Back to Multiple platform build/check report for BioC 3.14 |
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This page was generated on 2022-04-13 12:07:28 -0400 (Wed, 13 Apr 2022).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
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 tidybulk package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to [email protected]:packages/tidybulk.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 1950/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
tidybulk 1.6.1 (landing page) Stefano Mangiola
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: tidybulk |
Version: 1.6.1 |
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:tidybulk.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings tidybulk_1.6.1.tar.gz |
StartedAt: 2022-04-13 04:01:14 -0400 (Wed, 13 Apr 2022) |
EndedAt: 2022-04-13 04:15:50 -0400 (Wed, 13 Apr 2022) |
EllapsedTime: 876.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: tidybulk.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:tidybulk.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings tidybulk_1.6.1.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/tidybulk.Rcheck' * using R version 4.1.3 (2022-03-10) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'tidybulk/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'tidybulk' version '1.6.1' * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking whether package '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 R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * loading checks for arch 'i386' ** 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 * loading checks for arch 'x64' ** 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 .adjust_abundance_se: no visible binding for global variable '.' .adjust_abundance_se: no visible binding for global variable 'x' .aggregate_duplicates_se: no visible binding for global variable '.' .as_SummarizedExperiment: no visible binding for global variable '.' .cluster_elements_se: no visible binding for global variable '.' .deconvolve_cellularity_se: no visible binding for global variable 'X_cibersort' .deconvolve_cellularity_se: no visible binding for global variable '.' .describe_transcript: no visible binding for global variable '.' .describe_transcript_SE: no visible binding for global variable '.' .describe_transcript_SE: no visible binding for global variable 'transcript' .describe_transcript_SE: no visible binding for global variable 'description' .get_bibliography: no visible binding for global variable '.' .identify_abundant_se: no visible binding for global variable '.' .keep_abundant: no visible binding for global variable '.abundant' .keep_variable_se: no visible binding for global variable '.' .pivot_sample: no visible binding for global variable '.' .pivot_transcript: no visible binding for global variable '.' .reduce_dimensions_se: no visible binding for global variable '.' .rotate_dimensions_se: no visible binding for global variable '.' .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 '.' .scale_abundance_se: no visible binding for global variable 'x' .test_differential_abundance_se: no visible binding for global variable '.' .test_differential_cellularity: no visible binding for global variable 'X_cibersort' .test_differential_cellularity: no visible binding for global variable '.' .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_stratification_cellularity: no visible binding for global variable 'X_cibersort' .test_stratification_cellularity: no visible binding for global variable '.' .test_stratification_cellularity_SE: no visible binding for global variable 'X_cibersort' .test_stratification_cellularity_SE: no visible binding for global variable '.' .test_stratification_cellularity_SE: no visible binding for global variable '.cell_type' .tidybulk_se: no visible binding for global variable '.' .tidybulk_se: no visible binding for global variable 'feature' add_scaled_counts_bulk.calcNormFactor: no visible binding for global variable 'transcript' add_scaled_counts_bulk.get_low_expressed: no visible binding for global variable 'transcript' add_scaled_counts_bulk.get_low_expressed: no visible binding for global variable '.' 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' as_matrix: no visible binding for global variable 'variable' 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 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 '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_log_transformed: no visible binding for global variable 'm' fill_NA_using_formula: no visible binding for global variable 'ct_data' 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_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_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' initialise_tt_internals: no visible binding for global variable '.' 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' 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' symbol_to_entrez: no visible binding for global variable 'transcript_upper' symbol_to_entrez: no visible binding for global variable '.' 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 '.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 global function definition for 'egsea' 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_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 '.' adjust_abundance,RangedSummarizedExperiment: no visible binding for global variable 'x' adjust_abundance,SummarizedExperiment: no visible binding for global variable '.' adjust_abundance,SummarizedExperiment: no visible binding for global variable 'x' aggregate_duplicates,RangedSummarizedExperiment: no visible binding for global variable '.' aggregate_duplicates,SummarizedExperiment: no visible binding for global variable '.' as_SummarizedExperiment,spec_tbl_df: no visible binding for global variable '.' as_SummarizedExperiment,tbl_df: no visible binding for global variable '.' as_SummarizedExperiment,tidybulk: no visible binding for global variable '.' cluster_elements,RangedSummarizedExperiment: no visible binding for global variable '.' cluster_elements,SummarizedExperiment: no visible binding for global variable '.' deconvolve_cellularity,RangedSummarizedExperiment: no visible binding for global variable '.' deconvolve_cellularity,SummarizedExperiment: no visible binding for global variable '.' describe_transcript,RangedSummarizedExperiment: no visible binding for global variable '.' 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 '.' describe_transcript,SummarizedExperiment: no visible binding for global variable 'transcript' describe_transcript,SummarizedExperiment: no visible binding for global variable 'description' describe_transcript,spec_tbl_df: no visible binding for global variable '.' describe_transcript,tbl_df: no visible binding for global variable '.' describe_transcript,tidybulk: no visible binding for global variable '.' get_bibliography,RangedSummarizedExperiment: no visible binding for global variable '.' get_bibliography,SummarizedExperiment: no visible binding for global variable '.' get_bibliography,spec_tbl_df: no visible binding for global variable '.' get_bibliography,tbl: no visible binding for global variable '.' get_bibliography,tbl_df: no visible binding for global variable '.' get_bibliography,tidybulk: no visible binding for global variable '.' identify_abundant,RangedSummarizedExperiment: no visible binding for global variable '.' identify_abundant,SummarizedExperiment: no visible binding for global variable '.' 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' keep_variable,RangedSummarizedExperiment: no visible binding for global variable '.' keep_variable,SummarizedExperiment: no visible binding for global variable '.' pivot_sample,RangedSummarizedExperiment: no visible binding for global variable '.' pivot_sample,SummarizedExperiment: no visible binding for global variable '.' pivot_transcript,RangedSummarizedExperiment: no visible binding for global variable '.' pivot_transcript,SummarizedExperiment: no visible binding for global variable '.' reduce_dimensions,RangedSummarizedExperiment: no visible binding for global variable '.' reduce_dimensions,SummarizedExperiment: no visible binding for global variable '.' rotate_dimensions,RangedSummarizedExperiment: no visible binding for global variable '.' rotate_dimensions,SummarizedExperiment: no visible binding for global variable '.' scale_abundance,RangedSummarizedExperiment: no visible binding for global variable '.' scale_abundance,RangedSummarizedExperiment: no visible binding for global variable 'x' scale_abundance,SummarizedExperiment: no visible binding for global variable '.' 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_abundance,RangedSummarizedExperiment: no visible binding for global variable '.' test_differential_abundance,SummarizedExperiment: no visible binding for global variable '.' 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,spec_tbl_df: no visible binding for global variable '.' test_differential_cellularity,tbl_df: no visible binding for global variable 'X_cibersort' test_differential_cellularity,tbl_df: no visible binding for global variable '.' test_differential_cellularity,tidybulk: no visible binding for global variable 'X_cibersort' test_differential_cellularity,tidybulk: no visible binding for global variable '.' 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_stratification_cellularity,RangedSummarizedExperiment: no visible binding for global variable 'X_cibersort' test_stratification_cellularity,RangedSummarizedExperiment: no visible binding for global variable '.' 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 '.' 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,spec_tbl_df: no visible binding for global variable '.' test_stratification_cellularity,tbl_df: no visible binding for global variable 'X_cibersort' test_stratification_cellularity,tbl_df: no visible binding for global variable '.' test_stratification_cellularity,tidybulk: no visible binding for global variable 'X_cibersort' test_stratification_cellularity,tidybulk: no visible binding for global variable '.' tidybulk,RangedSummarizedExperiment: no visible binding for global variable '.' tidybulk,RangedSummarizedExperiment: no visible binding for global variable 'feature' tidybulk,SummarizedExperiment: no visible binding for global variable '.' tidybulk,SummarizedExperiment: no visible binding for global variable 'feature' Undefined global functions or variables: (Intercept) . .abundance_scaled .abundant .cell_type .feature .proportion Component Component value EPIC GeneID Status X_cibersort Y abundance buildCustomIdx buildIdx cell_type cell_type_proportions cluster cluster kmeans correlation counts cov_data ct_data data_base description egsea element ensembl_id entrez feature fit geneID genes gs_cat item1 m med multiplier my_n n_aggr name nf pathway prop rc read count ref_genome rotated dimensions sample 1 sample 2 sample a sample b sample_idx samples sdev seurat_clusters surv_test temp term test tot tot_filt transcript transcript_upper tt_columns value variable web_page x Consider adding importFrom("base", "sample") importFrom("stats", "kmeans") to your NAMESPACE file. * checking Rd files ... NOTE prepare_Rd: remove_redundancy-methods.Rd:136-138: Dropping empty section \details * 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 ... OK * 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 ... ** running examples for arch 'i386' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed test_differential_cellularity-methods 14.25 0.04 14.43 test_differential_abundance-methods 12.58 0.46 13.03 test_stratification_cellularity-methods 7.57 0.00 7.56 ** running examples for arch 'x64' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed test_differential_cellularity-methods 13.46 0.03 13.5 test_differential_abundance-methods 13.01 0.09 13.1 test_stratification_cellularity-methods 7.98 0.02 8.0 * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'testthat.R' OK ** running tests for arch 'x64' ... Running 'testthat.R' OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See 'C:/Users/biocbuild/bbs-3.14-bioc/meat/tidybulk.Rcheck/00check.log' for details.
tidybulk.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/tidybulk_1.6.1.tar.gz && rm -rf tidybulk.buildbin-libdir && mkdir tidybulk.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=tidybulk.buildbin-libdir tidybulk_1.6.1.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL tidybulk_1.6.1.zip && rm tidybulk_1.6.1.tar.gz tidybulk_1.6.1.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 35 3550k 35 1257k 0 0 1206k 0 0:00:02 0:00:01 0:00:01 1206k 98 3550k 98 3506k 0 0 1717k 0 0:00:02 0:00:02 --:--:-- 1717k 100 3550k 100 3550k 0 0 1733k 0 0:00:02 0:00:02 --:--:-- 1733k install for i386 * 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 'floor' Note: wrong number of arguments to 'floor' ** help *** installing help indices converting help for package 'tidybulk' finding HTML links ... done X_cibersort html adjust_abundance-methods html aggregate_duplicates-methods html arrange-methods html as_SummarizedExperiment-methods html as_matrix html bind-methods html breast_tcga_mini_SE html check_if_counts_is_na html check_if_duplicated_genes html check_if_wrong_input html cluster_elements-methods html counts_SE html counts_ensembl html deconvolve_cellularity-methods html describe_transcript-methods html distinct-methods html dplyr-methods html ensembl_symbol_mapping html ensembl_to_symbol-methods html fill_missing_abundance-methods html filter-methods html flybaseIDs html get_bibliography-methods html get_reduced_dimensions_UMAP_bulk html get_reduced_dimensions_UMAP_bulk_SE html group_by-methods html identify_abundant-methods html impute_missing_abundance-methods html join-methods html keep_abundant-methods html keep_variable-methods html log10_reverse_trans html logit_trans html mutate-methods html nest-methods html pipe html pivot_sample-methods html pivot_transcript-methods html reduce_dimensions-methods html reexports html remove_redundancy-methods html rename-methods html rotate_dimensions-methods html rowwise-methods html scale_abundance-methods html se html se_mini html summarise-methods html symbol_to_entrez html test_deseq2_df html test_differential_abundance-methods html test_differential_cellularity-methods html test_gene_enrichment-methods html test_gene_overrepresentation-methods html test_gene_rank-methods html test_stratification_cellularity-methods html tidybulk-methods html tidybulk_SAM_BAM-methods html vignette_manuscript_signature_boxplot html vignette_manuscript_signature_tsne html vignette_manuscript_signature_tsne2 html *** 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 install for x64 * installing *source* package 'tidybulk' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'tidybulk' as tidybulk_1.6.1.zip * DONE (tidybulk) * installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library' package 'tidybulk' successfully unpacked and MD5 sums checked
tidybulk.Rcheck/tests_i386/testthat.Rout R version 4.1.3 (2022-03-10) -- "One Push-Up" Copyright (C) 2022 The R Foundation for Statistical Computing Platform: i386-w64-mingw32/i386 (32-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(tidybulk) ======================================== tidybulk version 1.6.1 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 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 0.05 seconds (sparsity = 0.490437)! Learning embedding... Iteration 50: error is 55.923458 (50 iterations in 0.05 seconds) Iteration 100: error is 53.433488 (50 iterations in 0.05 seconds) Iteration 150: error is 55.281806 (50 iterations in 0.06 seconds) Iteration 200: error is 54.967648 (50 iterations in 0.05 seconds) Iteration 250: error is 55.971976 (50 iterations in 0.05 seconds) Iteration 300: error is 1.012080 (50 iterations in 0.05 seconds) Iteration 350: error is 0.842669 (50 iterations in 0.05 seconds) Iteration 400: error is 0.806371 (50 iterations in 0.03 seconds) Iteration 450: error is 0.801135 (50 iterations in 0.03 seconds) Iteration 500: error is 0.786040 (50 iterations in 0.05 seconds) Iteration 550: error is 0.781440 (50 iterations in 0.03 seconds) Iteration 600: error is 0.780893 (50 iterations in 0.03 seconds) Iteration 650: error is 0.780526 (50 iterations in 0.05 seconds) Iteration 700: error is 0.779401 (50 iterations in 0.03 seconds) Iteration 750: error is 0.779206 (50 iterations in 0.03 seconds) Iteration 800: error is 0.778141 (50 iterations in 0.05 seconds) Iteration 850: error is 0.777425 (50 iterations in 0.03 seconds) Iteration 900: error is 0.777316 (50 iterations in 0.03 seconds) Iteration 950: error is 0.777144 (50 iterations in 0.03 seconds) Iteration 1000: error is 0.776572 (50 iterations in 0.03 seconds) Fitting performed in 0.80 seconds. [ FAIL 0 | WARN 24 | SKIP 0 | PASS 212 ] [ FAIL 0 | WARN 24 | SKIP 0 | PASS 212 ] > > proc.time() user system elapsed 236.81 19.75 256.65 |
tidybulk.Rcheck/tests_x64/testthat.Rout R version 4.1.3 (2022-03-10) -- "One Push-Up" Copyright (C) 2022 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(testthat) > library(tidybulk) ======================================== tidybulk version 1.6.1 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 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 0.05 seconds (sparsity = 0.490437)! Learning embedding... Iteration 50: error is 55.923458 (50 iterations in 0.03 seconds) Iteration 100: error is 53.433488 (50 iterations in 0.05 seconds) Iteration 150: error is 55.281806 (50 iterations in 0.05 seconds) Iteration 200: error is 54.967648 (50 iterations in 0.05 seconds) Iteration 250: error is 55.971976 (50 iterations in 0.05 seconds) Iteration 300: error is 1.012080 (50 iterations in 0.05 seconds) Iteration 350: error is 0.842669 (50 iterations in 0.03 seconds) Iteration 400: error is 0.806371 (50 iterations in 0.03 seconds) Iteration 450: error is 0.801135 (50 iterations in 0.03 seconds) Iteration 500: error is 0.786040 (50 iterations in 0.03 seconds) Iteration 550: error is 0.781440 (50 iterations in 0.03 seconds) Iteration 600: error is 0.780893 (50 iterations in 0.03 seconds) Iteration 650: error is 0.780526 (50 iterations in 0.03 seconds) Iteration 700: error is 0.779401 (50 iterations in 0.03 seconds) Iteration 750: error is 0.779206 (50 iterations in 0.05 seconds) Iteration 800: error is 0.778141 (50 iterations in 0.03 seconds) Iteration 850: error is 0.777425 (50 iterations in 0.03 seconds) Iteration 900: error is 0.777316 (50 iterations in 0.03 seconds) Iteration 950: error is 0.777144 (50 iterations in 0.03 seconds) Iteration 1000: error is 0.776572 (50 iterations in 0.03 seconds) Fitting performed in 0.72 seconds. [ FAIL 0 | WARN 24 | SKIP 0 | PASS 212 ] [ FAIL 0 | WARN 24 | SKIP 0 | PASS 212 ] > > proc.time() user system elapsed 252.20 4.45 256.75 |
tidybulk.Rcheck/examples_i386/tidybulk-Ex.timings
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tidybulk.Rcheck/examples_x64/tidybulk-Ex.timings
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