Package: CoRegFlux

Version: 1.0.0

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_1.0.0.tar.gz

StartedAt: 2019-10-16 01:47:24 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 01:51:55 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 271.1 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_1.0.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/CoRegFlux.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.0.0’
* 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      35.313  3.451  26.585
ODCurveToFluxCurves                 26.882  0.366  27.513
ODCurveToMetabolicGeneCurves        13.430  0.593  14.460
Simulation                           8.287  0.216   8.558
get_fva_intervals_from_observations  6.149  0.022   6.172
* 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 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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 [53.5 s]

⠏ |   0       | DFBAsimulationFunctions
⠋ |   1       | 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"
1: expect_lt(euler_step_metabolites(met_concentrations_t0 = 10, fluxes = -1, rate = 0.1, 
       time_step = 0.1, biomass_t0 = 0.3), expected = 10) at testthat//test_DFBAsimulationFunctions.R:41
2: quasi_label(enquo(object), label, arg = "object")
3: eval_bare(get_expr(quo), get_env(quo))

test_DFBAsimulationFunctions.R:49: error: positive fluxes increase metabolite concentrations
could not find function "euler_step_metabolites"
1: expect_gt(euler_step_metabolites(met_concentrations_t0 = 10, fluxes = 1, rate = 0.1, 
       time_step = 0.1, biomass_t0 = 0.3), expected = 10) at testthat//test_DFBAsimulationFunctions.R:49
2: quasi_label(enquo(object), label, arg = "object")
3: eval_bare(get_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"
1: .handleSimpleError(function (e) 
   {
       handled <<- TRUE
       test_error <<- e
       options(expressions = expressions_opt_new)
       on.exit(options(expressions = expressions_opt), add = TRUE)
       e$expectation_calls <- frame_calls(11, 2)
       test_error <<- e
       register_expectation(e)
       e$handled <- TRUE
       test_error <<- e
   }, "could not find function \"update_uptake_fluxes_constraints_metabolites\"", base::quote(update_uptake_fluxes_constraints_metabolites(model = iMM904, 
       met_fluxes_indexes = 550, biomass_t0 = 0.3, met_concentrations_t0 = 1e-06, time_step = 1))) at testthat//test_DFBAsimulationFunctions.R:59
2: eval(code, test_env)
────────────────────────────────────────────────────────────────────────────────

⠏ |   0       | MetabolicModelFunctions
⠋ |   0 1     | MetabolicModelFunctions
✖ |   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"
1: expect_true(is.data.frame(convert_metabolites_to_model_names(metabolites = metabolites, 
       model = iMM904))) at testthat//test_MetabolicModelFunctions.R:13
2: quasi_label(enquo(object), label, arg = "object")
3: eval_bare(get_expr(quo), get_env(quo))
4: is.data.frame(convert_metabolites_to_model_names(metabolites = metabolites, model = iMM904))
────────────────────────────────────────────────────────────────────────────────

══ Results ═════════════════════════════════════════════════════════════════════
Duration: 57.0 s

OK:       29
Failed:   4
Warnings: 0
Skipped:  0
> 
> proc.time()
   user  system elapsed 
 77.123   8.020  61.080 

name	user	system	elapsed
ODCurveToFluxCurves	26.882	0.366	27.513
ODCurveToMetabolicGeneCurves	13.430	0.593	14.460
Simulation	8.287	0.216	8.558
adjust_constraints_to_observed_rates	0.141	0.004	0.145
build_exchange_met	0.143	0.003	0.145
coregflux_static	1.599	0.040	1.709
get_biomass_flux_position	0.128	0.002	0.131
get_fba_fluxes_from_observations	0.427	0.004	0.431
get_fva_intervals_from_observations	6.149	0.022	6.172
get_metabolites_exchange_fluxes	0.149	0.003	0.152
predict_linear_model_influence	35.313	3.451	26.585
update_fluxes_constraints_geneKOOV	0.156	0.012	0.168
update_fluxes_constraints_influence	0.465	0.012	0.477
visFluxCurves	0.443	0.009	0.451
visMetabolicGeneCurves	0.533	0.035	0.568