| Back to Multiple platform build/check report for BioC 3.12 |
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This page was generated on 2021-05-06 12:27:15 -0400 (Thu, 06 May 2021).
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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 377/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CoRegFlux 1.6.0 (landing page) Pauline Trébulle and Mohamed Elati
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | ERROR | OK | |||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | ERROR | OK | |||||||||
| Package: CoRegFlux |
| Version: 1.6.0 |
| Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:CoRegFlux.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings CoRegFlux_1.6.0.tar.gz |
| StartedAt: 2021-05-06 00:27:42 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 00:31:17 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 215.5 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: CoRegFlux.Rcheck |
| Warnings: NA |
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### Running command:
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### /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:CoRegFlux.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings CoRegFlux_1.6.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/CoRegFlux.Rcheck’
* using R version 4.0.5 (2021-03-31)
* 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 ‘1.6.0’
* 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 32.208 0.584 23.754
ODCurveToFluxCurves 24.880 0.168 25.240
ODCurveToMetabolicGeneCurves 8.588 0.112 8.709
Simulation 6.972 0.136 7.125
get_fva_intervals_from_observations 5.100 0.016 5.120
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘Test.R’
ERROR
Running the tests in ‘tests/Test.R’ failed.
Last 13 lines of output:
────────────────────────────────────────────────────────────────────────────────
Error (test_MetabolicModelFunctions.R:13:6): Metabolites names to model names works and return a
data.frame
Error: 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: 54.4 s
[ FAIL 4 | WARN 0 | SKIP 0 | PASS 29 ]
Error: Test failures
Execution halted
* 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: 1 ERROR
See
‘/home/biocbuild/bbs-3.12-bioc/meat/CoRegFlux.Rcheck/00check.log’
for details.
CoRegFlux.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL CoRegFlux ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.12-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.fail
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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 | CoregfluxAndFVAFunctions
⠏ | 0 | CoregfluxAndFVAFonctions
⠋ | 1 | CoregfluxAndFVAFonctions
⠹ | 3 | CoregfluxAndFVAFonctions
✔ | 6 | CoregfluxAndFVAFonctions [50.9 s]
⠏ | 0 | DFBAsimulationFunctions
⠏ | 0 | DFBAsimulationFunctions
⠋ | 1 | DFBAsimulationFunctions
⠧ | 5 3 | DFBAsimulationFunctions
⠹ | 10 3 | DFBAsimulationFunctions
✖ | 17 3 | DFBAsimulationFunctions [3.2 s]
────────────────────────────────────────────────────────────────────────────────
Error (test_DFBAsimulationFunctions.R:41:6): uptake fluxes diminish metabolite concentrations
Error: 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))
Error (test_DFBAsimulationFunctions.R:49:6): positive fluxes increase metabolite concentrations
Error: 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))
Error (test_DFBAsimulationFunctions.R:59:16): update_uptake_fluxes_constraints_metabolites check that
bounds are changed
Error: could not find function "update_uptake_fluxes_constraints_metabolites"
────────────────────────────────────────────────────────────────────────────────
⠏ | 0 | MetabolicModelFunctions
⠏ | 0 | MetabolicModelFunctions
⠋ | 0 1 | MetabolicModelFunctions
✖ | 6 1 | MetabolicModelFunctions [0.2 s]
────────────────────────────────────────────────────────────────────────────────
Error (test_MetabolicModelFunctions.R:13:6): Metabolites names to model names works and return a
data.frame
Error: 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: 54.4 s
[ FAIL 4 | WARN 0 | SKIP 0 | PASS 29 ]
Error: Test failures
Execution halted
CoRegFlux.Rcheck/CoRegFlux-Ex.timings
| name | user | system | elapsed | |
| ODCurveToFluxCurves | 24.880 | 0.168 | 25.240 | |
| ODCurveToMetabolicGeneCurves | 8.588 | 0.112 | 8.709 | |
| Simulation | 6.972 | 0.136 | 7.125 | |
| adjust_constraints_to_observed_rates | 0.120 | 0.012 | 0.130 | |
| build_exchange_met | 0.112 | 0.008 | 0.120 | |
| coregflux_static | 1.384 | 0.084 | 1.468 | |
| get_biomass_flux_position | 0.096 | 0.008 | 0.104 | |
| get_fba_fluxes_from_observations | 0.400 | 0.020 | 0.419 | |
| get_fva_intervals_from_observations | 5.100 | 0.016 | 5.120 | |
| get_metabolites_exchange_fluxes | 0.084 | 0.012 | 0.096 | |
| predict_linear_model_influence | 32.208 | 0.584 | 23.754 | |
| update_fluxes_constraints_geneKOOV | 0.088 | 0.012 | 0.098 | |
| update_fluxes_constraints_influence | 0.404 | 0.128 | 0.538 | |
| visFluxCurves | 0.248 | 0.020 | 0.271 | |
| visMetabolicGeneCurves | 0.372 | 0.012 | 0.388 | |