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CHECK report for CoRegFlux on tokay1

This page was generated on 2021-05-06 12:30:29 -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: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CoRegFlux.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings CoRegFlux_1.6.0.tar.gz
StartedAt: 2021-05-06 01:46:51 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 01:52:19 -0400 (Thu, 06 May 2021)
EllapsedTime: 328.1 seconds
RetCode: 1
Status:   ERROR   
CheckDir: CoRegFlux.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CoRegFlux.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings CoRegFlux_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/CoRegFlux.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                     user system elapsed
predict_linear_model_influence      27.55   0.37   27.92
get_fva_intervals_from_observations  6.49   0.08    6.56
Simulation                           5.77   0.45    6.39
ODCurveToFluxCurves                  4.31   0.29    5.22
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                user system elapsed
predict_linear_model_influence 23.88   0.22   24.09
Simulation                      5.32   0.19    6.44
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  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: 54.3 s
  
  [ FAIL 4 | WARN 0 | SKIP 0 | PASS 29 ]
  Error: Test failures
  Execution halted
** running tests for arch 'x64' ...
  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: 61.1 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: 2 ERRORs
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/CoRegFlux.Rcheck/00check.log'
for details.

Installation output

CoRegFlux.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/CoRegFlux_1.6.0.tar.gz && rm -rf CoRegFlux.buildbin-libdir && mkdir CoRegFlux.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CoRegFlux.buildbin-libdir CoRegFlux_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL CoRegFlux_1.6.0.zip && rm CoRegFlux_1.6.0.tar.gz CoRegFlux_1.6.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 4574k  100 4574k    0     0  39.6M      0 --:--:-- --:--:-- --:--:-- 40.2M

install for i386

* installing *source* package 'CoRegFlux' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'CoRegFlux'
    finding HTML links ... done
    FBA_step                                html  
    ODCurveToFluxCurves                     html  
    ODCurveToMetabolicGeneCurves            html  
    ODToFluxBounds                          html  
    ODcurveToMetCurve                       html  
    ODtoflux                                html  
    PredictedGeneState                      html  
    SC_EXP_DATA                             html  
    SC_GRN_1                                html  
    SC_Test_data                            html  
    SC_experiment_influence                 html  
    Simulation                              html  
    Simulation_Step                         html  
    adjust_constraints_to_observed_rates    html  
    aliases_SC                              html  
    build_exchange_met                      html  
    continuous_gpr                          html  
    convert_metabolites_to_model_names      html  
    coregflux_static                        html  
    euler_step_biomass                      html  
    euler_step_metabolites                  html  
    get_biomass_flux_position               html  
    get_fba_fluxes_from_observations        html  
    get_fva_intervals_from_observations     html  
    get_linear_model                        html  
    get_metabolites_exchange_fluxes         html  
    gpr_expression                          html  
    iMM904                                  html  
    perturbation_function                   html  
    predict_linear_model_influence          html  
    train_continuous_model                  html  
    update_fluxes_constraints_GRegulation   html  
    update_fluxes_constraints_geneKOOV      html  
    update_fluxes_constraints_influence     html  
    update_fluxes_state                     html  
    update_system_state                     html  
    update_uptake_fluxes_constraints_metabolites
                                            html  
    visFluxCurves                           html  
    visMetabolicGeneCurves                  html  
** 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

install for x64

* installing *source* package 'CoRegFlux' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CoRegFlux' as CoRegFlux_1.6.0.zip
* DONE (CoRegFlux)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'CoRegFlux' successfully unpacked and MD5 sums checked

Tests output

CoRegFlux.Rcheck/tests_i386/Test.Rout.fail


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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/")
v |  OK F W S | Context

/ |   0       | CoregfluxAndFVAFunctions                                        
/ |   0       | CoregfluxAndFVAFonctions                                        
- |   1       | CoregfluxAndFVAFonctions                                        
| |   3       | CoregfluxAndFVAFonctions                                        
v |   6       | CoregfluxAndFVAFonctions [50.8 s]

/ |   0       | DFBAsimulationFunctions                                         
/ |   0       | DFBAsimulationFunctions                                         
- |   1       | DFBAsimulationFunctions                                         
/ |   5 3     | DFBAsimulationFunctions                                         
\ |   7 3     | DFBAsimulationFunctions                                         
x |  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                                         
x |   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: 54.3 s

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

CoRegFlux.Rcheck/tests_x64/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-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(CoRegFlux)
> library(testthat)
> 
> testthat::test_dir("testthat/")
v |  OK F W S | Context

/ |   0       | CoregfluxAndFVAFunctions                                        
/ |   0       | CoregfluxAndFVAFonctions                                        
- |   1       | CoregfluxAndFVAFonctions                                        
| |   3       | CoregfluxAndFVAFonctions                                        
v |   6       | CoregfluxAndFVAFonctions [58.4 s]

/ |   0       | DFBAsimulationFunctions                                         
/ |   0       | DFBAsimulationFunctions                                         
- |   1       | DFBAsimulationFunctions                                         
/ |   5 3     | DFBAsimulationFunctions                                         
x |  17 3     | DFBAsimulationFunctions [2.5 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                                         
x |   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: 61.1 s

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

Example timings

CoRegFlux.Rcheck/examples_i386/CoRegFlux-Ex.timings

nameusersystemelapsed
ODCurveToFluxCurves4.310.295.22
ODCurveToMetabolicGeneCurves1.170.111.46
Simulation5.770.456.39
adjust_constraints_to_observed_rates0.100.000.11
build_exchange_met0.100.040.13
coregflux_static1.080.231.31
get_biomass_flux_position0.120.050.17
get_fba_fluxes_from_observations0.450.010.47
get_fva_intervals_from_observations6.490.086.56
get_metabolites_exchange_fluxes0.140.050.19
predict_linear_model_influence27.55 0.3727.92
update_fluxes_constraints_geneKOOV0.150.020.17
update_fluxes_constraints_influence0.580.200.79
visFluxCurves0.310.030.34
visMetabolicGeneCurves0.330.030.36

CoRegFlux.Rcheck/examples_x64/CoRegFlux-Ex.timings

nameusersystemelapsed
ODCurveToFluxCurves4.690.164.84
ODCurveToMetabolicGeneCurves1.000.041.05
Simulation5.320.196.44
adjust_constraints_to_observed_rates0.090.020.11
build_exchange_met0.090.010.11
coregflux_static1.410.191.59
get_biomass_flux_position0.080.020.10
get_fba_fluxes_from_observations0.260.030.29
get_fva_intervals_from_observations4.240.014.25
get_metabolites_exchange_fluxes0.090.030.13
predict_linear_model_influence23.88 0.2224.09
update_fluxes_constraints_geneKOOV0.150.020.17
update_fluxes_constraints_influence0.490.230.72
visFluxCurves0.360.030.39
visMetabolicGeneCurves0.320.070.39