Pauline Trébulle and Mohamed Elati
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/CoRegFlux |
| Branch: master |
| Last Commit: 0dd0327 |
| Last Changed Date: 2019-03-14 04:53:37 -0400 (Thu, 14 Mar 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 11:52:48 -0400 (Tue, 09 Apr 2019).
| Package 341/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| CoRegFlux 0.99.22 Pauline Trébulle and Mohamed Elati
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
| Package: CoRegFlux |
| Version: 0.99.22 |
| Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:CoRegFlux.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings CoRegFlux_0.99.22.tar.gz |
| StartedAt: 2019-04-08 23:44:28 -0400 (Mon, 08 Apr 2019) |
| EndedAt: 2019-04-08 23:47:48 -0400 (Mon, 08 Apr 2019) |
| EllapsedTime: 200.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CoRegFlux.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:CoRegFlux.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings CoRegFlux_0.99.22.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/CoRegFlux.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-pc-linux-gnu (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 ‘0.99.22’
* 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 29.624 0.612 22.193
ODCurveToFluxCurves 24.292 0.115 24.828
ODCurveToMetabolicGeneCurves 8.851 0.096 8.988
Simulation 6.802 0.108 6.929
* 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
CoRegFlux.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL CoRegFlux ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/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)
CoRegFlux.Rcheck/tests/Test.Rout
R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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
⠙ | 2 | CoregfluxAndFVAFonctions
⠹ | 3 | CoregfluxAndFVAFonctions
⠸ | 4 | CoregfluxAndFVAFonctions
⠼ | 5 | CoregfluxAndFVAFonctions
⠴ | 6 | CoregfluxAndFVAFonctions
✔ | 6 | CoregfluxAndFVAFonctions [43.4 s]
⠏ | 0 | DFBAsimulationFunctions
⠋ | 1 | DFBAsimulationFunctions
⠙ | 2 | DFBAsimulationFunctions
⠹ | 3 | DFBAsimulationFunctions
⠸ | 4 | DFBAsimulationFunctions
⠼ | 4 1 | DFBAsimulationFunctions
⠴ | 4 2 | DFBAsimulationFunctions
⠦ | 4 3 | DFBAsimulationFunctions
⠧ | 5 3 | DFBAsimulationFunctions
⠇ | 6 3 | DFBAsimulationFunctions
⠏ | 7 3 | DFBAsimulationFunctions
⠋ | 8 3 | DFBAsimulationFunctions
⠙ | 9 3 | DFBAsimulationFunctions
⠹ | 10 3 | DFBAsimulationFunctions
⠸ | 11 3 | DFBAsimulationFunctions
⠼ | 12 3 | DFBAsimulationFunctions
⠴ | 13 3 | DFBAsimulationFunctions
⠦ | 14 3 | DFBAsimulationFunctions
⠧ | 15 3 | DFBAsimulationFunctions
⠇ | 16 3 | DFBAsimulationFunctions
⠏ | 17 3 | DFBAsimulationFunctions
✖ | 17 3 | DFBAsimulationFunctions [3.1 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)
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)
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
⠙ | 1 1 | MetabolicModelFunctions
⠹ | 2 1 | MetabolicModelFunctions
⠸ | 3 1 | MetabolicModelFunctions
⠼ | 4 1 | MetabolicModelFunctions
⠴ | 5 1 | MetabolicModelFunctions
⠦ | 6 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"
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)
3: eval_bare(get_expr(quo), get_env(quo))
4: is.data.frame(convert_metabolites_to_model_names(metabolites = metabolites, model = iMM904))
────────────────────────────────────────────────────────────────────────────────
══ Results ═════════════════════════════════════════════════════════════════════
Duration: 46.8 s
OK: 29
Failed: 4
Warnings: 0
Skipped: 0
Frustration is a natural part of programming :)
>
> proc.time()
user system elapsed
63.432 1.273 49.841
CoRegFlux.Rcheck/CoRegFlux-Ex.timings
| name | user | system | elapsed | |
| ODCurveToFluxCurves | 24.292 | 0.115 | 24.828 | |
| ODCurveToMetabolicGeneCurves | 8.851 | 0.096 | 8.988 | |
| Simulation | 6.802 | 0.108 | 6.929 | |
| adjust_constraints_to_observed_rates | 0.124 | 0.016 | 0.140 | |
| build_exchange_met | 0.103 | 0.016 | 0.119 | |
| coregflux_static | 1.571 | 0.112 | 1.683 | |
| get_biomass_flux_position | 0.096 | 0.008 | 0.105 | |
| get_fba_fluxes_from_observations | 0.351 | 0.004 | 0.355 | |
| get_fva_intervals_from_observations | 4.613 | 0.012 | 4.629 | |
| get_metabolites_exchange_fluxes | 0.129 | 0.008 | 0.137 | |
| predict_linear_model_influence | 29.624 | 0.612 | 22.193 | |
| update_fluxes_constraints_geneKOOV | 0.122 | 0.012 | 0.134 | |
| update_fluxes_constraints_influence | 0.451 | 0.108 | 0.559 | |
| visFluxCurves | 0.366 | 0.024 | 0.389 | |
| visMetabolicGeneCurves | 0.370 | 0.028 | 0.398 | |