Ricard Argelaguet
| Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024) |
| git_url: https://git.bioconductor.org/packages/MOFA2 |
| git_branch: RELEASE_3_20 |
| git_last_commit: deed7fb |
| git_last_commit_date: 2024-10-29 10:52:01 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-12-23 12:06 -0500 (Mon, 23 Dec 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 1300/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MOFA2 1.16.0 (landing page) Ricard Argelaguet
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
|
To the developers/maintainers of the MOFA2 package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MOFA2.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: MOFA2 |
| Version: 1.16.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MOFA2.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MOFA2_1.16.0.tar.gz |
| StartedAt: 2024-12-20 06:15:26 -0500 (Fri, 20 Dec 2024) |
| EndedAt: 2024-12-20 06:22:36 -0500 (Fri, 20 Dec 2024) |
| EllapsedTime: 429.5 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: MOFA2.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MOFA2.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MOFA2_1.16.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/MOFA2.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MOFA2/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MOFA2’ version ‘1.16.0’
* 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 ‘MOFA2’ can be installed ... NOTE
Found the following notes/warnings:
Non-staged installation was used
See ‘/Users/biocbuild/bbs-3.20-bioc/meat/MOFA2.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 code 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 ... NOTE
.plot_factors_vs_cov_1d: no visible binding for global variable
‘value.factor’
.plot_factors_vs_cov_1d: no visible binding for global variable
‘value_scaled’
.plot_factors_vs_cov_1d: no visible binding for global variable
‘value.covariate’
.plot_factors_vs_cov_1d: no visible binding for global variable ‘value’
.plot_factors_vs_cov_2d: no visible binding for global variable
‘value.factor’
.set_xax: no visible binding for global variable ‘value’
add_mofa_factors_to_seurat: no visible global function definition for
‘CreateDimReducObject’
create_mofa_from_SingleCellExperiment: no visible global function
definition for ‘colData’
get_interpolated_factors: no visible binding for global variable ‘L1’
get_interpolated_factors: no visible binding for global variable ‘L2’
get_interpolated_factors: no visible binding for global variable
‘value’
get_interpolated_factors: no visible binding for global variable
‘covariate’
get_interpolated_factors: no visible binding for global variable
‘covariate_value’
get_interpolated_factors: no visible binding for global variable
‘sample_id’
interpolate_factors: no visible binding for global variable ‘.’
plot_alignment: no visible binding for global variable ‘group’
plot_alignment: no visible binding for global variable ‘value.warped’
plot_alignment: no visible binding for global variable
‘value.unaligned’
plot_contribution_scores: no visible binding for global variable ‘view’
plot_data_overview: no visible binding for global variable ‘view’
plot_data_overview: no visible binding for global variable ‘ptotal’
plot_data_overview: no visible binding for global variable ‘ntotal’
plot_data_overview: no visible binding for global variable ‘group’
plot_data_overview: no visible binding for global variable
‘group_label’
plot_dimred: no visible binding for global variable ‘.’
plot_enrichment_detailed: no visible binding for global variable
‘pathway’
plot_enrichment_detailed: no visible binding for global variable
‘feature.statistic’
plot_factors_vs_cov: no visible binding for global variable ‘E2’
plot_factors_vs_cov: no visible binding for global variable ‘value’
plot_interpolation_vs_covariate: no visible binding for global variable
‘variance’
plot_interpolation_vs_covariate: no visible binding for global variable
‘group’
plot_interpolation_vs_covariate: no visible binding for global variable
‘value.covariate’
plot_interpolation_vs_covariate: no visible binding for global variable
‘value.factor’
plot_interpolation_vs_covariate: no visible binding for global variable
‘ymin’
plot_interpolation_vs_covariate: no visible binding for global variable
‘ymax’
plot_sharedness: no visible binding for global variable ‘sharedness’
plot_sharedness: no visible binding for global variable ‘value’
plot_smoothness: no visible binding for global variable ‘value’
plot_smoothness: no visible binding for global variable ‘smoothness’
plot_top_weights: no visible binding for global variable ‘value’
plot_weights: no visible binding for global variable ‘value’
plot_weights: no visible binding for global variable ‘.’
summarise_factors: no visible binding for global variable ‘value’
summarise_factors: no visible binding for global variable ‘level’
summarise_factors: no visible binding for global variable ‘group’
Undefined global functions or variables:
. CreateDimReducObject E2 L1 L2 colData covariate covariate_value
feature.statistic group group_label level ntotal pathway ptotal
sample_id sharedness smoothness value value.covariate value.factor
value.unaligned value.warped value_scaled variance view ymax ymin
* checking Rd files ... NOTE
checkRd: (-1) calculate_contribution_scores.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) calculate_contribution_scores.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) calculate_contribution_scores.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) correlate_factors_with_covariates.Rd:24-25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) correlate_factors_with_covariates.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) create_mofa.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) create_mofa.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) create_mofa.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) create_mofa.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) create_mofa.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_default_data_options.Rd:24-25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_default_data_options.Rd:26-27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_default_data_options.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_default_model_options.Rd:24-25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_default_model_options.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_default_model_options.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_default_model_options.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_default_model_options.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_default_model_options.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_default_stochastic_options.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_default_stochastic_options.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_default_stochastic_options.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_default_stochastic_options.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_default_training_options.Rd:24-25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_default_training_options.Rd:26-27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_default_training_options.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_default_training_options.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_default_training_options.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_default_training_options.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_default_training_options.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_default_training_options.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_default_training_options.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_default_training_options.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_expectations.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_expectations.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) impute.Rd:24: Lost braces; missing escapes or markup?
24 | \item \strong{response}:{gives mean for gaussian and poisson and probabilities for bernoulli.}
| ^
checkRd: (-1) impute.Rd:25: Lost braces; missing escapes or markup?
25 | \item \strong{link}: {gives the linear predictions.}
| ^
checkRd: (-1) impute.Rd:26: Lost braces; missing escapes or markup?
26 | \item \strong{inRange}: {rounds the fitted values from "terms" for integer-valued distributions to the next integer (default).}
| ^
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: ‘PCGSE’
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from Rd file 'create_mofa_from_Seurat.Rd':
create_mofa_from_Seurat
Code: function(seurat, groups = NULL, assays = NULL, layer = "data",
features = NULL, extract_metadata = FALSE)
Docs: function(seurat, groups = NULL, assays = NULL, slot =
"scale.data", features = NULL, extract_metadata =
FALSE)
Argument names in code not in docs:
layer
Argument names in docs not in code:
slot
Mismatches in argument names:
Position: 4 Code: layer Docs: slot
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in shell scripts ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plot_dimred 5.558 0.081 5.666
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 4 NOTEs
See
‘/Users/biocbuild/bbs-3.20-bioc/meat/MOFA2.Rcheck/00check.log’
for details.
MOFA2.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MOFA2 ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘MOFA2’ ... ** using non-staged installation via StagedInstall field ** R ** inst ** byte-compile and prepare package for lazy loading Creating a generic function for ‘rownames’ from package ‘base’ in package ‘MOFA2’ Creating a generic function for ‘colnames’ from package ‘base’ in package ‘MOFA2’ Creating a generic function for ‘nrow’ from package ‘base’ in package ‘MOFA2’ Creating a generic function for ‘ncol’ from package ‘base’ in package ‘MOFA2’ Creating a generic function for ‘rownames<-’ from package ‘base’ in package ‘MOFA2’ Creating a generic function for ‘colnames<-’ from package ‘base’ in package ‘MOFA2’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (MOFA2)
MOFA2.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
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(testthat)
> library(MOFA2)
Attaching package: 'MOFA2'
The following object is masked from 'package:stats':
predict
>
> test_check("MOFA2")
single_group
100
____________
| |
view_0 1000 | 100% |
|____________|
____________
| |
view_1 1000 | 100% |
|____________|
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 25 ]
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 25 ]
>
> # setwd("/Users/rargelaguet/mofa/MOFA2/tests/testthat")
>
> proc.time()
user system elapsed
23.920 1.344 25.495
MOFA2.Rcheck/MOFA2-Ex.timings
| name | user | system | elapsed | |
| add_mofa_factors_to_seurat | 0.010 | 0.001 | 0.011 | |
| calculate_contribution_scores | 0.423 | 0.036 | 0.466 | |
| calculate_variance_explained | 4.406 | 0.276 | 4.737 | |
| calculate_variance_explained_per_sample | 0.357 | 0.021 | 0.381 | |
| cluster_samples | 0.337 | 0.018 | 0.358 | |
| compare_elbo | 0.674 | 0.041 | 0.723 | |
| compare_factors | 0.727 | 0.036 | 0.767 | |
| covariates_names | 0.465 | 0.027 | 0.507 | |
| create_mofa | 1.016 | 0.074 | 1.099 | |
| create_mofa_from_df | 1.458 | 0.055 | 1.524 | |
| create_mofa_from_matrix | 0.025 | 0.000 | 0.025 | |
| factors_names | 0.328 | 0.015 | 0.346 | |
| features_metadata | 0.395 | 0.098 | 0.499 | |
| features_names | 0.357 | 0.083 | 0.450 | |
| get_covariates | 0.438 | 0.023 | 0.469 | |
| get_data | 0.810 | 0.039 | 0.857 | |
| get_default_data_options | 1.478 | 0.053 | 1.549 | |
| get_default_mefisto_options | 0.240 | 0.020 | 0.261 | |
| get_default_model_options | 0.873 | 0.035 | 0.910 | |
| get_default_stochastic_options | 0.958 | 0.051 | 1.126 | |
| get_default_training_options | 0.915 | 0.041 | 1.166 | |
| get_dimensions | 0.327 | 0.018 | 0.345 | |
| get_elbo | 0.344 | 0.018 | 0.384 | |
| get_expectations | 0.340 | 0.018 | 0.369 | |
| get_factors | 0.332 | 0.015 | 0.348 | |
| get_imputed_data | 0.353 | 0.018 | 0.373 | |
| get_lengthscales | 0.430 | 0.020 | 0.452 | |
| get_scales | 0.432 | 0.019 | 0.453 | |
| get_variance_explained | 0.340 | 0.019 | 0.359 | |
| get_weights | 0.384 | 0.024 | 0.415 | |
| groups_names | 0.332 | 0.029 | 0.362 | |
| impute | 0.352 | 0.018 | 0.369 | |
| interpolate_factors | 0.478 | 0.021 | 0.500 | |
| load_model | 0.324 | 0.016 | 0.340 | |
| make_example_data | 0.004 | 0.000 | 0.005 | |
| plot_ascii_data | 0.369 | 0.026 | 0.396 | |
| plot_data_heatmap | 0.425 | 0.022 | 0.450 | |
| plot_data_overview | 0.724 | 0.022 | 0.754 | |
| plot_data_scatter | 3.125 | 0.108 | 3.269 | |
| plot_data_vs_cov | 1.052 | 0.030 | 1.096 | |
| plot_dimred | 5.558 | 0.081 | 5.666 | |
| plot_factor | 2.617 | 0.039 | 2.676 | |
| plot_factor_cor | 0.332 | 0.018 | 0.351 | |
| plot_factors | 1.250 | 0.028 | 1.293 | |
| plot_factors_vs_cov | 1.075 | 0.029 | 1.113 | |
| plot_group_kernel | 0.806 | 0.023 | 0.835 | |
| plot_interpolation_vs_covariate | 1.175 | 0.027 | 1.218 | |
| plot_smoothness | 0.490 | 0.021 | 0.519 | |
| plot_top_weights | 1.760 | 0.027 | 1.818 | |
| plot_variance_explained | 3.242 | 0.049 | 3.392 | |
| plot_variance_explained_by_covariates | 2.409 | 0.038 | 2.480 | |
| plot_variance_explained_per_feature | 0.736 | 0.024 | 0.787 | |
| plot_weights | 4.650 | 0.080 | 4.772 | |
| plot_weights_heatmap | 0.734 | 0.039 | 0.779 | |
| plot_weights_scatter | 0.740 | 0.037 | 0.786 | |
| predict | 0.354 | 0.020 | 0.381 | |
| prepare_mofa | 0.926 | 0.026 | 0.958 | |
| run_mofa | 0.957 | 0.043 | 1.006 | |
| run_tsne | 0.348 | 0.021 | 0.370 | |
| run_umap | 0.339 | 0.015 | 0.357 | |
| samples_metadata | 0.337 | 0.021 | 0.361 | |
| samples_names | 0.349 | 0.021 | 0.372 | |
| set_covariates | 0.056 | 0.002 | 0.059 | |
| subset_factors | 0.377 | 0.042 | 0.421 | |
| subset_groups | 0.354 | 0.017 | 0.376 | |
| subset_samples | 0.349 | 0.016 | 0.373 | |
| subset_views | 0.350 | 0.017 | 0.372 | |
| views_names | 0.342 | 0.015 | 0.357 | |