Package: CoRegFlux

Version: 1.3.0

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_1.3.0.tar.gz

StartedAt: 2020-01-16 03:15:33 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 03:20:43 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 310.2 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_1.3.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/CoRegFlux.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘1.3.0’
* 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 (user + system) or elapsed time > 5s
                                      user system elapsed
predict_linear_model_influence      38.667  3.675  29.419
ODCurveToFluxCurves                 29.777  0.418  30.576
ODCurveToMetabolicGeneCurves        15.054  0.576  16.143
Simulation                           8.730  0.260   9.112
get_fva_intervals_from_observations  7.162  0.050   7.391
* 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/4.0/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 Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
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
✔ |   6       | CoregfluxAndFVAFonctions [66.3 s]

⠏ |   0       | DFBAsimulationFunctions
⠋ |   1       | DFBAsimulationFunctions
⠼ |   4 1     | DFBAsimulationFunctions
⠧ |   5 3     | DFBAsimulationFunctions
⠏ |   7 3     | DFBAsimulationFunctions
✖ |  17 3     | DFBAsimulationFunctions [3.9 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: 70.7 s

OK:       29
Failed:   4
Warnings: 0
Skipped:  0
> 
> proc.time()
   user  system elapsed 
 89.673   7.352  76.055 

name	user	system	elapsed
ODCurveToFluxCurves	29.777	0.418	30.576
ODCurveToMetabolicGeneCurves	15.054	0.576	16.143
Simulation	8.730	0.260	9.112
adjust_constraints_to_observed_rates	0.158	0.005	0.162
build_exchange_met	0.141	0.003	0.143
coregflux_static	1.705	0.063	1.768
get_biomass_flux_position	0.117	0.003	0.121
get_fba_fluxes_from_observations	0.458	0.005	0.533
get_fva_intervals_from_observations	7.162	0.050	7.391
get_metabolites_exchange_fluxes	0.143	0.003	0.146
predict_linear_model_influence	38.667	3.675	29.419
update_fluxes_constraints_geneKOOV	0.158	0.013	0.171
update_fluxes_constraints_influence	0.427	0.013	0.440
visFluxCurves	0.566	0.068	0.635
visMetabolicGeneCurves	0.450	0.015	0.466