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CHECK report for CoRegFlux on malbec1

This page was generated on 2021-05-06 12:27:15 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the CoRegFlux package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 377/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CoRegFlux 1.6.0  (landing page)
Pauline Trébulle and Mohamed Elati
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/CoRegFlux
Branch: RELEASE_3_12
Last Commit: 6e77093
Last Changed Date: 2020-10-27 11:43:27 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    ERROR  
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    ERROR    OK  
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    ERROR    OK  

Summary

Package: CoRegFlux
Version: 1.6.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:CoRegFlux.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings CoRegFlux_1.6.0.tar.gz
StartedAt: 2021-05-06 00:27:42 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 00:31:17 -0400 (Thu, 06 May 2021)
EllapsedTime: 215.5 seconds
RetCode: 1
Status:   ERROR  
CheckDir: CoRegFlux.Rcheck
Warnings: NA

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:CoRegFlux.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings CoRegFlux_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/CoRegFlux.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CoRegFlux/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CoRegFlux’ version ‘1.6.0’
* package encoding: UTF-8
* 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 ‘CoRegFlux’ 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 ... OK
* 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
predict_linear_model_influence      32.208  0.584  23.754
ODCurveToFluxCurves                 24.880  0.168  25.240
ODCurveToMetabolicGeneCurves         8.588  0.112   8.709
Simulation                           6.972  0.136   7.125
get_fva_intervals_from_observations  5.100  0.016   5.120
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘Test.R’
 ERROR
Running the tests in ‘tests/Test.R’ failed.
Last 13 lines of output:
  ────────────────────────────────────────────────────────────────────────────────
  Error (test_MetabolicModelFunctions.R:13:6): Metabolites names to model names works and return a
                       data.frame
  Error: could not find function "convert_metabolites_to_model_names"
  Backtrace:
   1. testthat::expect_true(...) test_MetabolicModelFunctions.R:13:5
   4. base::is.data.frame(...)
  ────────────────────────────────────────────────────────────────────────────────
  
  ══ Results ═════════════════════════════════════════════════════════════════════
  Duration: 54.4 s
  
  [ FAIL 4 | WARN 0 | SKIP 0 | PASS 29 ]
  Error: Test failures
  Execution halted
* 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 ERROR
See
  ‘/home/biocbuild/bbs-3.12-bioc/meat/CoRegFlux.Rcheck/00check.log’
for details.

Installation output

CoRegFlux.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL CoRegFlux
###
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘CoRegFlux’ ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** 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 (CoRegFlux)

Tests output

CoRegFlux.Rcheck/tests/Test.Rout.fail


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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(CoRegFlux)
> library(testthat)
> 
> testthat::test_dir("testthat/")
✔ |  OK F W S | Context

⠏ |   0       | CoregfluxAndFVAFunctions                                        
⠏ |   0       | CoregfluxAndFVAFonctions                                        
⠋ |   1       | CoregfluxAndFVAFonctions                                        
⠹ |   3       | CoregfluxAndFVAFonctions                                        
✔ |   6       | CoregfluxAndFVAFonctions [50.9 s]

⠏ |   0       | DFBAsimulationFunctions                                         
⠏ |   0       | DFBAsimulationFunctions                                         
⠋ |   1       | DFBAsimulationFunctions                                         
⠧ |   5 3     | DFBAsimulationFunctions                                         
⠹ |  10 3     | DFBAsimulationFunctions                                         
✖ |  17 3     | DFBAsimulationFunctions [3.2 s]
────────────────────────────────────────────────────────────────────────────────
Error (test_DFBAsimulationFunctions.R:41:6): uptake fluxes diminish metabolite concentrations
Error: could not find function "euler_step_metabolites"
Backtrace:
 1. testthat::expect_lt(...) test_DFBAsimulationFunctions.R:41:5
 2. testthat::quasi_label(enquo(object), label, arg = "object")
 3. rlang::eval_bare(expr, quo_get_env(quo))

Error (test_DFBAsimulationFunctions.R:49:6): positive fluxes increase metabolite concentrations
Error: could not find function "euler_step_metabolites"
Backtrace:
 1. testthat::expect_gt(...) test_DFBAsimulationFunctions.R:49:5
 2. testthat::quasi_label(enquo(object), label, arg = "object")
 3. rlang::eval_bare(expr, quo_get_env(quo))

Error (test_DFBAsimulationFunctions.R:59:16): update_uptake_fluxes_constraints_metabolites check that
 bounds are changed
Error: could not find function "update_uptake_fluxes_constraints_metabolites"
────────────────────────────────────────────────────────────────────────────────

⠏ |   0       | MetabolicModelFunctions                                         
⠏ |   0       | MetabolicModelFunctions                                         
⠋ |   0 1     | MetabolicModelFunctions                                         
✖ |   6 1     | MetabolicModelFunctions [0.2 s]
────────────────────────────────────────────────────────────────────────────────
Error (test_MetabolicModelFunctions.R:13:6): Metabolites names to model names works and return a
                     data.frame
Error: could not find function "convert_metabolites_to_model_names"
Backtrace:
 1. testthat::expect_true(...) test_MetabolicModelFunctions.R:13:5
 4. base::is.data.frame(...)
────────────────────────────────────────────────────────────────────────────────

══ Results ═════════════════════════════════════════════════════════════════════
Duration: 54.4 s

[ FAIL 4 | WARN 0 | SKIP 0 | PASS 29 ]
Error: Test failures
Execution halted

Example timings

CoRegFlux.Rcheck/CoRegFlux-Ex.timings

nameusersystemelapsed
ODCurveToFluxCurves24.880 0.16825.240
ODCurveToMetabolicGeneCurves8.5880.1128.709
Simulation6.9720.1367.125
adjust_constraints_to_observed_rates0.1200.0120.130
build_exchange_met0.1120.0080.120
coregflux_static1.3840.0841.468
get_biomass_flux_position0.0960.0080.104
get_fba_fluxes_from_observations0.4000.0200.419
get_fva_intervals_from_observations5.1000.0165.120
get_metabolites_exchange_fluxes0.0840.0120.096
predict_linear_model_influence32.208 0.58423.754
update_fluxes_constraints_geneKOOV0.0880.0120.098
update_fluxes_constraints_influence0.4040.1280.538
visFluxCurves0.2480.0200.271
visMetabolicGeneCurves0.3720.0120.388