Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-02-08 01:15:15 -0000 (Wed, 08 Feb 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4164 |
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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 |
############################################################################## ############################################################################## ### ### Running 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 ### ############################################################################## ############################################################################## * 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. ######################################################### ### __ __ ____ ______ ### ### | \/ |/ __ \| ____/\ _ ### ### | \ / | | | | |__ / \ _| |_ ### ### | |\/| | | | | __/ /\ \_ _| ### ### | | | | |__| | | / ____ \|_| ### ### |_| |_|\____/|_|/_/ \_\ ### ### ### ######################################################### 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. 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-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/getting_started_R_files/figure-html/unnamed-chunk-9-1.png" but not available. ######################################################### ### __ __ ____ ______ ### ### | \/ |/ __ \| ____/\ _ ### ### | \ / | | | | |__ / \ _| |_ ### ### | |\/| | | | | __/ /\ \_ _| ### ### | | | | |__| | | / ____ \|_| ### ### |_| |_|\____/|_|/_/ \_\ ### ### ### ######################################################### 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 Iteration 46: time=0.10, ELBO=-237360.34, deltaELBO=35.419 (0.00221065%), Factors=10 Iteration 47: time=0.09, Factors=10 Iteration 48: time=0.08, Factors=10 Iteration 49: time=0.09, Factors=10 Iteration 50: time=0.09, Factors=10 Iteration 51: time=0.33, ELBO=-237328.29, deltaELBO=32.048 (0.00200026%), Factors=10 Iteration 52: time=0.12, Factors=10 Iteration 53: time=0.12, Factors=10 Iteration 54: time=0.14, Factors=10 Iteration 55: time=0.26, Factors=10 Iteration 56: time=0.16, ELBO=-237299.17, deltaELBO=29.115 (0.00181716%), Factors=10 Iteration 57: time=0.11, Factors=10 Iteration 58: time=0.07, Factors=10 Iteration 59: time=0.09, Factors=10 Iteration 60: time=0.08, Factors=10 Iteration 61: time=0.11, ELBO=-237272.58, deltaELBO=26.598 (0.00166010%), Factors=10 Iteration 62: time=0.09, Factors=10 Iteration 63: time=0.09, Factors=10 Iteration 64: time=0.07, Factors=10 Iteration 65: time=0.10, Factors=10 Iteration 66: time=0.12, ELBO=-237248.19, deltaELBO=24.389 (0.00152223%), Factors=10 Iteration 67: time=0.09, Factors=10 Iteration 68: time=0.08, Factors=10 Iteration 69: time=0.09, Factors=10 Iteration 70: time=0.22, Factors=10 Iteration 71: time=0.28, ELBO=-237225.73, deltaELBO=22.454 (0.00140141%), Factors=10 Iteration 72: time=0.09, Factors=10 Iteration 73: time=0.10, Factors=10 Iteration 74: time=0.08, Factors=10 Iteration 75: time=0.09, Factors=10 Iteration 76: time=0.09, ELBO=-237204.92, deltaELBO=20.812 (0.00129895%), Factors=10 Iteration 77: time=0.10, Factors=10 Iteration 78: time=0.10, Factors=10 Iteration 79: time=0.09, Factors=10 Iteration 80: time=0.12, Factors=10 Iteration 81: time=0.10, ELBO=-237185.62, deltaELBO=19.301 (0.00120464%), Factors=10 Iteration 82: time=0.10, Factors=10 Iteration 83: time=0.10, Factors=10 Iteration 84: time=0.10, Factors=10 Iteration 85: time=0.08, Factors=10 Iteration 86: time=0.09, ELBO=-237167.58, deltaELBO=18.038 (0.00112582%), Factors=10 Iteration 87: time=0.13, Factors=10 Iteration 88: time=0.10, Factors=10 Iteration 89: time=0.07, Factors=10 Iteration 90: time=0.08, Factors=10 Iteration 91: time=0.10, ELBO=-237150.65, deltaELBO=16.935 (0.00105695%), Factors=10 Iteration 92: time=0.11, Factors=10 Iteration 93: time=0.08, Factors=10 Iteration 94: time=0.09, Factors=10 Iteration 95: time=0.13, Factors=10 Iteration 96: time=0.08, ELBO=-237134.74, deltaELBO=15.912 (0.00099310%), Factors=10 Iteration 97: time=0.06, Factors=10 Iteration 98: time=0.05, Factors=10 Iteration 99: time=0.05, Factors=10 Iteration 100: time=0.08, Factors=10 Iteration 101: time=0.10, ELBO=-237119.68, deltaELBO=15.055 (0.00093961%), Factors=10 Iteration 102: time=0.09, Factors=10 Iteration 103: time=0.08, Factors=10 Iteration 104: time=0.05, Factors=10 Iteration 105: time=0.04, Factors=10 Iteration 106: time=0.05, ELBO=-237105.47, deltaELBO=14.214 (0.00088716%), Factors=10 Iteration 107: time=0.05, Factors=10 Iteration 108: time=0.04, Factors=10 Iteration 109: time=0.04, Factors=10 Iteration 110: time=0.04, Factors=10 Iteration 111: time=0.05, ELBO=-237091.95, deltaELBO=13.516 (0.00084360%), Factors=10 Iteration 112: time=0.05, Factors=10 Iteration 113: time=0.08, Factors=10 Iteration 114: time=0.10, Factors=10 Iteration 115: time=0.16, Factors=10 Iteration 116: time=0.14, ELBO=-237079.07, deltaELBO=12.886 (0.00080424%), Factors=10 Iteration 117: time=0.12, Factors=10 Iteration 118: time=0.09, Factors=10 Iteration 119: time=0.07, Factors=10 Iteration 120: time=0.06, Factors=10 Iteration 121: time=0.05, ELBO=-237066.81, deltaELBO=12.255 (0.00076487%), Factors=10 Iteration 122: time=0.05, Factors=10 Iteration 123: time=0.04, Factors=10 Iteration 124: time=0.04, Factors=10 Iteration 125: time=0.04, Factors=10 Iteration 126: time=0.05, ELBO=-237055.06, deltaELBO=11.754 (0.00073363%), Factors=10 Iteration 127: time=0.09, Factors=10 Iteration 128: time=0.17, Factors=10 Iteration 129: time=0.14, Factors=10 Iteration 130: time=0.19, Factors=10 Iteration 131: time=0.16, ELBO=-237043.82, deltaELBO=11.235 (0.00070119%), Factors=10 Iteration 132: time=0.20, Factors=10 Iteration 133: time=0.17, Factors=10 Iteration 134: time=0.14, Factors=10 Iteration 135: time=0.13, Factors=10 Iteration 136: time=0.19, ELBO=-237033.06, deltaELBO=10.767 (0.00067198%), Factors=10 Iteration 137: time=0.09, Factors=10 Iteration 138: time=0.07, Factors=10 Iteration 139: time=0.07, Factors=10 Iteration 140: time=0.07, Factors=10 Iteration 141: time=0.09, ELBO=-237022.63, deltaELBO=10.422 (0.00065048%), 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time=0.04, Factors=10 Iteration 164: time=0.04, Factors=10 Iteration 165: time=0.04, Factors=10 Iteration 166: time=0.09, ELBO=-236975.95, deltaELBO=8.725 (0.00054455%), Factors=10 Iteration 167: time=0.08, Factors=10 Iteration 168: time=0.37, Factors=10 Iteration 169: time=0.09, Factors=10 Iteration 170: time=0.14, Factors=10 Iteration 171: time=0.44, ELBO=-236967.60, deltaELBO=8.350 (0.00052119%), Factors=10 Iteration 172: time=0.15, Factors=10 Iteration 173: time=0.11, Factors=10 Iteration 174: time=0.05, Factors=10 Iteration 175: time=0.05, Factors=10 Iteration 176: time=0.05, ELBO=-236959.48, deltaELBO=8.119 (0.00050673%), Factors=10 Iteration 177: time=0.05, Factors=10 Iteration 178: time=0.05, Factors=10 Iteration 179: time=0.07, Factors=10 Iteration 180: time=1.57, Factors=10 Iteration 181: time=0.20, ELBO=-236951.71, deltaELBO=7.775 (0.00048526%), Factors=10 Iteration 182: time=0.16, Factors=10 Iteration 183: time=0.06, Factors=10 Iteration 184: time=0.05, Factors=10 Iteration 185: time=0.06, Factors=10 Iteration 186: time=0.05, ELBO=-236944.19, deltaELBO=7.523 (0.00046954%), Factors=10 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 | |