Stefano Mangiola
| Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022) |
| git_url: https://git.bioconductor.org/packages/tidybulk |
| git_branch: RELEASE_3_14 |
| git_last_commit: 13706d8 |
| git_last_commit_date: 2021-10-28 23:23:06 -0400 (Thu, 28 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.14 |
|
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 git@git.bioconductor.org: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 |
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###
### 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
###
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* 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
|
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tidybulk.Rcheck/examples_i386/tidybulk-Ex.timings
|
tidybulk.Rcheck/examples_x64/tidybulk-Ex.timings
|