Package: CoRegFlux

Version: 1.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CoRegFlux.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CoRegFlux_1.2.0.tar.gz

StartedAt: 2020-04-15 01:27:30 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 01:31:06 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 215.5 seconds

RetCode: 0

Status:  OK

CheckDir: CoRegFlux.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CoRegFlux.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CoRegFlux_1.2.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/CoRegFlux.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.2.0’
* 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 or elapsed time > 5s
                                 user system elapsed
predict_linear_model_influence 29.255  1.753  22.234
ODCurveToFluxCurves            26.130  0.227  26.891
ODCurveToMetabolicGeneCurves   10.608  0.311  11.083
Simulation                      6.864  0.110   6.992
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL CoRegFlux
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/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)

R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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       | CoregfluxAndFVAFonctions
⠋ |   1       | CoregfluxAndFVAFonctions
⠹ |   3       | CoregfluxAndFVAFonctions
✔ |   6       | CoregfluxAndFVAFonctions [41.8 s]

⠏ |   0       | DFBAsimulationFunctions
⠋ |   1       | DFBAsimulationFunctions
⠦ |   4 3     | DFBAsimulationFunctions
⠧ |   5 3     | DFBAsimulationFunctions
⠸ |  11 3     | DFBAsimulationFunctions
✖ |  17 3     | DFBAsimulationFunctions [3.2 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
✖ |   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: 45.4 s

OK:       29
Failed:   4
Warnings: 0
Skipped:  0
> 
> proc.time()
   user  system elapsed 
 62.426   3.498  49.078 

name	user	system	elapsed
ODCurveToFluxCurves	26.130	0.227	26.891
ODCurveToMetabolicGeneCurves	10.608	0.311	11.083
Simulation	6.864	0.110	6.992
adjust_constraints_to_observed_rates	0.104	0.002	0.106
build_exchange_met	0.086	0.001	0.087
coregflux_static	1.276	0.022	1.299
get_biomass_flux_position	0.091	0.001	0.092
get_fba_fluxes_from_observations	0.313	0.002	0.315
get_fva_intervals_from_observations	4.686	0.014	4.711
get_metabolites_exchange_fluxes	0.105	0.002	0.106
predict_linear_model_influence	29.255	1.753	22.234
update_fluxes_constraints_geneKOOV	0.157	0.018	0.175
update_fluxes_constraints_influence	0.405	0.007	0.413
visFluxCurves	0.299	0.004	0.303
visMetabolicGeneCurves	0.333	0.015	0.348