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This page was generated on 2021-10-15 15:05:38 -0400 (Fri, 15 Oct 2021).

CHECK results for CoRegFlux on nebbiolo1

To the developers/maintainers of the CoRegFlux package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CoRegFlux.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
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raw results

Package 391/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CoRegFlux 1.8.0  (landing page)
Pauline Trébulle and Mohamed Elati
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/CoRegFlux
git_branch: RELEASE_3_13
git_last_commit: 8f1dfd8
git_last_commit_date: 2021-05-19 12:41:32 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    ERROR  
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    ERROR    OK  
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    ERROR    OK  

Summary

Package: CoRegFlux
Version: 1.8.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:CoRegFlux.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings CoRegFlux_1.8.0.tar.gz
StartedAt: 2021-10-14 09:23:37 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 09:26:02 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 145.3 seconds
RetCode: 1
Status:   ERROR  
CheckDir: CoRegFlux.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:CoRegFlux.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings CoRegFlux_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/CoRegFlux.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.8.0’
* 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 ... WARNING
Found the following significant warnings:
  Warning: Package 'CoRegFlux' is deprecated and will be removed from Bioconductor
See ‘/home/biocbuild/bbs-3.13-bioc/meat/CoRegFlux.Rcheck/00install.out’ for details.
* 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 19.503  0.788  14.772
ODCurveToFluxCurves            15.396  0.163  15.565
ODCurveToMetabolicGeneCurves    7.152  0.160   7.312
* 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 in `convert_metabolites_to_model_names(metabolites = metabolites, 
      model = iMM904)`: 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: 32.3 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, 1 WARNING
See
  ‘/home/biocbuild/bbs-3.13-bioc/meat/CoRegFlux.Rcheck/00check.log’
for details.


Installation output

CoRegFlux.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL CoRegFlux
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-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
Warning: Package 'CoRegFlux' is deprecated and will be removed from Bioconductor
  version 3.14
** testing if installed package can be loaded from final location
Warning: Package 'CoRegFlux' is deprecated and will be removed from Bioconductor
  version 3.14
** testing if installed package keeps a record of temporary installation path
* DONE (CoRegFlux)

Tests output

CoRegFlux.Rcheck/tests/Test.Rout.fail


R version 4.1.1 (2021-08-10) -- "Kick Things"
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)
Warning message:
Package 'CoRegFlux' is deprecated and will be removed from Bioconductor
  version 3.14 
> library(testthat)
> 
> testthat::test_dir("testthat/")
✔ | F W S  OK | Context

⠏ |         0 | CoregfluxAndFVAFunctions                                        
⠏ |         0 | CoregfluxAndFVAFonctions                                        
⠋ |         1 | CoregfluxAndFVAFonctions                                        
⠹ |         3 | CoregfluxAndFVAFonctions                                        
✔ |         6 | CoregfluxAndFVAFonctions [30.1s]

⠏ |         0 | DFBAsimulationFunctions                                         
⠏ |         0 | DFBAsimulationFunctions                                         
⠋ |         1 | DFBAsimulationFunctions                                         
⠧ | 3       5 | DFBAsimulationFunctions                                         
✖ | 3      17 | DFBAsimulationFunctions [2.0s]
────────────────────────────────────────────────────────────────────────────────
Error (test_DFBAsimulationFunctions.R:41:6): uptake fluxes diminish metabolite concentrations
Error in `euler_step_metabolites(met_concentrations_t0 = 10, fluxes = -1, 
    rate = 0.1, time_step = 0.1, biomass_t0 = 0.3)`: 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 in `euler_step_metabolites(met_concentrations_t0 = 10, fluxes = 1, 
    rate = 0.1, time_step = 0.1, biomass_t0 = 0.3)`: 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 in `update_uptake_fluxes_constraints_metabolites(model = iMM904, 
    met_fluxes_indexes = 550, biomass_t0 = 0.3, met_concentrations_t0 = 1e-06, 
    time_step = 1)`: could not find function "update_uptake_fluxes_constraints_metabolites"
────────────────────────────────────────────────────────────────────────────────

⠏ |         0 | MetabolicModelFunctions                                         
⠏ |         0 | MetabolicModelFunctions                                         
⠼ | 1       4 | MetabolicModelFunctions                                         
✖ | 1       6 | MetabolicModelFunctions [0.1s]
────────────────────────────────────────────────────────────────────────────────
Error (test_MetabolicModelFunctions.R:13:6): Metabolites names to model names works and return a
                     data.frame
Error in `convert_metabolites_to_model_names(metabolites = metabolites, 
    model = iMM904)`: 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: 32.3 s

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

Example timings

CoRegFlux.Rcheck/CoRegFlux-Ex.timings

nameusersystemelapsed
ODCurveToFluxCurves15.396 0.16315.565
ODCurveToMetabolicGeneCurves7.1520.1607.312
Simulation4.8160.0674.883
adjust_constraints_to_observed_rates0.0750.0020.078
build_exchange_met0.0690.0040.073
coregflux_static0.8760.0250.901
get_biomass_flux_position0.0590.0080.067
get_fba_fluxes_from_observations0.3210.0000.324
get_fva_intervals_from_observations3.3890.3433.733
get_metabolites_exchange_fluxes0.0810.0120.093
predict_linear_model_influence19.503 0.78814.772
update_fluxes_constraints_geneKOOV0.0830.0000.084
update_fluxes_constraints_influence0.2520.0040.256
visFluxCurves0.1840.0240.209
visMetabolicGeneCurves0.2090.0000.210