| Back to Build/check report for BioC 3.17 |
|
This page was generated on 2023-01-02 09:00:39 -0500 (Mon, 02 Jan 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| palomino5 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" | 4165 |
| 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 | ||||
|
To the developers/maintainers of the MOFA2 package: Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1227/2158 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MOFA2 1.9.0 (landing page) Ricard Argelaguet
| palomino5 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ||||||||
| Package: MOFA2 |
| Version: 1.9.0 |
| Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MOFA2.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings MOFA2_1.9.0.tar.gz |
| StartedAt: 2022-12-29 01:31:43 -0500 (Thu, 29 Dec 2022) |
| EndedAt: 2022-12-29 01:34:17 -0500 (Thu, 29 Dec 2022) |
| EllapsedTime: 153.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MOFA2.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MOFA2.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings MOFA2_1.9.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/MOFA2.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
gcc.exe (GCC) 10.4.0
GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'MOFA2/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MOFA2' version '1.9.0'
* 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 'MOFA2' can be installed ... NOTE
Found the following notes/warnings:
Non-staged installation was used
See 'F:/biocbuild/bbs-3.17-bioc-rtools43/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 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 ... 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_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 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 ... OK
* 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 ... OK
* 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
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'testthat.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: 3 NOTEs
See
'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/MOFA2.Rcheck/00check.log'
for details.
MOFA2.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL MOFA2 ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.17-bioc/R/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 Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2022 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(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 6 | SKIP 0 | PASS 26 ]
[ FAIL 0 | WARN 6 | SKIP 0 | PASS 26 ]
>
> proc.time()
user system elapsed
7.85 0.60 8.45
MOFA2.Rcheck/MOFA2-Ex.timings
| name | user | system | elapsed | |
| add_mofa_factors_to_seurat | 0.02 | 0.00 | 0.01 | |
| calculate_contribution_scores | 0.14 | 0.00 | 0.17 | |
| calculate_variance_explained | 1.38 | 0.08 | 1.45 | |
| calculate_variance_explained_per_sample | 0.48 | 0.03 | 0.52 | |
| cluster_samples | 0.13 | 0.03 | 0.15 | |
| compare_elbo | 0.23 | 0.05 | 0.28 | |
| compare_factors | 0.38 | 0.00 | 0.38 | |
| covariates_names | 0.17 | 0.00 | 0.17 | |
| create_mofa | 0.75 | 0.03 | 0.78 | |
| create_mofa_from_df | 0.33 | 0.03 | 0.36 | |
| create_mofa_from_matrix | 0.01 | 0.00 | 0.02 | |
| factors_names | 0.13 | 0.00 | 0.12 | |
| features_metadata | 0.14 | 0.03 | 0.17 | |
| features_names | 0.12 | 0.02 | 0.15 | |
| get_covariates | 0.14 | 0.01 | 0.15 | |
| get_data | 0.65 | 0.05 | 0.69 | |
| get_default_data_options | 0.35 | 0.03 | 0.39 | |
| get_default_mefisto_options | 0.13 | 0.00 | 0.12 | |
| get_default_model_options | 0.62 | 0.06 | 0.69 | |
| get_default_stochastic_options | 0.36 | 0.05 | 0.41 | |
| get_default_training_options | 0.29 | 0.09 | 0.37 | |
| get_dimensions | 0.10 | 0.02 | 0.13 | |
| get_elbo | 0.08 | 0.06 | 0.14 | |
| get_expectations | 0.11 | 0.02 | 0.12 | |
| get_factors | 0.11 | 0.03 | 0.14 | |
| get_imputed_data | 0.14 | 0.01 | 0.16 | |
| get_lengthscales | 0.13 | 0.02 | 0.14 | |
| get_scales | 0.14 | 0.02 | 0.16 | |
| get_variance_explained | 0.12 | 0.00 | 0.12 | |
| get_weights | 0.11 | 0.01 | 0.12 | |
| groups_names | 0.15 | 0.00 | 0.16 | |
| impute | 0.08 | 0.08 | 0.16 | |
| interpolate_factors | 0.17 | 0.00 | 0.17 | |
| load_model | 0.42 | 0.01 | 0.44 | |
| make_example_data | 0.02 | 0.00 | 0.02 | |
| plot_ascii_data | 0.12 | 0.02 | 0.14 | |
| plot_data_heatmap | 0.14 | 0.02 | 0.15 | |
| plot_data_overview | 0.24 | 0.02 | 0.25 | |
| plot_data_scatter | 1.09 | 0.04 | 1.14 | |
| plot_data_vs_cov | 0.39 | 0.02 | 0.41 | |
| plot_dimred | 2.93 | 0.06 | 2.92 | |
| plot_factor | 0.90 | 0.03 | 0.92 | |
| plot_factor_cor | 0.13 | 0.01 | 0.14 | |
| plot_factors | 0.45 | 0.02 | 0.47 | |
| plot_factors_vs_cov | 0.31 | 0.05 | 0.36 | |
| plot_group_kernel | 0.27 | 0.01 | 0.28 | |
| plot_interpolation_vs_covariate | 0.39 | 0.03 | 0.42 | |
| plot_smoothness | 0.14 | 0.02 | 0.15 | |
| plot_top_weights | 0.58 | 0.03 | 0.61 | |
| plot_variance_explained | 1.11 | 0.00 | 1.11 | |
| plot_variance_explained_by_covariates | 0.78 | 0.03 | 0.81 | |
| plot_variance_explained_per_feature | 0.26 | 0.00 | 0.27 | |
| plot_weights | 1.52 | 0.08 | 1.59 | |
| plot_weights_heatmap | 0.25 | 0.03 | 0.30 | |
| plot_weights_scatter | 0.26 | 0.03 | 0.29 | |
| predict | 0.13 | 0.01 | 0.15 | |
| prepare_mofa | 0.83 | 0.04 | 0.85 | |
| run_mofa | 0.54 | 0.00 | 0.55 | |
| run_tsne | 0.11 | 0.03 | 0.14 | |
| run_umap | 0.13 | 0.00 | 0.13 | |
| samples_metadata | 0.12 | 0.01 | 0.14 | |
| samples_names | 0.13 | 0.00 | 0.12 | |
| set_covariates | 0.03 | 0.00 | 0.03 | |
| subset_factors | 0.14 | 0.02 | 0.16 | |
| subset_groups | 0.13 | 0.00 | 0.13 | |
| subset_samples | 0.12 | 0.00 | 0.12 | |
| subset_views | 0.13 | 0.00 | 0.13 | |
| views_names | 0.11 | 0.03 | 0.14 | |