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 12:44:43 -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: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CoRegFlux.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings CoRegFlux_0.99.22.tar.gz |
| StartedAt: 2019-04-09 02:01:08 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 02:07:33 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 385.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CoRegFlux.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CoRegFlux.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings CoRegFlux_0.99.22.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/CoRegFlux.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* 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 '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 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 or elapsed time > 5s
user system elapsed
predict_linear_model_influence 27.38 0.39 27.78
ODCurveToFluxCurves 21.49 0.27 21.93
ODCurveToMetabolicGeneCurves 9.93 0.16 10.16
Simulation 7.58 0.43 8.03
get_fva_intervals_from_observations 5.93 0.03 5.99
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
predict_linear_model_influence 20.93 0.31 21.24
ODCurveToFluxCurves 16.89 0.11 17.00
ODCurveToMetabolicGeneCurves 8.88 0.10 9.04
Simulation 5.55 0.33 5.87
* 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
CoRegFlux.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/CoRegFlux_0.99.22.tar.gz && rm -rf CoRegFlux.buildbin-libdir && mkdir CoRegFlux.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CoRegFlux.buildbin-libdir CoRegFlux_0.99.22.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL CoRegFlux_0.99.22.zip && rm CoRegFlux_0.99.22.tar.gz CoRegFlux_0.99.22.zip
###
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% 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 33.2M 0 --:--:-- --:--:-- --:--:-- 35.1M
install for i386
* installing *source* package 'CoRegFlux' ...
** 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_0.99.22.zip
* DONE (CoRegFlux)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'CoRegFlux' successfully unpacked and MD5 sums checked
|
CoRegFlux.Rcheck/tests_i386/Test.Rout
R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
Copyright (C) 2019 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
\ | 2 | CoregfluxAndFVAFonctions
| | 3 | CoregfluxAndFVAFonctions
/ | 4 | CoregfluxAndFVAFonctions
- | 5 | CoregfluxAndFVAFonctions
\ | 6 | CoregfluxAndFVAFonctions
v | 6 | CoregfluxAndFVAFonctions [48.6 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
x | 17 3 | DFBAsimulationFunctions [2.9 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
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"
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: 51.8 s
OK: 29
Failed: 4
Warnings: 0
Skipped: 0
>
> proc.time()
user system elapsed
54.03 0.92 54.93
|
CoRegFlux.Rcheck/tests_x64/Test.Rout
R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
Copyright (C) 2019 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
\ | 2 | CoregfluxAndFVAFonctions
| | 3 | CoregfluxAndFVAFonctions
/ | 4 | CoregfluxAndFVAFonctions
- | 5 | CoregfluxAndFVAFonctions
\ | 6 | CoregfluxAndFVAFonctions
v | 6 | CoregfluxAndFVAFonctions [72.8 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
x | 17 3 | DFBAsimulationFunctions [3.6 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
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"
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: 76.9 s
OK: 29
Failed: 4
Warnings: 0
Skipped: 0
>
> proc.time()
user system elapsed
78.32 1.20 81.37
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CoRegFlux.Rcheck/examples_i386/CoRegFlux-Ex.timings
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CoRegFlux.Rcheck/examples_x64/CoRegFlux-Ex.timings
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