.29
fg_save38.25 0.8239.10
fg_save_plots39.72 0.7540.49
fg_set_layout0.200.000.21
fg_summary0.370.000.37
flowGraph-class000
flowGraph101
flowGraphSubset000
flowGraphSubset_summary_adjust000
flowGraphSubset_summary_pars000
get_phen_list0.020.000.02
get_phen_meta000
ggdf0.220.010.23
loop_ind_f000
meandiff000
plot_gr1.080.051.47
set_layout_graph0.260.010.28
summary_table000
time_output000
tstr000