| Back to Build/check report for BioC 3.17 |
|
This page was generated on 2023-02-08 01:15:15 -0000 (Wed, 08 Feb 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4164 |
| 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: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1230/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MOFA2 1.9.0 (landing page) Ricard Argelaguet
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
| Package: MOFA2 |
| Version: 1.9.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:MOFA2.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings MOFA2_1.9.0.tar.gz |
| StartedAt: 2023-02-07 08:44:39 -0000 (Tue, 07 Feb 2023) |
| EndedAt: 2023-02-07 08:52:31 -0000 (Tue, 07 Feb 2023) |
| EllapsedTime: 471.7 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: MOFA2.Rcheck |
| Warnings: NA |
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### Running command:
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### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:MOFA2.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings MOFA2_1.9.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/MOFA2.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* 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 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 ‘/home/biocbuild/bbs-3.17-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 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’
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
|____________|
____________
| |
view_1 1000 | 100% |
|____________|
[ FAIL 1 | WARN 7 | SKIP 0 | PASS 25 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_plot.R:18'): plot data scatter ───────────────────────────────
`p <- plot_data_scatter(test_mofa2, view = 1, factor = 1)` produced warnings.
[ FAIL 1 | WARN 7 | SKIP 0 | PASS 25 ]
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 ...
‘MEFISTO_temporal.Rmd’ using ‘UTF-8’... OK
‘downstream_analysis.Rmd’ using ‘UTF-8’... OK
‘getting_started_R.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘MEFISTO_temporal.Rmd’ using rmarkdown
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MOFA2.Rcheck/vign_test/MOFA2/vignettes/MEFISTO_temporal_files/figure-html/unnamed-chunk-3-1.png" but not available.
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use_float32 set to True: replacing float64 arrays by float32 arrays to speed up computations...
Successfully loaded view='view_1' group='group1' with N=200 samples and D=200 features...
Successfully loaded view='view_2' group='group1' with N=200 samples and D=200 features...
Successfully loaded view='view_3' group='group1' with N=200 samples and D=200 features...
Successfully loaded view='view_4' group='group1' with N=200 samples and D=200 features...
Loaded 1 covariate(s) for each sample...
Model options:
- Automatic Relevance Determination prior on the factors: False
- Automatic Relevance Determination prior on the weights: True
- Spike-and-slab prior on the factors: False
- Spike-and-slab prior on the weights: False
Likelihoods:
- View 0 (view_1): gaussian
- View 1 (view_2): gaussian
- View 2 (view_3): gaussian
- View 3 (view_4): gaussian
######################################
## Training the model with seed 42 ##
######################################
ELBO before training: -668156.69
Iteration 1: time=0.25, ELBO=-112628.56, deltaELBO=555528.126 (83.14339043%), Factors=4
Iteration 2: time=0.15, Factors=4
Iteration 3: time=0.15, Factors=4
Iteration 4: time=0.17, Factors=4
Iteration 5: time=0.15, Factors=4
Iteration 6: time=0.20, ELBO=-60038.12, deltaELBO=52590.443 (7.87097448%), Factors=4
Iteration 7: time=0.07, Factors=4
Iteration 8: time=0.07, Factors=4
Iteration 9: time=0.07, Factors=4
Iteration 10: time=0.09, Factors=4
Iteration 11: time=0.13, ELBO=-59874.45, deltaELBO=163.676 (0.02449672%), Factors=4
Iteration 12: time=0.07, Factors=4
Iteration 13: time=0.08, Factors=4
Iteration 14: time=0.11, Factors=4
Iteration 15: time=0.09, Factors=4
Iteration 16: time=0.09, ELBO=-59706.33, deltaELBO=168.117 (0.02516128%), Factors=4
Iteration 17: time=0.07, Factors=4
Iteration 18: time=0.07, Factors=4
Iteration 19: time=0.07, Factors=4
Optimising sigma node...
Iteration 20: time=12.10, Factors=4
Iteration 21: time=0.09, ELBO=-58693.09, deltaELBO=1013.241 (0.15164714%), Factors=4
Iteration 22: time=0.07, Factors=4
Iteration 23: time=0.07, Factors=4
Iteration 24: time=0.07, Factors=4
Iteration 25: time=0.07, Factors=4
Iteration 26: time=0.09, ELBO=-58472.74, deltaELBO=220.352 (0.03297904%), Factors=4
Iteration 27: time=0.07, Factors=4
Iteration 28: time=0.07, Factors=4
Iteration 29: time=0.12, Factors=4
Optimising sigma node...
Iteration 30: time=10.32, Factors=4
Iteration 31: time=0.10, ELBO=-58287.06, deltaELBO=185.678 (0.02778958%), Factors=4
Iteration 32: time=0.07, Factors=4
Iteration 33: time=0.07, Factors=4
Iteration 34: time=0.07, Factors=4
Iteration 35: time=0.10, Factors=4
Iteration 36: time=0.16, ELBO=-58181.29, deltaELBO=105.766 (0.01582952%), Factors=4
Iteration 37: time=0.09, Factors=4
Iteration 38: time=0.11, Factors=4
Iteration 39: time=0.11, Factors=4
Optimising sigma node...
Iteration 40: time=8.80, Factors=4
Iteration 41: time=0.09, ELBO=-58026.91, deltaELBO=154.380 (0.02310532%), Factors=4
Iteration 42: time=0.08, Factors=4
Iteration 43: time=0.12, Factors=4
Iteration 44: time=0.10, Factors=4
Iteration 45: time=0.11, Factors=4
Iteration 46: time=0.16, ELBO=-57938.97, deltaELBO=87.944 (0.01316221%), Factors=4
Iteration 47: time=0.12, Factors=4
Iteration 48: time=0.09, Factors=4
Iteration 49: time=0.07, Factors=4
Optimising sigma node...
Iteration 50: time=8.96, Factors=4
Iteration 51: time=0.11, ELBO=-57831.56, deltaELBO=107.406 (0.01607498%), Factors=4
Iteration 52: time=0.13, Factors=4
Iteration 53: time=0.09, Factors=4
Iteration 54: time=0.07, Factors=4
Iteration 55: time=0.07, Factors=4
Iteration 56: time=0.09, ELBO=-57760.44, deltaELBO=71.125 (0.01064494%), Factors=4
Iteration 57: time=0.07, Factors=4
Iteration 58: time=0.07, Factors=4
Iteration 59: time=0.09, Factors=4
Optimising sigma node...
Iteration 60: time=6.51, Factors=4
Iteration 61: time=0.09, ELBO=-57683.55, deltaELBO=76.889 (0.01150765%), Factors=4
Iteration 62: time=0.09, Factors=4
Iteration 63: time=0.07, Factors=4
Iteration 64: time=0.07, Factors=4
Iteration 65: time=0.08, Factors=4
Iteration 66: time=0.09, ELBO=-57646.15, deltaELBO=37.397 (0.00559706%), Factors=4
Iteration 67: time=0.08, Factors=4
Iteration 68: time=0.12, Factors=4
Iteration 69: time=0.08, Factors=4
Optimising sigma node...
Iteration 70: time=8.24, Factors=4
Iteration 71: time=0.15, ELBO=-57618.65, deltaELBO=27.504 (0.00411637%), Factors=4
Iteration 72: time=0.10, Factors=4
Iteration 73: time=0.07, Factors=4
Iteration 74: time=0.07, Factors=4
Iteration 75: time=0.07, Factors=4
Iteration 76: time=0.09, ELBO=-57601.36, deltaELBO=17.283 (0.00258664%), Factors=4
Iteration 77: time=0.27, Factors=4
Iteration 78: time=0.16, Factors=4
Iteration 79: time=0.14, Factors=4
Optimising sigma node...
Iteration 80: time=11.74, Factors=4
Iteration 81: time=0.09, ELBO=-57581.25, deltaELBO=20.115 (0.00301053%), Factors=4
Iteration 82: time=0.07, Factors=4
Iteration 83: time=0.08, Factors=4
Iteration 84: time=0.07, Factors=4
Iteration 85: time=0.10, Factors=4
Iteration 86: time=0.10, ELBO=-57565.76, deltaELBO=15.492 (0.00231869%), Factors=4
Iteration 87: time=0.08, Factors=4
Iteration 88: time=0.07, Factors=4
Iteration 89: time=0.08, Factors=4
Optimising sigma node...
Iteration 90: time=12.27, Factors=4
Iteration 91: time=0.11, ELBO=-57548.33, deltaELBO=17.423 (0.00260760%), Factors=4
Iteration 92: time=0.07, Factors=4
Iteration 93: time=0.08, Factors=4
Iteration 94: time=0.16, Factors=4
Iteration 95: time=0.13, Factors=4
Iteration 96: time=0.21, ELBO=-57534.18, deltaELBO=14.156 (0.00211860%), Factors=4
Iteration 97: time=0.16, Factors=4
Iteration 98: time=0.17, Factors=4
Iteration 99: time=0.18, Factors=4
#######################
## Training finished ##
#######################
Saving model in /tmp/RtmpOmzMiF/model.hdf5...
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MOFA2.Rcheck/vign_test/MOFA2/vignettes/MEFISTO_temporal_files/figure-html/unnamed-chunk-8-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MOFA2.Rcheck/vign_test/MOFA2/vignettes/MEFISTO_temporal_files/figure-html/unnamed-chunk-8-2.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MOFA2.Rcheck/vign_test/MOFA2/vignettes/MEFISTO_temporal_files/figure-html/unnamed-chunk-10-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MOFA2.Rcheck/vign_test/MOFA2/vignettes/MEFISTO_temporal_files/figure-html/unnamed-chunk-12-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MOFA2.Rcheck/vign_test/MOFA2/vignettes/MEFISTO_temporal_files/figure-html/unnamed-chunk-12-2.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MOFA2.Rcheck/vign_test/MOFA2/vignettes/MEFISTO_temporal_files/figure-html/unnamed-chunk-13-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MOFA2.Rcheck/vign_test/MOFA2/vignettes/MEFISTO_temporal_files/figure-html/unnamed-chunk-14-1.png" but not available.
--- finished re-building ‘MEFISTO_temporal.Rmd’
--- re-building ‘downstream_analysis.Rmd’ using rmarkdown
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MOFA2.Rcheck/vign_test/MOFA2/vignettes/downstream_analysis_files/figure-html/unnamed-chunk-3-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MOFA2.Rcheck/vign_test/MOFA2/vignettes/downstream_analysis_files/figure-html/unnamed-chunk-6-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MOFA2.Rcheck/vign_test/MOFA2/vignettes/downstream_analysis_files/figure-html/unnamed-chunk-7-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MOFA2.Rcheck/vign_test/MOFA2/vignettes/downstream_analysis_files/figure-html/unnamed-chunk-8-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MOFA2.Rcheck/vign_test/MOFA2/vignettes/downstream_analysis_files/figure-html/unnamed-chunk-9-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MOFA2.Rcheck/vign_test/MOFA2/vignettes/downstream_analysis_files/figure-html/unnamed-chunk-10-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MOFA2.Rcheck/vign_test/MOFA2/vignettes/downstream_analysis_files/figure-html/unnamed-chunk-11-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MOFA2.Rcheck/vign_test/MOFA2/vignettes/downstream_analysis_files/figure-html/unnamed-chunk-12-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MOFA2.Rcheck/vign_test/MOFA2/vignettes/downstream_analysis_files/figure-html/unnamed-chunk-13-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MOFA2.Rcheck/vign_test/MOFA2/vignettes/downstream_analysis_files/figure-html/unnamed-chunk-14-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MOFA2.Rcheck/vign_test/MOFA2/vignettes/downstream_analysis_files/figure-html/unnamed-chunk-16-1.png" but not available.
--- finished re-building ‘downstream_analysis.Rmd’
--- re-building ‘getting_started_R.Rmd’ using rmarkdown
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MOFA2.Rcheck/vign_test/MOFA2/vignettes/getting_started_R_files/figure-html/unnamed-chunk-4-1.png" but not available.
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#########################################################
use_float32 set to True: replacing float64 arrays by float32 arrays to speed up computations...
Successfully loaded view='view_0' group='single_group' with N=100 samples and D=1000 features...
Successfully loaded view='view_1' group='single_group' with N=100 samples and D=1000 features...
Model options:
- Automatic Relevance Determination prior on the factors: False
- Automatic Relevance Determination prior on the weights: True
- Spike-and-slab prior on the factors: False
- Spike-and-slab prior on the weights: False
Likelihoods:
- View 0 (view_0): gaussian
- View 1 (view_1): gaussian
######################################
## Training the model with seed 42 ##
######################################
ELBO before training: -1602212.69
Iteration 1: time=0.14, ELBO=-281808.02, deltaELBO=1320404.677 (82.41132294%), Factors=10
Iteration 2: time=0.08, Factors=10
Iteration 3: time=0.11, Factors=10
Iteration 4: time=0.12, Factors=10
Iteration 5: time=0.12, Factors=10
Iteration 6: time=0.10, ELBO=-237882.85, deltaELBO=43925.169 (2.74153173%), Factors=10
Iteration 7: time=0.19, Factors=10
Iteration 8: time=0.09, Factors=10
Iteration 9: time=0.10, Factors=10
Iteration 10: time=0.08, Factors=10
Iteration 11: time=0.12, ELBO=-237719.38, deltaELBO=163.463 (0.01020230%), Factors=10
Iteration 12: time=0.09, Factors=10
Iteration 13: time=0.09, Factors=10
Iteration 14: time=0.25, Factors=10
Iteration 15: time=0.12, Factors=10
Iteration 16: time=0.18, ELBO=-237643.62, deltaELBO=75.763 (0.00472864%), Factors=10
Iteration 17: time=0.17, Factors=10
Iteration 18: time=0.07, Factors=10
Iteration 19: time=0.11, Factors=10
Iteration 20: time=0.12, Factors=10
Iteration 21: time=0.10, ELBO=-237581.47, deltaELBO=62.157 (0.00387942%), Factors=10
Iteration 22: time=0.12, Factors=10
Iteration 23: time=0.25, Factors=10
Iteration 24: time=0.19, Factors=10
Iteration 25: time=0.15, Factors=10
Iteration 26: time=0.09, ELBO=-237526.96, deltaELBO=54.509 (0.00340211%), Factors=10
Iteration 27: time=0.10, Factors=10
Iteration 28: time=0.09, Factors=10
Iteration 29: time=0.15, Factors=10
Iteration 30: time=0.07, Factors=10
Iteration 31: time=0.10, ELBO=-237478.41, deltaELBO=48.542 (0.00302967%), Factors=10
Iteration 32: time=0.09, Factors=10
Iteration 33: time=0.09, Factors=10
Iteration 34: time=0.13, Factors=10
Iteration 35: time=0.16, Factors=10
Iteration 36: time=0.21, ELBO=-237434.94, deltaELBO=43.474 (0.00271336%), Factors=10
Iteration 37: time=0.11, Factors=10
Iteration 38: time=0.19, Factors=10
Iteration 39: time=0.14, Factors=10
Iteration 40: time=0.23, Factors=10
Iteration 41: time=0.19, ELBO=-237395.76, deltaELBO=39.184 (0.00244559%), Factors=10
Iteration 42: time=0.12, Factors=10
Iteration 43: time=0.17, Factors=10
Iteration 44: time=0.15, Factors=10
Iteration 45: time=0.13, Factors=10
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Converged!
#######################
## Training finished ##
#######################
Saving model in /tmp/RtmpNBWUGX/model.hdf5...
Quitting from lines 213-215 (getting_started_R.Rmd)
Error: processing vignette 'getting_started_R.Rmd' failed with diagnostics:
AttributeError: module 'numpy' has no attribute 'float'
--- failed re-building ‘getting_started_R.Rmd’
SUMMARY: processing the following file failed:
‘getting_started_R.Rmd’
Error: Vignette re-building failed.
Execution halted
* checking PDF version of manual ... OK
* DONE
Status: 2 ERRORs, 3 NOTEs
See
‘/home/biocbuild/bbs-3.17-bioc/meat/MOFA2.Rcheck/00check.log’
for details.
MOFA2.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL MOFA2 ### ############################################################################## ############################################################################## * installing to library ‘/home/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.fail
R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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(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 1 | WARN 7 | SKIP 0 | PASS 25 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_plot.R:18'): plot data scatter ───────────────────────────────
`p <- plot_data_scatter(test_mofa2, view = 1, factor = 1)` produced warnings.
[ FAIL 1 | WARN 7 | SKIP 0 | PASS 25 ]
Error: Test failures
Execution halted
MOFA2.Rcheck/MOFA2-Ex.timings
| name | user | system | elapsed | |
| add_mofa_factors_to_seurat | 0.007 | 0.000 | 0.020 | |
| calculate_contribution_scores | 0.267 | 0.008 | 0.480 | |
| calculate_variance_explained | 2.195 | 0.112 | 2.428 | |
| calculate_variance_explained_per_sample | 0.754 | 0.023 | 0.870 | |
| cluster_samples | 0.219 | 0.004 | 0.237 | |
| compare_elbo | 0.430 | 0.012 | 0.442 | |
| compare_factors | 0.490 | 0.004 | 0.581 | |
| covariates_names | 0.298 | 0.008 | 0.343 | |
| create_mofa | 1.168 | 0.020 | 1.338 | |
| create_mofa_from_df | 0.659 | 0.004 | 0.696 | |
| create_mofa_from_matrix | 0.014 | 0.000 | 0.014 | |
| factors_names | 0.225 | 0.000 | 0.225 | |
| features_metadata | 0.227 | 0.012 | 0.247 | |
| features_names | 0.232 | 0.008 | 0.258 | |
| get_covariates | 0.271 | 0.004 | 0.316 | |
| get_data | 1.122 | 0.004 | 1.413 | |
| get_default_data_options | 1.142 | 0.003 | 1.213 | |
| get_default_mefisto_options | 0.169 | 0.004 | 0.181 | |
| get_default_model_options | 0.657 | 0.004 | 0.662 | |
| get_default_stochastic_options | 0.678 | 0.002 | 0.682 | |
| get_default_training_options | 0.657 | 0.003 | 0.660 | |
| get_dimensions | 0.215 | 0.001 | 0.237 | |
| get_elbo | 0.224 | 0.008 | 0.295 | |
| get_expectations | 0.209 | 0.012 | 0.221 | |
| get_factors | 0.222 | 0.000 | 0.222 | |
| get_imputed_data | 0.228 | 0.012 | 0.239 | |
| get_lengthscales | 0.282 | 0.004 | 0.318 | |
| get_scales | 0.263 | 0.008 | 0.273 | |
| get_variance_explained | 0.211 | 0.008 | 0.221 | |
| get_weights | 0.241 | 0.012 | 0.287 | |
| groups_names | 0.221 | 0.000 | 0.251 | |
| impute | 0.248 | 0.004 | 0.253 | |
| interpolate_factors | 0.311 | 0.004 | 0.363 | |
| load_model | 0.214 | 0.008 | 0.266 | |
| make_example_data | 0.003 | 0.000 | 0.019 | |
| plot_ascii_data | 0.222 | 0.000 | 0.222 | |
| plot_data_heatmap | 0.286 | 0.004 | 0.293 | |
| plot_data_overview | 0.428 | 0.008 | 0.464 | |
| plot_data_scatter | 1.891 | 0.024 | 2.167 | |
| plot_data_vs_cov | 0.673 | 0.004 | 0.730 | |
| plot_dimred | 4.014 | 0.032 | 4.659 | |
| plot_factor | 1.647 | 0.008 | 1.877 | |
| plot_factor_cor | 0.243 | 0.000 | 0.335 | |
| plot_factors | 0.758 | 0.008 | 0.799 | |
| plot_factors_vs_cov | 0.660 | 0.004 | 0.840 | |
| plot_group_kernel | 0.483 | 0.004 | 0.503 | |
| plot_interpolation_vs_covariate | 0.753 | 0.008 | 0.969 | |
| plot_smoothness | 0.290 | 0.004 | 0.297 | |
| plot_top_weights | 1.021 | 0.016 | 1.380 | |
| plot_variance_explained | 2.043 | 0.004 | 2.100 | |
| plot_variance_explained_by_covariates | 1.449 | 0.008 | 1.670 | |
| plot_variance_explained_per_feature | 0.449 | 0.012 | 0.478 | |
| plot_weights | 2.817 | 0.000 | 3.082 | |
| plot_weights_heatmap | 0.480 | 0.004 | 0.491 | |
| plot_weights_scatter | 0.424 | 0.020 | 0.448 | |
| predict | 0.230 | 0.012 | 0.242 | |
| prepare_mofa | 0.665 | 0.008 | 0.819 | |
| run_mofa | 0.703 | 0.008 | 0.808 | |
| run_tsne | 0.227 | 0.000 | 0.246 | |
| run_umap | 0.218 | 0.000 | 0.244 | |
| samples_metadata | 0.213 | 0.000 | 0.213 | |
| samples_names | 0.206 | 0.005 | 0.211 | |
| set_covariates | 0.050 | 0.002 | 0.052 | |
| subset_factors | 0.286 | 0.004 | 0.482 | |
| subset_groups | 0.234 | 0.000 | 0.234 | |
| subset_samples | 0.232 | 0.008 | 0.240 | |
| subset_views | 0.216 | 0.008 | 0.225 | |
| views_names | 0.222 | 0.000 | 0.224 | |