| Back to Multiple platform build/check report for BioC 3.11 |
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This page was generated on 2020-10-17 11:56:22 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE CoRegFlux PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 374/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| CoRegFlux 1.4.0 Pauline Trébulle and Mohamed Elati
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK |  | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |
| Package: CoRegFlux |
| Version: 1.4.0 |
| Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CoRegFlux.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings CoRegFlux_1.4.0.tar.gz |
| StartedAt: 2020-10-17 02:57:00 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 03:03:46 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 405.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CoRegFlux.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CoRegFlux.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings CoRegFlux_1.4.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/CoRegFlux.Rcheck'
* using R version 4.0.3 (2020-10-10)
* 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 '1.4.0'
* 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 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 (user + system) or elapsed time > 5s
user system elapsed
predict_linear_model_influence 33.09 0.41 33.50
ODCurveToFluxCurves 21.37 0.22 21.91
ODCurveToMetabolicGeneCurves 11.52 0.22 11.76
Simulation 8.11 0.36 8.47
get_fva_intervals_from_observations 5.45 0.08 5.53
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
predict_linear_model_influence 21.42 0.27 21.69
ODCurveToFluxCurves 18.28 0.13 23.25
ODCurveToMetabolicGeneCurves 7.67 0.22 25.43
Simulation 5.78 0.25 6.03
* 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/3.11/bioc/src/contrib/CoRegFlux_1.4.0.tar.gz && rm -rf CoRegFlux.buildbin-libdir && mkdir CoRegFlux.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CoRegFlux.buildbin-libdir CoRegFlux_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL CoRegFlux_1.4.0.zip && rm CoRegFlux_1.4.0.tar.gz CoRegFlux_1.4.0.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 17.5M 0 --:--:-- --:--:-- --:--:-- 18.0M
install for i386
* installing *source* package 'CoRegFlux' ...
** using staged installation
** 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_1.4.0.zip
* DONE (CoRegFlux)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'CoRegFlux' successfully unpacked and MD5 sums checked
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CoRegFlux.Rcheck/tests_i386/Test.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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
| | 3 | CoregfluxAndFVAFonctions
v | 6 | CoregfluxAndFVAFonctions [48.1 s]
/ | 0 | DFBAsimulationFunctions
- | 1 | DFBAsimulationFunctions
/ | 5 3 | DFBAsimulationFunctions
x | 17 3 | DFBAsimulationFunctions [3.1 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
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"
Backtrace:
1. testthat::expect_true(...) test_MetabolicModelFunctions.R:13:5
4. base::is.data.frame(...)
--------------------------------------------------------------------------------
== Results =====================================================================
Duration: 51.6 s
OK: 29
Failed: 4
Warnings: 0
Skipped: 0
>
> proc.time()
user system elapsed
53.85 0.89 54.75
|
CoRegFlux.Rcheck/tests_x64/Test.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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
| | 3 | CoregfluxAndFVAFonctions
v | 6 | CoregfluxAndFVAFonctions [52.6 s]
/ | 0 | DFBAsimulationFunctions
- | 1 | DFBAsimulationFunctions
/ | 5 3 | DFBAsimulationFunctions
x | 17 3 | DFBAsimulationFunctions [2.6 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
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"
Backtrace:
1. testthat::expect_true(...) test_MetabolicModelFunctions.R:13:5
4. base::is.data.frame(...)
--------------------------------------------------------------------------------
== Results =====================================================================
Duration: 55.5 s
OK: 29
Failed: 4
Warnings: 0
Skipped: 0
>
> proc.time()
user system elapsed
58.45 0.64 59.07
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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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