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CHECK report for CoRegFlux on tokay2

This page was generated on 2020-10-17 11:56:22 -0400 (Sat, 17 Oct 2020).

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 374/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CoRegFlux 1.4.0
Pauline Trébulle and Mohamed Elati
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/CoRegFlux
Branch: RELEASE_3_11
Last Commit: 1ce49af
Last Changed Date: 2020-04-27 15:24:11 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: CoRegFlux
Version: 1.4.0
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CoRegFlux.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings CoRegFlux_1.4.0.tar.gz
StartedAt: 2020-10-17 02:57:00 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 03:03:46 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 405.3 seconds
RetCode: 0
Status:  OK  
CheckDir: CoRegFlux.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CoRegFlux.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings CoRegFlux_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/CoRegFlux.Rcheck'
* using R version 4.0.3 (2020-10-10)
* 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 '1.4.0'
* 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      33.09   0.41   33.50
ODCurveToFluxCurves                 21.37   0.22   21.91
ODCurveToMetabolicGeneCurves        11.52   0.22   11.76
Simulation                           8.11   0.36    8.47
get_fva_intervals_from_observations  5.45   0.08    5.53
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                user system elapsed
predict_linear_model_influence 21.42   0.27   21.69
ODCurveToFluxCurves            18.28   0.13   23.25
ODCurveToMetabolicGeneCurves    7.67   0.22   25.43
Simulation                      5.78   0.25    6.03
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'Test.R'
 OK
** running tests for arch 'x64' ...
  Running 'Test.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: OK


Installation output

CoRegFlux.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/CoRegFlux_1.4.0.tar.gz && rm -rf CoRegFlux.buildbin-libdir && mkdir CoRegFlux.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CoRegFlux.buildbin-libdir CoRegFlux_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL CoRegFlux_1.4.0.zip && rm CoRegFlux_1.4.0.tar.gz CoRegFlux_1.4.0.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 4573k  100 4573k    0     0  17.5M      0 --:--:-- --:--:-- --:--:-- 18.0M

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_1.4.0.zip
* DONE (CoRegFlux)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'CoRegFlux' successfully unpacked and MD5 sums checked

Tests output

CoRegFlux.Rcheck/tests_i386/Test.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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       | CoregfluxAndFVAFonctions
- |   1       | CoregfluxAndFVAFonctions
| |   3       | CoregfluxAndFVAFonctions
v |   6       | CoregfluxAndFVAFonctions [48.1 s]

/ |   0       | DFBAsimulationFunctions
- |   1       | DFBAsimulationFunctions
/ |   5 3     | DFBAsimulationFunctions
x |  17 3     | DFBAsimulationFunctions [3.1 s]
--------------------------------------------------------------------------------
test_DFBAsimulationFunctions.R:41: error: uptake fluxes diminish metabolite concentrations
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))

test_DFBAsimulationFunctions.R:49: error: positive fluxes increase metabolite concentrations
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))

test_DFBAsimulationFunctions.R:59: error: update_uptake_fluxes_constraints_metabolites check that
 bounds are changed
could not find function "update_uptake_fluxes_constraints_metabolites"
--------------------------------------------------------------------------------

/ |   0       | MetabolicModelFunctions
- |   0 1     | MetabolicModelFunctions
x |   6 1     | MetabolicModelFunctions [0.1 s]
--------------------------------------------------------------------------------
test_MetabolicModelFunctions.R:13: error: Metabolites names to model names works and return a
                     data.frame
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: 51.6 s

OK:       29
Failed:   4
Warnings: 0
Skipped:  0
> 
> proc.time()
   user  system elapsed 
  53.85    0.89   54.75 

CoRegFlux.Rcheck/tests_x64/Test.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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       | CoregfluxAndFVAFonctions
- |   1       | CoregfluxAndFVAFonctions
| |   3       | CoregfluxAndFVAFonctions
v |   6       | CoregfluxAndFVAFonctions [52.6 s]

/ |   0       | DFBAsimulationFunctions
- |   1       | DFBAsimulationFunctions
/ |   5 3     | DFBAsimulationFunctions
x |  17 3     | DFBAsimulationFunctions [2.6 s]
--------------------------------------------------------------------------------
test_DFBAsimulationFunctions.R:41: error: uptake fluxes diminish metabolite concentrations
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))

test_DFBAsimulationFunctions.R:49: error: positive fluxes increase metabolite concentrations
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))

test_DFBAsimulationFunctions.R:59: error: update_uptake_fluxes_constraints_metabolites check that
 bounds are changed
could not find function "update_uptake_fluxes_constraints_metabolites"
--------------------------------------------------------------------------------

/ |   0       | MetabolicModelFunctions
- |   0 1     | MetabolicModelFunctions
x |   6 1     | MetabolicModelFunctions [0.2 s]
--------------------------------------------------------------------------------
test_MetabolicModelFunctions.R:13: error: Metabolites names to model names works and return a
                     data.frame
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: 55.5 s

OK:       29
Failed:   4
Warnings: 0
Skipped:  0
> 
> proc.time()
   user  system elapsed 
  58.45    0.64   59.07 

Example timings

CoRegFlux.Rcheck/examples_i386/CoRegFlux-Ex.timings

nameusersystemelapsed
ODCurveToFluxCurves21.37 0.2221.91
ODCurveToMetabolicGeneCurves11.52 0.2211.76
Simulation8.110.368.47
adjust_constraints_to_observed_rates0.110.060.17
build_exchange_met0.130.050.17
coregflux_static1.690.342.03
get_biomass_flux_position0.110.050.16
get_fba_fluxes_from_observations0.450.030.48
get_fva_intervals_from_observations5.450.085.53
get_metabolites_exchange_fluxes0.140.040.19
predict_linear_model_influence33.09 0.4133.50
update_fluxes_constraints_geneKOOV0.110.080.18
update_fluxes_constraints_influence0.520.280.80
visFluxCurves0.310.030.34
visMetabolicGeneCurves0.280.090.38

CoRegFlux.Rcheck/examples_x64/CoRegFlux-Ex.timings

nameusersystemelapsed
ODCurveToFluxCurves18.28 0.1323.25
ODCurveToMetabolicGeneCurves 7.67 0.2225.43
Simulation5.780.256.03
adjust_constraints_to_observed_rates0.080.030.11
build_exchange_met0.050.050.09
coregflux_static1.010.251.27
get_biomass_flux_position0.080.010.10
get_fba_fluxes_from_observations0.310.030.34
get_fva_intervals_from_observations4.260.004.27
get_metabolites_exchange_fluxes0.100.030.12
predict_linear_model_influence21.42 0.2721.69
update_fluxes_constraints_geneKOOV0.110.020.12
update_fluxes_constraints_influence0.360.200.57
visFluxCurves0.250.010.26
visMetabolicGeneCurves0.190.050.24