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This page was generated on 2024-06-18 17:59 -0400 (Tue, 18 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4758
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4492
merida1macOS 12.7.4 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4464
kjohnson1macOS 13.6.6 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4464
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 1313/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MOFA2 1.14.0  (landing page)
Ricard Argelaguet
Snapshot Date: 2024-06-16 14:00 -0400 (Sun, 16 Jun 2024)
git_url: https://git.bioconductor.org/packages/MOFA2
git_branch: RELEASE_3_19
git_last_commit: f09c92e
git_last_commit_date: 2024-04-30 11:28:22 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published


CHECK results for MOFA2 on palomino3

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.

raw results


Summary

Package: MOFA2
Version: 1.14.0
Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MOFA2.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings MOFA2_1.14.0.tar.gz
StartedAt: 2024-06-17 07:06:05 -0400 (Mon, 17 Jun 2024)
EndedAt: 2024-06-17 07:13:22 -0400 (Mon, 17 Jun 2024)
EllapsedTime: 437.3 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: MOFA2.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MOFA2.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings MOFA2_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/MOFA2.Rcheck'
* using R version 4.4.0 (2024-04-24 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 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 '1.14.0'
* 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-3.19-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
* 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
  'F:/biocbuild/bbs-3.19-bioc/meat/MOFA2.Rcheck/00check.log'
for details.


Installation output

MOFA2.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL MOFA2
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.19-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)

Tests output

MOFA2.Rcheck/tests/testthat.Rout


R version 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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 
  11.37   11.14   22.78 

Example timings

MOFA2.Rcheck/MOFA2-Ex.timings

nameusersystemelapsed
add_mofa_factors_to_seurat000
calculate_contribution_scores0.160.080.25
calculate_variance_explained1.890.202.10
calculate_variance_explained_per_sample0.640.050.69
cluster_samples0.160.030.20
compare_elbo0.250.070.33
compare_factors0.370.070.44
covariates_names0.190.040.25
create_mofa0.970.021.00
create_mofa_from_df0.540.000.54
create_mofa_from_matrix000
factors_names0.140.020.16
features_metadata0.180.030.20
features_names0.180.060.27
get_covariates0.210.000.20
get_data0.980.031.02
get_default_data_options0.640.020.65
get_default_mefisto_options0.190.010.33
get_default_model_options0.620.020.64
get_default_stochastic_options0.680.000.67
get_default_training_options1.150.031.19
get_dimensions0.220.010.23
get_elbo0.190.040.22
get_expectations0.190.010.21
get_factors0.110.030.14
get_imputed_data0.140.020.15
get_lengthscales0.140.040.19
get_scales0.190.020.21
get_variance_explained0.140.020.15
get_weights0.170.010.18
groups_names0.140.030.18
impute0.180.070.23
interpolate_factors0.250.030.28
load_model0.170.040.22
make_example_data000
plot_ascii_data0.150.000.15
plot_data_heatmap0.190.030.22
plot_data_overview0.310.000.33
plot_data_scatter1.310.181.84
plot_data_vs_cov0.440.040.50
plot_dimred3.710.213.96
plot_factor1.180.011.19
plot_factor_cor0.20.00.2
plot_factors0.660.020.67
plot_factors_vs_cov0.450.030.48
plot_group_kernel0.330.050.38
plot_interpolation_vs_covariate0.470.030.50
plot_smoothness0.240.030.26
plot_top_weights0.870.000.88
plot_variance_explained1.380.061.45
plot_variance_explained_by_covariates1.250.031.28
plot_variance_explained_per_feature0.290.020.31
plot_weights3.110.033.14
plot_weights_heatmap0.330.010.35
plot_weights_scatter0.270.040.31
predict0.120.030.16
prepare_mofa0.470.030.50
run_mofa0.560.010.57
run_tsne0.190.020.21
run_umap0.120.060.18
samples_metadata0.160.020.18
samples_names0.140.000.15
set_covariates0.050.000.05
subset_factors0.220.020.23
subset_groups0.120.050.18
subset_samples0.170.000.19
subset_views0.180.000.19
views_names0.180.020.20