| Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:32 -0400 (Fri, 15 Oct 2021).
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To the developers/maintainers of the CoRegFlux package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CoRegFlux.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 391/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Pauline Trébulle and Mohamed Elati
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | ERROR | OK | |||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | ERROR | OK | |||||||||
| Package: CoRegFlux |
| Version: 1.8.0 |
| 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_1.8.0.tar.gz |
| StartedAt: 2021-10-14 17:48:54 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 17:52:31 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 216.1 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: CoRegFlux.Rcheck |
| Warnings: NA |
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### Running 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_1.8.0.tar.gz
###
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##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/CoRegFlux.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.8.0’
* 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 ... NOTE
Found the following hidden files and directories:
.git_fetch_output.txt
.git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘CoRegFlux’ can be installed ... WARNING
Found the following significant warnings:
Warning: Package 'CoRegFlux' is deprecated and will be removed from Bioconductor
See ‘/Users/biocbuild/bbs-3.13-bioc/meat/CoRegFlux.Rcheck/00install.out’ for details.
* 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 30.585 1.830 23.526
ODCurveToFluxCurves 19.985 0.211 20.239
ODCurveToMetabolicGeneCurves 9.515 0.265 9.785
Simulation 7.068 0.083 7.161
* 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 in `convert_metabolites_to_model_names(metabolites = metabolites,
model = iMM904)`: 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: 45.8 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, 1 WARNING, 1 NOTE
See
‘/Users/biocbuild/bbs-3.13-bioc/meat/CoRegFlux.Rcheck/00check.log’
for details.
CoRegFlux.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL CoRegFlux ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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 Warning: Package 'CoRegFlux' is deprecated and will be removed from Bioconductor version 3.14 ** testing if installed package can be loaded from final location Warning: Package 'CoRegFlux' is deprecated and will be removed from Bioconductor version 3.14 ** testing if installed package keeps a record of temporary installation path * DONE (CoRegFlux)
CoRegFlux.Rcheck/tests/Test.Rout.fail
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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)
Warning message:
Package 'CoRegFlux' is deprecated and will be removed from Bioconductor
version 3.14
> library(testthat)
>
> testthat::test_dir("testthat/")
✔ | F W S OK | Context
⠏ | 0 | CoregfluxAndFVAFunctions
⠏ | 0 | CoregfluxAndFVAFonctions
⠋ | 1 | CoregfluxAndFVAFonctions
⠹ | 3 | CoregfluxAndFVAFonctions
✔ | 6 | CoregfluxAndFVAFonctions [42.6s]
⠏ | 0 | DFBAsimulationFunctions
⠏ | 0 | DFBAsimulationFunctions
⠋ | 1 | DFBAsimulationFunctions
⠦ | 3 4 | DFBAsimulationFunctions
⠧ | 3 5 | DFBAsimulationFunctions
✖ | 3 17 | DFBAsimulationFunctions [3.0s]
────────────────────────────────────────────────────────────────────────────────
Error (test_DFBAsimulationFunctions.R:41:6): uptake fluxes diminish metabolite concentrations
Error in `euler_step_metabolites(met_concentrations_t0 = 10, fluxes = -1,
rate = 0.1, time_step = 0.1, biomass_t0 = 0.3)`: 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 in `euler_step_metabolites(met_concentrations_t0 = 10, fluxes = 1,
rate = 0.1, time_step = 0.1, biomass_t0 = 0.3)`: 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 in `update_uptake_fluxes_constraints_metabolites(model = iMM904,
met_fluxes_indexes = 550, biomass_t0 = 0.3, met_concentrations_t0 = 1e-06,
time_step = 1)`: could not find function "update_uptake_fluxes_constraints_metabolites"
────────────────────────────────────────────────────────────────────────────────
⠏ | 0 | MetabolicModelFunctions
⠏ | 0 | MetabolicModelFunctions
⠋ | 1 0 | MetabolicModelFunctions
✖ | 1 6 | MetabolicModelFunctions [0.2s]
────────────────────────────────────────────────────────────────────────────────
Error (test_MetabolicModelFunctions.R:13:6): Metabolites names to model names works and return a
data.frame
Error in `convert_metabolites_to_model_names(metabolites = metabolites,
model = iMM904)`: 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: 45.8 s
[ FAIL 4 | WARN 0 | SKIP 0 | PASS 29 ]
Error: Test failures
Execution halted
CoRegFlux.Rcheck/CoRegFlux-Ex.timings
| name | user | system | elapsed | |
| ODCurveToFluxCurves | 19.985 | 0.211 | 20.239 | |
| ODCurveToMetabolicGeneCurves | 9.515 | 0.265 | 9.785 | |
| Simulation | 7.068 | 0.083 | 7.161 | |
| adjust_constraints_to_observed_rates | 0.110 | 0.006 | 0.116 | |
| build_exchange_met | 0.091 | 0.002 | 0.094 | |
| coregflux_static | 1.353 | 0.024 | 1.378 | |
| get_biomass_flux_position | 0.083 | 0.002 | 0.085 | |
| get_fba_fluxes_from_observations | 0.328 | 0.004 | 0.331 | |
| get_fva_intervals_from_observations | 4.445 | 0.018 | 4.465 | |
| get_metabolites_exchange_fluxes | 0.113 | 0.005 | 0.118 | |
| predict_linear_model_influence | 30.585 | 1.830 | 23.526 | |
| update_fluxes_constraints_geneKOOV | 0.100 | 0.007 | 0.107 | |
| update_fluxes_constraints_influence | 0.379 | 0.010 | 0.389 | |
| visFluxCurves | 0.360 | 0.022 | 0.383 | |
| visMetabolicGeneCurves | 0.322 | 0.023 | 0.347 | |