Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:04 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 2139/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
tidybulk 1.18.0 (landing page) Stefano Mangiola
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the tidybulk package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/tidybulk.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: tidybulk |
Version: 1.18.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:tidybulk.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings tidybulk_1.18.0.tar.gz |
StartedAt: 2024-12-20 06:08:16 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 06:17:34 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 557.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: tidybulk.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:tidybulk.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings tidybulk_1.18.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/tidybulk.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘tidybulk/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘tidybulk’ version ‘1.18.0’ * 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 ‘tidybulk’ can be installed ... OK * 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 loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... 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 .adjust_abundance_se: no visible binding for global variable ‘x’ .aggregate_duplicates_se: no visible binding for global variable ‘group_name’ .aggregate_duplicates_se: no visible binding for global variable ‘group’ .deconvolve_cellularity_se: no visible binding for global variable ‘X_cibersort’ .describe_transcript_SE: no visible binding for global variable ‘transcript’ .describe_transcript_SE: no visible binding for global variable ‘description’ .identify_abundant: no visible binding for global variable ‘.abundant’ .keep_abundant: no visible binding for global variable ‘.abundant’ .pivot_sample: no visible binding for global variable ‘.’ .quantile_normalise_abundance: no visible binding for global variable ‘x’ .quantile_normalise_abundance_se: no visible binding for global variable ‘x’ .resolve_complete_confounders_of_non_interest: no visible global function definition for ‘combn’ .scale_abundance: no visible binding for global variable ‘x’ .scale_abundance: no visible binding for global variable ‘multiplier’ .scale_abundance_se: no visible binding for global variable ‘x’ .test_differential_abundance_se: no visible binding for global variable ‘.contrasts’ .test_differential_abundance_se: no visible binding for global variable ‘action’ .test_differential_cellularity: no visible binding for global variable ‘X_cibersort’ .test_differential_cellularity_se: no visible binding for global variable ‘X_cibersort’ .test_differential_cellularity_se: no visible binding for global variable ‘cell_type’ .test_differential_cellularity_se: no visible binding for global variable ‘prop’ .test_differential_cellularity_se: no visible binding for global variable ‘.cell_type’ .test_gene_enrichment_SE: no visible global function definition for ‘buildCustomIdx’ .test_gene_enrichment_SE: no visible global function definition for ‘buildIdx’ .test_gene_enrichment_SE: no visible global function definition for ‘egsea’ .test_gene_enrichment_SE: no visible binding for global variable ‘pathway’ .test_gene_enrichment_SE: no visible binding for global variable ‘data_base’ .test_gene_enrichment_SE: no visible binding for global variable ‘web_page’ .test_gene_overrepresentation: no visible binding for global variable ‘my_do_test’ .test_gene_overrepresentation_SE: no visible binding for global variable ‘my_do_test’ .test_gene_rank: no visible global function definition for ‘with_groups’ .test_gene_rank: no visible global function definition for ‘desc’ .test_gene_rank_SE: no visible global function definition for ‘desc’ .test_stratification_cellularity: no visible binding for global variable ‘X_cibersort’ .test_stratification_cellularity_SE: no visible binding for global variable ‘X_cibersort’ .test_stratification_cellularity_SE: no visible binding for global variable ‘.cell_type’ add_scaled_counts_bulk.calcNormFactor: no visible binding for global variable ‘transcript’ aggregate_duplicated_transcripts_DT: no visible binding for global variable ‘.abundance_scaled’ aggregate_duplicated_transcripts_bulk: no visible binding for global variable ‘.abundance_scaled’ aggregate_duplicated_transcripts_bulk: no visible binding for global variable ‘n_aggr’ aggregate_duplicated_transcripts_bulk: no visible global function definition for ‘where’ as_matrix: no visible binding for global variable ‘variable’ call_core: no visible binding for global variable ‘nulldist’ change_reserved_column_names: no visible binding for global variable ‘.’ check_if_duplicated_genes: no visible binding for global variable ‘transcript’ check_if_duplicated_genes: no visible binding for global variable ‘read count’ counts_scaled_exist_SE: no visible binding for global variable ‘tt_columns’ counts_scaled_exist_SE: no visible binding for global variable ‘.’ create_tt_from_bam_sam_bulk: no visible binding for global variable ‘.’ create_tt_from_bam_sam_bulk: no visible binding for global variable ‘temp’ create_tt_from_bam_sam_bulk: no visible binding for global variable ‘Status’ create_tt_from_bam_sam_bulk: no visible binding for global variable ‘counts’ create_tt_from_bam_sam_bulk: no visible binding for global variable ‘GeneID’ create_tt_from_bam_sam_bulk: no visible binding for global variable ‘genes’ create_tt_from_bam_sam_bulk: no visible binding for global variable ‘samples’ create_tt_from_bam_sam_bulk: no visible binding for global variable ‘transcript’ eliminate_sparse_transcripts: no visible global function definition for ‘add_count’ eliminate_sparse_transcripts: no visible binding for global variable ‘my_n’ entrez_over_to_gsea: no visible binding for global variable ‘gs_cat’ entrez_over_to_gsea: no visible binding for global variable ‘test’ entrez_over_to_gsea: no visible binding for global variable ‘geneID’ entrez_rank_to_gsea: no visible binding for global variable ‘gs_cat’ entrez_rank_to_gsea: no visible binding for global variable ‘.’ entrez_rank_to_gsea: no visible binding for global variable ‘entrez_gene’ entrez_rank_to_gsea: no visible binding for global variable ‘fit’ error_if_duplicated_genes: no visible binding for global variable ‘transcript’ error_if_duplicated_genes: no visible binding for global variable ‘read count’ error_if_duplicated_genes: no visible global function definition for ‘desc’ error_if_log_transformed: no visible binding for global variable ‘m’ fill_NA_matrix_with_factor_colwise: no visible binding for global variable ‘.’ fill_NA_using_formula: no visible binding for global variable ‘NUL’ fill_NA_using_formula: no visible binding for global variable ‘ct_data’ fill_NA_using_formula: no visible binding for global variable ‘library_size__’ fill_NA_using_formula: no visible binding for global variable ‘cov_data’ filter_genes_on_condition: no visible binding for global variable ‘.feature’ get_abundance_norm_if_exists: no visible binding for global variable ‘.abundance_scaled’ get_adjusted_counts_for_unwanted_variation_bulk: no visible binding for global variable ‘.’ get_adjusted_counts_for_unwanted_variation_bulk: no visible global function definition for ‘all_of’ get_assay_scaled_if_exists_SE: no visible binding for global variable ‘tt_columns’ get_assay_scaled_if_exists_SE: no visible binding for global variable ‘.abundance_scaled’ get_cell_type_proportions: no visible binding for global variable ‘.’ get_clusters_SNN_bulk: no visible binding for global variable ‘seurat_clusters’ get_clusters_SNN_bulk_SE: no visible binding for global variable ‘.’ get_clusters_SNN_bulk_SE: no visible binding for global variable ‘seurat_clusters’ get_clusters_kmeans_bulk: no visible binding for global variable ‘.’ get_clusters_kmeans_bulk: no visible binding for global variable ‘cluster’ get_clusters_kmeans_bulk: no visible binding for global variable ‘cluster kmeans’ get_clusters_kmeans_bulk_SE: no visible binding for global variable ‘.’ get_clusters_kmeans_bulk_SE: no visible binding for global variable ‘cluster’ get_differential_transcript_abundance_bulk: no visible binding for global variable ‘.’ get_differential_transcript_abundance_bulk_SE: no visible binding for global variable ‘.’ get_differential_transcript_abundance_bulk_voom: no visible binding for global variable ‘.’ get_differential_transcript_abundance_bulk_voom_SE: no visible binding for global variable ‘.’ get_differential_transcript_abundance_deseq2: no visible binding for global variable ‘counts’ get_differential_transcript_abundance_deseq2: no visible binding for global variable ‘.’ get_differential_transcript_abundance_deseq2_SE: no visible binding for global variable ‘.’ get_differential_transcript_abundance_glmmSeq: no visible binding for global variable ‘tagwise.dispersion’ get_differential_transcript_abundance_glmmSeq: no visible binding for global variable ‘.’ get_differential_transcript_abundance_glmmSeq_SE: no visible binding for global variable ‘tagwise.dispersion’ get_differential_transcript_abundance_glmmSeq_SE: no visible binding for global variable ‘.’ get_reduced_dimensions_MDS_bulk: no visible binding for global variable ‘Component’ get_reduced_dimensions_MDS_bulk: no visible binding for global variable ‘Component value’ get_reduced_dimensions_MDS_bulk_SE: no visible binding for global variable ‘Component’ get_reduced_dimensions_MDS_bulk_SE: no visible binding for global variable ‘Component value’ get_reduced_dimensions_PCA_bulk: no visible binding for global variable ‘sdev’ get_reduced_dimensions_PCA_bulk: no visible binding for global variable ‘name’ get_reduced_dimensions_PCA_bulk: no visible binding for global variable ‘value’ get_reduced_dimensions_PCA_bulk: no visible binding for global variable ‘x’ get_reduced_dimensions_PCA_bulk_SE: no visible binding for global variable ‘sdev’ get_reduced_dimensions_PCA_bulk_SE: no visible binding for global variable ‘name’ get_reduced_dimensions_PCA_bulk_SE: no visible binding for global variable ‘value’ get_reduced_dimensions_PCA_bulk_SE: no visible binding for global variable ‘x’ get_reduced_dimensions_TSNE_bulk: no visible binding for global variable ‘Y’ get_reduced_dimensions_TSNE_bulk_SE: no visible binding for global variable ‘Y’ get_reduced_dimensions_UMAP_bulk_SE: no visible binding for global variable ‘x’ get_rotated_dimensions: no visible binding for global variable ‘value’ get_rotated_dimensions: no visible binding for global variable ‘rotated dimensions’ get_scaled_counts_bulk: no visible binding for global variable ‘med’ get_scaled_counts_bulk: no visible binding for global variable ‘tot_filt’ get_scaled_counts_bulk: no visible binding for global variable ‘nf’ get_scaled_counts_bulk: no visible binding for global variable ‘.’ get_scaled_counts_bulk: no visible binding for global variable ‘tot’ get_symbol_from_ensembl: no visible binding for global variable ‘ensembl_id’ get_symbol_from_ensembl: no visible binding for global variable ‘transcript’ get_symbol_from_ensembl: no visible binding for global variable ‘ref_genome’ get_tt_columns: no visible binding for global variable ‘tt_columns’ glmerCore: no visible global function definition for ‘coef’ glmerCore: no visible global function definition for ‘vcov’ glmerCore: no visible global function definition for ‘AIC’ glmerCore: no visible global function definition for ‘logLik’ glmerCore: no visible global function definition for ‘anova’ glmerCore: no visible global function definition for ‘predict’ glmmSeq: no visible global function definition for ‘update.formula’ glmmTMB_to_confidence_intervals_random_effects: no visible binding for global variable ‘group_id’ glmmTMB_to_confidence_intervals_random_effects: no visible binding for global variable ‘parameter’ glmmTMB_to_confidence_intervals_random_effects: no visible binding for global variable ‘CI’ glmmTMB_to_confidence_intervals_random_effects: no visible binding for global variable ‘lower’ glmmTMB_to_confidence_intervals_random_effects: no visible binding for global variable ‘upper’ glmmTMBcore: no visible global function definition for ‘coef’ glmmTMBcore: no visible global function definition for ‘vcov’ glmmTMBcore: no visible global function definition for ‘AIC’ glmmTMBcore: no visible global function definition for ‘logLik’ glmmTMBcore: no visible global function definition for ‘anova’ glmmTMBcore: no visible global function definition for ‘predict’ initialise_tt_internals: no visible binding for global variable ‘.’ lmer_to_confidence_intervals_random_effects: no visible binding for global variable ‘group_id’ lmer_to_confidence_intervals_random_effects: no visible binding for global variable ‘parameter’ lmer_to_confidence_intervals_random_effects: no visible binding for global variable ‘CI’ lmer_to_confidence_intervals_random_effects: no visible binding for global variable ‘lower’ lmer_to_confidence_intervals_random_effects: no visible binding for global variable ‘upper’ memorise_methods_used: no visible binding for global variable ‘.’ multivariable_differential_tissue_composition: no visible binding for global variable ‘.’ multivariable_differential_tissue_composition: no visible binding for global variable ‘.cell_type’ multivariable_differential_tissue_composition: no visible binding for global variable ‘term’ multivariable_differential_tissue_composition_SE: no visible binding for global variable ‘.’ multivariable_differential_tissue_composition_SE: no visible binding for global variable ‘.cell_type’ multivariable_differential_tissue_composition_SE: no visible binding for global variable ‘term’ remove_redundancy_elements_though_reduced_dimensions: no visible binding for global variable ‘sample b’ remove_redundancy_elements_though_reduced_dimensions: no visible binding for global variable ‘sample a’ remove_redundancy_elements_though_reduced_dimensions: no visible binding for global variable ‘sample 1’ remove_redundancy_elements_though_reduced_dimensions: no visible binding for global variable ‘sample 2’ remove_redundancy_elements_though_reduced_dimensions_SE: no visible binding for global variable ‘sample b’ remove_redundancy_elements_though_reduced_dimensions_SE: no visible binding for global variable ‘sample a’ remove_redundancy_elements_though_reduced_dimensions_SE: no visible binding for global variable ‘sample 1’ remove_redundancy_elements_though_reduced_dimensions_SE: no visible binding for global variable ‘sample 2’ remove_redundancy_elements_through_correlation: no visible binding for global variable ‘rc’ remove_redundancy_elements_through_correlation: no visible binding for global variable ‘transcript’ remove_redundancy_elements_through_correlation: no visible binding for global variable ‘correlation’ remove_redundancy_elements_through_correlation: no visible binding for global variable ‘item1’ remove_redundancy_elements_through_correlation_SE: no visible binding for global variable ‘abundance’ remove_redundancy_elements_through_correlation_SE: no visible binding for global variable ‘transcript’ remove_redundancy_elements_through_correlation_SE: no visible binding for global variable ‘element’ remove_redundancy_elements_through_correlation_SE: no visible binding for global variable ‘feature’ remove_redundancy_elements_through_correlation_SE: no visible binding for global variable ‘rc’ remove_redundancy_elements_through_correlation_SE: no visible binding for global variable ‘correlation’ remove_redundancy_elements_through_correlation_SE: no visible binding for global variable ‘item1’ resolve_complete_confounders_of_non_interest_pair_SE: no visible binding for global variable ‘rowid’ resolve_complete_confounders_of_non_interest_pair_SE: no visible global function definition for ‘desc’ resolve_complete_confounders_of_non_interest_pair_SE: no visible binding for global variable ‘n1’ resolve_complete_confounders_of_non_interest_pair_SE: no visible binding for global variable ‘n2’ resolve_complete_confounders_of_non_interest_pair_SE: no visible binding for global variable ‘se_data’ resolve_complete_confounders_of_non_interest_pair_SE: no visible global function definition for ‘DataFrame’ rowwise.tidybulk: no visible binding for global variable ‘.data’ run_epic: no visible global function definition for ‘EPIC’ run_llsr: no visible binding for global variable ‘X_cibersort’ scale_design: no visible binding for global variable ‘value’ scale_design: no visible binding for global variable ‘sample_idx’ scale_design: no visible binding for global variable ‘(Intercept)’ select_closest_pairs: no visible binding for global variable ‘sample 1’ select_closest_pairs: no visible binding for global variable ‘sample 2’ subset_tibble_output: no visible binding for global variable ‘.’ symbol_to_entrez: no visible binding for global variable ‘transcript_upper’ symbol_to_entrez: no visible binding for global variable ‘entrez’ test_differential_cellularity: no visible binding for global variable ‘X_cibersort’ test_differential_cellularity_: no visible binding for global variable ‘cell_type’ test_differential_cellularity_: no visible binding for global variable ‘prop’ test_differential_cellularity_: no visible binding for global variable ‘.’ test_differential_cellularity_: no visible binding for global variable ‘.cell_type’ test_gene_enrichment_bulk_EGSEA: no visible global function definition for ‘buildCustomIdx’ test_gene_enrichment_bulk_EGSEA: no visible global function definition for ‘buildIdx’ test_gene_enrichment_bulk_EGSEA: no visible binding for global variable ‘pathway’ test_gene_enrichment_bulk_EGSEA: no visible binding for global variable ‘data_base’ test_gene_enrichment_bulk_EGSEA: no visible binding for global variable ‘web_page’ test_gene_enrichment_bulk_EGSEA: no visible global function definition for ‘egsea’ test_stratification_cellularity: no visible binding for global variable ‘X_cibersort’ test_stratification_cellularity_: no visible binding for global variable ‘.cell_type’ tidybulk_to_SummarizedExperiment: no visible binding for global variable ‘.’ univariable_differential_tissue_composition: no visible binding for global variable ‘.proportion’ univariable_differential_tissue_composition: no visible binding for global variable ‘.cell_type’ univariable_differential_tissue_composition: no visible binding for global variable ‘cell_type_proportions’ univariable_differential_tissue_composition: no visible binding for global variable ‘surv_test’ univariable_differential_tissue_composition_SE: no visible binding for global variable ‘.proportion’ univariable_differential_tissue_composition_SE: no visible binding for global variable ‘.cell_type’ univariable_differential_tissue_composition_SE: no visible binding for global variable ‘cell_type_proportions’ univariable_differential_tissue_composition_SE: no visible binding for global variable ‘surv_test’ univariable_differential_tissue_stratification: no visible binding for global variable ‘.cell_type’ univariable_differential_tissue_stratification: no visible binding for global variable ‘cell_type_proportions’ univariable_differential_tissue_stratification: no visible binding for global variable ‘surv_test’ univariable_differential_tissue_stratification_SE: no visible binding for global variable ‘.cell_type’ univariable_differential_tissue_stratification_SE: no visible binding for global variable ‘cell_type_proportions’ univariable_differential_tissue_stratification_SE: no visible binding for global variable ‘surv_test’ adjust_abundance,RangedSummarizedExperiment: no visible binding for global variable ‘x’ adjust_abundance,SummarizedExperiment: no visible binding for global variable ‘x’ aggregate_duplicates,RangedSummarizedExperiment: no visible binding for global variable ‘group_name’ aggregate_duplicates,RangedSummarizedExperiment: no visible binding for global variable ‘group’ aggregate_duplicates,SummarizedExperiment: no visible binding for global variable ‘group_name’ aggregate_duplicates,SummarizedExperiment: no visible binding for global variable ‘group’ describe_transcript,RangedSummarizedExperiment: no visible binding for global variable ‘transcript’ describe_transcript,RangedSummarizedExperiment: no visible binding for global variable ‘description’ describe_transcript,SummarizedExperiment: no visible binding for global variable ‘transcript’ describe_transcript,SummarizedExperiment: no visible binding for global variable ‘description’ identify_abundant,spec_tbl_df: no visible binding for global variable ‘.abundant’ identify_abundant,tbl_df: no visible binding for global variable ‘.abundant’ identify_abundant,tidybulk: no visible binding for global variable ‘.abundant’ keep_abundant,spec_tbl_df: no visible binding for global variable ‘.abundant’ keep_abundant,tbl_df: no visible binding for global variable ‘.abundant’ keep_abundant,tidybulk: no visible binding for global variable ‘.abundant’ pivot_sample,RangedSummarizedExperiment: no visible binding for global variable ‘.’ pivot_sample,SummarizedExperiment: no visible binding for global variable ‘.’ quantile_normalise_abundance,RangedSummarizedExperiment: no visible binding for global variable ‘x’ quantile_normalise_abundance,SummarizedExperiment: no visible binding for global variable ‘x’ quantile_normalise_abundance,spec_tbl_df: no visible binding for global variable ‘x’ quantile_normalise_abundance,tbl_df: no visible binding for global variable ‘x’ quantile_normalise_abundance,tidybulk: no visible binding for global variable ‘x’ resolve_complete_confounders_of_non_interest,RangedSummarizedExperiment: no visible global function definition for ‘combn’ resolve_complete_confounders_of_non_interest,SummarizedExperiment: no visible global function definition for ‘combn’ scale_abundance,RangedSummarizedExperiment: no visible binding for global variable ‘x’ scale_abundance,SummarizedExperiment: no visible binding for global variable ‘x’ scale_abundance,spec_tbl_df: no visible binding for global variable ‘x’ scale_abundance,spec_tbl_df: no visible binding for global variable ‘multiplier’ scale_abundance,tbl_df: no visible binding for global variable ‘x’ scale_abundance,tbl_df: no visible binding for global variable ‘multiplier’ scale_abundance,tidybulk: no visible binding for global variable ‘x’ scale_abundance,tidybulk: no visible binding for global variable ‘multiplier’ test_differential_cellularity,RangedSummarizedExperiment: no visible binding for global variable ‘X_cibersort’ test_differential_cellularity,RangedSummarizedExperiment: no visible binding for global variable ‘cell_type’ test_differential_cellularity,RangedSummarizedExperiment: no visible binding for global variable ‘prop’ test_differential_cellularity,RangedSummarizedExperiment: no visible binding for global variable ‘.cell_type’ test_differential_cellularity,SummarizedExperiment: no visible binding for global variable ‘X_cibersort’ test_differential_cellularity,SummarizedExperiment: no visible binding for global variable ‘cell_type’ test_differential_cellularity,SummarizedExperiment: no visible binding for global variable ‘prop’ test_differential_cellularity,SummarizedExperiment: no visible binding for global variable ‘.cell_type’ test_differential_cellularity,spec_tbl_df: no visible binding for global variable ‘X_cibersort’ test_differential_cellularity,tbl_df: no visible binding for global variable ‘X_cibersort’ test_differential_cellularity,tidybulk: no visible binding for global variable ‘X_cibersort’ test_gene_enrichment,RangedSummarizedExperiment: no visible global function definition for ‘buildCustomIdx’ test_gene_enrichment,RangedSummarizedExperiment: no visible global function definition for ‘buildIdx’ test_gene_enrichment,RangedSummarizedExperiment: no visible global function definition for ‘egsea’ test_gene_enrichment,RangedSummarizedExperiment: no visible binding for global variable ‘pathway’ test_gene_enrichment,RangedSummarizedExperiment: no visible binding for global variable ‘data_base’ test_gene_enrichment,RangedSummarizedExperiment: no visible binding for global variable ‘web_page’ test_gene_enrichment,SummarizedExperiment: no visible global function definition for ‘buildCustomIdx’ test_gene_enrichment,SummarizedExperiment: no visible global function definition for ‘buildIdx’ test_gene_enrichment,SummarizedExperiment: no visible global function definition for ‘egsea’ test_gene_enrichment,SummarizedExperiment: no visible binding for global variable ‘pathway’ test_gene_enrichment,SummarizedExperiment: no visible binding for global variable ‘data_base’ test_gene_enrichment,SummarizedExperiment: no visible binding for global variable ‘web_page’ test_gene_overrepresentation,RangedSummarizedExperiment: no visible binding for global variable ‘my_do_test’ test_gene_overrepresentation,SummarizedExperiment: no visible binding for global variable ‘my_do_test’ test_gene_overrepresentation,spec_tbl_df: no visible binding for global variable ‘my_do_test’ test_gene_overrepresentation,tbl_df: no visible binding for global variable ‘my_do_test’ test_gene_overrepresentation,tidybulk: no visible binding for global variable ‘my_do_test’ test_gene_rank,RangedSummarizedExperiment: no visible global function definition for ‘desc’ test_gene_rank,SummarizedExperiment: no visible global function definition for ‘desc’ test_gene_rank,spec_tbl_df: no visible global function definition for ‘with_groups’ test_gene_rank,spec_tbl_df: no visible global function definition for ‘desc’ test_gene_rank,tbl_df: no visible global function definition for ‘with_groups’ test_gene_rank,tbl_df: no visible global function definition for ‘desc’ test_gene_rank,tidybulk: no visible global function definition for ‘with_groups’ test_gene_rank,tidybulk: no visible global function definition for ‘desc’ test_stratification_cellularity,RangedSummarizedExperiment: no visible binding for global variable ‘X_cibersort’ test_stratification_cellularity,RangedSummarizedExperiment: no visible binding for global variable ‘.cell_type’ test_stratification_cellularity,SummarizedExperiment: no visible binding for global variable ‘X_cibersort’ test_stratification_cellularity,SummarizedExperiment: no visible binding for global variable ‘.cell_type’ test_stratification_cellularity,spec_tbl_df: no visible binding for global variable ‘X_cibersort’ test_stratification_cellularity,tbl_df: no visible binding for global variable ‘X_cibersort’ test_stratification_cellularity,tidybulk: no visible binding for global variable ‘X_cibersort’ Undefined global functions or variables: (Intercept) . .abundance_scaled .abundant .cell_type .contrasts .data .feature .proportion AIC CI Component Component value DataFrame EPIC GeneID NUL Status X_cibersort Y abundance action add_count all_of anova buildCustomIdx buildIdx cell_type cell_type_proportions cluster cluster kmeans coef combn correlation counts cov_data ct_data data_base desc description egsea element ensembl_id entrez entrez_gene feature fit geneID genes group group_id group_name gs_cat item1 library_size__ logLik lower m med multiplier my_do_test my_n n1 n2 n_aggr name nf nulldist parameter pathway predict prop rc read count ref_genome rotated dimensions rowid sample 1 sample 2 sample a sample b sample_idx samples sdev se_data seurat_clusters surv_test tagwise.dispersion temp term test tot tot_filt transcript transcript_upper tt_columns update.formula upper value variable vcov web_page where with_groups x Consider adding importFrom("base", "sample") importFrom("stats", "AIC", "anova", "coef", "kmeans", "logLik", "predict", "update.formula", "vcov") importFrom("utils", "combn") to your NAMESPACE file. * checking Rd files ... NOTE checkRd: (-1) remove_redundancy-methods.Rd:158-175: Lost braces 158 | select_closest_pairs = function(df) { | ^ checkRd: (-1) remove_redundancy-methods.Rd:161-171: Lost braces 161 | while (df |> nrow() > 0) { | ^ checkRd: (-1) rotate_dimensions-methods.Rd:126-134: Lost braces 126 | rotation = function(m, d) { | ^ * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... NOTE Documented arguments not in \usage in Rd file 'get_reduced_dimensions_UMAP_bulk.Rd': ‘log_transform’ Documented arguments not in \usage in Rd file 'get_reduced_dimensions_UMAP_bulk_SE.Rd': ‘.abundance’ ‘.feature’ ‘.element’ Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed test_differential_abundance-methods 49.330 0.365 49.700 test_differential_cellularity-methods 15.036 0.108 15.144 test_stratification_cellularity-methods 8.249 0.083 8.333 deconvolve_cellularity-methods 6.865 0.061 6.928 adjust_abundance-methods 4.900 0.214 5.113 * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 3 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/tidybulk.Rcheck/00check.log’ for details.
tidybulk.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL tidybulk ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘tidybulk’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Note: wrong number of arguments to 'expm1' Note: wrong number of arguments to 'expm1' Note: wrong number of arguments to 'expm1' Note: wrong number of arguments to 'expm1' Note: wrong number of arguments to 'expm1' Note: wrong number of arguments to 'expm1' Note: wrong number of arguments to 'expm1' Note: wrong number of arguments to 'floor' Note: wrong number of arguments to 'floor' ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (tidybulk)
tidybulk.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu 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(tidybulk) Loading required package: ttservice ======================================== tidybulk version 1.18.0 If you use TIDYBULK in published research, please cite: Mangiola et al. tidybulk: an R tidy framework for modular transcriptomic data analysis. Genome Biology 2021. This message can be suppressed by: suppressPackageStartupMessages(library(tidybulk)) ======================================== Attaching package: 'tidybulk' The following object is masked from 'package:stats': filter > > test_check("tidybulk") Coefficients not estimable: conditionTRUE Coefficients not estimable: conditionTRUE Time difference of 3.751675 secs Time difference of 3.570194 secs Found 2 batches Using null model in ComBat-seq. Adjusting for 1 covariate(s) or covariate level(s) Estimating dispersions Fitting the GLM model Apply shrinkage - computing posterior estimates for parameters Using 100 random genes for Monte Carlo integration Adjusting the data Found 2 batches Using null model in ComBat-seq. Adjusting for 1 covariate(s) or covariate level(s) Estimating dispersions Fitting the GLM model Apply shrinkage - computing posterior estimates for parameters Using 100 random genes for Monte Carlo integration Adjusting the data Found 2 batches Using null model in ComBat-seq. Adjusting for 1 covariate(s) or covariate level(s) Estimating dispersions Fitting the GLM model Apply shrinkage - computing posterior estimates for parameters Using 100 random genes for Monte Carlo integration Adjusting the data Time difference of 9.749014 secs Time difference of 9.011614 secs Performing PCA Read the 251 x 50 data matrix successfully! OpenMP is working. 1 threads. Using no_dims = 2, perplexity = 30.000000, and theta = 0.500000 Computing input similarities... Building tree... Done in 0.02 seconds (sparsity = 0.490437)! Learning embedding... Iteration 50: error is 56.524826 (50 iterations in 0.04 seconds) Iteration 100: error is 56.234503 (50 iterations in 0.04 seconds) Iteration 150: error is 58.141695 (50 iterations in 0.04 seconds) Iteration 200: error is 57.075857 (50 iterations in 0.04 seconds) Iteration 250: error is 56.052760 (50 iterations in 0.04 seconds) Iteration 300: error is 1.009544 (50 iterations in 0.04 seconds) Iteration 350: error is 0.825040 (50 iterations in 0.04 seconds) Iteration 400: error is 0.815341 (50 iterations in 0.03 seconds) Iteration 450: error is 0.805331 (50 iterations in 0.03 seconds) Iteration 500: error is 0.806034 (50 iterations in 0.03 seconds) Iteration 550: error is 0.803248 (50 iterations in 0.03 seconds) Iteration 600: error is 0.801136 (50 iterations in 0.03 seconds) Iteration 650: error is 0.800800 (50 iterations in 0.03 seconds) Iteration 700: error is 0.799081 (50 iterations in 0.03 seconds) Iteration 750: error is 0.798706 (50 iterations in 0.03 seconds) Iteration 800: error is 0.799409 (50 iterations in 0.03 seconds) Iteration 850: error is 0.799236 (50 iterations in 0.03 seconds) Iteration 900: error is 0.799730 (50 iterations in 0.03 seconds) Iteration 950: error is 0.799898 (50 iterations in 0.03 seconds) Iteration 1000: error is 0.800068 (50 iterations in 0.03 seconds) Fitting performed in 0.66 seconds. [ FAIL 0 | WARN 48 | SKIP 4 | PASS 225 ] ══ Skipped tests (4) ═══════════════════════════════════════════════════════════ • empty test (4): 'test-bulk_methods.R:1064:1', 'test-bulk_methods_SummarizedExperiment.R:449:1', 'test-tximeta_GRnges_IRanges.R:3:1', 'test-tximeta_GRnges_IRanges.R:19:1' [ FAIL 0 | WARN 48 | SKIP 4 | PASS 225 ] > > proc.time() user system elapsed 236.512 5.169 241.678
tidybulk.Rcheck/tidybulk-Ex.timings
name | user | system | elapsed | |
adjust_abundance-methods | 4.900 | 0.214 | 5.113 | |
aggregate_duplicates-methods | 0.073 | 0.000 | 0.073 | |
arrange-methods | 0.008 | 0.000 | 0.008 | |
as_matrix | 0.009 | 0.000 | 0.009 | |
bind_rows | 0.225 | 0.024 | 0.250 | |
cluster_elements-methods | 0.051 | 0.009 | 0.060 | |
deconvolve_cellularity-methods | 6.865 | 0.061 | 6.928 | |
describe_transcript-methods | 1.098 | 0.108 | 1.206 | |
distinct-methods | 0.081 | 0.018 | 0.099 | |
dplyr-methods | 0.201 | 0.027 | 0.228 | |
ensembl_to_symbol-methods | 0.674 | 0.019 | 0.693 | |
fill_missing_abundance-methods | 0 | 0 | 0 | |
filter-methods | 0.231 | 0.004 | 0.235 | |
get_bibliography-methods | 0.002 | 0.000 | 0.002 | |
group_by-methods | 0.003 | 0.000 | 0.003 | |
identify_abundant-methods | 0.010 | 0.001 | 0.012 | |
impute_missing_abundance-methods | 0.06 | 0.00 | 0.06 | |
join-methods | 1.180 | 0.090 | 1.269 | |
keep_abundant-methods | 0.029 | 0.001 | 0.030 | |
keep_variable-methods | 0.028 | 0.002 | 0.029 | |
log10_reverse_trans | 0.159 | 0.006 | 0.163 | |
logit_trans | 0.119 | 0.003 | 0.121 | |
mutate-methods | 0.046 | 0.004 | 0.051 | |
nest-methods | 0.357 | 0.027 | 0.384 | |
pivot_sample-methods | 0.024 | 0.000 | 0.025 | |
pivot_transcript-methods | 0.016 | 0.000 | 0.016 | |
quantile_normalise_abundance-methods | 0.023 | 0.000 | 0.023 | |
reduce_dimensions-methods | 0.153 | 0.000 | 0.154 | |
remove_redundancy-methods | 0.317 | 0.005 | 0.323 | |
rename-methods | 0.022 | 0.000 | 0.022 | |
resolve_complete_confounders_of_non_interest-methods | 0 | 0 | 0 | |
rotate_dimensions-methods | 0.124 | 0.000 | 0.123 | |
rowwise-methods | 0.002 | 0.000 | 0.002 | |
scale_abundance-methods | 0.056 | 0.000 | 0.056 | |
summarise-methods | 0.003 | 0.000 | 0.002 | |
symbol_to_entrez | 0.544 | 0.018 | 0.562 | |
test_differential_abundance-methods | 49.330 | 0.365 | 49.700 | |
test_differential_cellularity-methods | 15.036 | 0.108 | 15.144 | |
test_gene_enrichment-methods | 0 | 0 | 0 | |
test_gene_overrepresentation-methods | 0.000 | 0.000 | 0.001 | |
test_gene_rank-methods | 0 | 0 | 0 | |
test_stratification_cellularity-methods | 8.249 | 0.083 | 8.333 | |
tidybulk-methods | 0.072 | 0.001 | 0.073 | |