Stefano Mangiola
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/tidybulk |
| Branch: RELEASE_3_11 |
| Last Commit: bfa4dd1 |
| Last Changed Date: 2020-06-08 00:40:18 -0400 (Mon, 08 Jun 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:57:56 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE tidybulk PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1797/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| tidybulk 1.0.2 Stefano Mangiola
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | [ OK ] | OK | WARNINGS | NA | |||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |
| Package: tidybulk |
| Version: 1.0.2 |
| Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/tidybulk_1.0.2.tar.gz && rm -rf tidybulk.buildbin-libdir && mkdir tidybulk.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=tidybulk.buildbin-libdir tidybulk_1.0.2.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL tidybulk_1.0.2.zip && rm tidybulk_1.0.2.tar.gz tidybulk_1.0.2.zip |
| StartedAt: 2020-10-16 17:14:23 -0400 (Fri, 16 Oct 2020) |
| EndedAt: 2020-10-16 17:15:58 -0400 (Fri, 16 Oct 2020) |
| EllapsedTime: 95.1 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/tidybulk_1.0.2.tar.gz && rm -rf tidybulk.buildbin-libdir && mkdir tidybulk.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=tidybulk.buildbin-libdir tidybulk_1.0.2.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL tidybulk_1.0.2.zip && rm tidybulk_1.0.2.tar.gz tidybulk_1.0.2.zip
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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
in method for 'tidybulk' with signature '"SummarizedExperiment"': no definition for class "SummarizedExperiment"
in method for 'tidybulk' with signature '"RangedSummarizedExperiment"': no definition for class "RangedSummarizedExperiment"
in method for 'scale_abundance' with signature '"SummarizedExperiment"': no definition for class "SummarizedExperiment"
in method for 'scale_abundance' with signature '"RangedSummarizedExperiment"': no definition for class "RangedSummarizedExperiment"
in method for 'cluster_elements' with signature '"SummarizedExperiment"': no definition for class "SummarizedExperiment"
in method for 'cluster_elements' with signature '"RangedSummarizedExperiment"': no definition for class "RangedSummarizedExperiment"
in method for 'reduce_dimensions' with signature '"SummarizedExperiment"': no definition for class "SummarizedExperiment"
in method for 'reduce_dimensions' with signature '"RangedSummarizedExperiment"': no definition for class "RangedSummarizedExperiment"
in method for 'rotate_dimensions' with signature '"SummarizedExperiment"': no definition for class "SummarizedExperiment"
in method for 'rotate_dimensions' with signature '"RangedSummarizedExperiment"': no definition for class "RangedSummarizedExperiment"
in method for 'remove_redundancy' with signature '"SummarizedExperiment"': no definition for class "SummarizedExperiment"
in method for 'remove_redundancy' with signature '"RangedSummarizedExperiment"': no definition for class "RangedSummarizedExperiment"
in method for 'adjust_abundance' with signature '"SummarizedExperiment"': no definition for class "SummarizedExperiment"
in method for 'adjust_abundance' with signature '"RangedSummarizedExperiment"': no definition for class "RangedSummarizedExperiment"
in method for 'aggregate_duplicates' with signature '"SummarizedExperiment"': no definition for class "SummarizedExperiment"
in method for 'aggregate_duplicates' with signature '"RangedSummarizedExperiment"': no definition for class "RangedSummarizedExperiment"
in method for 'deconvolve_cellularity' with signature '"SummarizedExperiment"': no definition for class "SummarizedExperiment"
in method for 'deconvolve_cellularity' with signature '"RangedSummarizedExperiment"': no definition for class "RangedSummarizedExperiment"
in method for 'test_differential_abundance' with signature '"SummarizedExperiment"': no definition for class "SummarizedExperiment"
in method for 'test_differential_abundance' with signature '"RangedSummarizedExperiment"': no definition for class "RangedSummarizedExperiment"
in method for 'keep_variable' with signature '"SummarizedExperiment"': no definition for class "SummarizedExperiment"
in method for 'keep_variable' with signature '"RangedSummarizedExperiment"': no definition for class "RangedSummarizedExperiment"
in method for 'keep_abundant' with signature '"SummarizedExperiment"': no definition for class "SummarizedExperiment"
in method for 'keep_abundant' with signature '"RangedSummarizedExperiment"': no definition for class "RangedSummarizedExperiment"
in method for 'impute_abundance' with signature '"SummarizedExperiment"': no definition for class "SummarizedExperiment"
in method for 'impute_abundance' with signature '"RangedSummarizedExperiment"': no definition for class "RangedSummarizedExperiment"
Note: wrong number of arguments to '!'
Note: wrong number of arguments to '>'
Note: wrong number of arguments to '>'
Note: wrong number of arguments to '<'
Note: wrong number of arguments to '>'
Note: wrong number of arguments to '!'
Note: wrong number of arguments to '<'
Note: wrong number of arguments to '>'
Note: wrong number of arguments to '<'
Note: wrong number of arguments to '<'
Note: wrong number of arguments to '!'
Note: wrong number of arguments to '!'
Note: wrong number of arguments to '^'
Note: wrong number of arguments to '/'
Note: wrong number of arguments to 'floor'
Note: wrong number of arguments to '>'
Note: wrong number of arguments to '<'
** help
*** installing help indices
converting help for package 'tidybulk'
finding HTML links ... done
X_cibersort html
add_attr html
add_class html
add_scaled_counts_bulk.calcNormFactor html
add_scaled_counts_bulk.get_low_expressed
html
adjust_abundance-methods html
aggregate_duplicated_transcripts_bulk html
aggregate_duplicates-methods html
as_matrix html
bind html
breast_tcga_mini html
check_if_counts_is_na html
check_if_duplicated_genes html
check_if_wrong_input html
cluster_elements-methods html
counts html
counts_ensembl html
counts_mini html
create_tt_from_bam_sam_bulk html
create_tt_from_tibble_bulk html
deconvolve_cellularity-methods html
distinct html
dplyr-methods html
drop_attr html
drop_class html
ensembl_symbol_mapping html
ensembl_to_symbol-methods html
error_if_counts_is_na html
error_if_duplicated_genes html
error_if_log_transformed html
error_if_wrong_input html
fill_NA_using_formula html
fill_NA_with_row_median html
filter html
flybaseIDs html
full_join html
get_abundance_norm_if_exists html
get_adjusted_counts_for_unwanted_variation_bulk
html
get_cell_type_proportions html
get_clusters_SNN_bulk html
get_clusters_kmeans_bulk html
get_differential_transcript_abundance_bulk
html
get_elements html
get_elements_features html
get_elements_features_abundance html
get_reduced_dimensions_MDS_bulk html
get_reduced_dimensions_PCA_bulk html
get_reduced_dimensions_TSNE_bulk html
get_rotated_dimensions html
get_sample html
get_sample_counts html
get_sample_transcript html
get_sample_transcript_counts html
get_scaled_counts_bulk html
get_symbol_from_ensembl html
get_transcript html
get_x_y_annotation_columns html
group_by html
ifelse2_pipe html
ifelse_pipe html
impute_abundance-methods html
inner_join html
keep_abundant-methods html
keep_variable-methods html
keep_variable_transcripts html
left_join html
mutate html
parse_formula html
pivot_sample-methods html
pivot_transcript-methods html
prepend html
reduce_dimensions-methods html
reexports html
remove_redundancy-methods html
remove_redundancy_elements_though_reduced_dimensions
html
remove_redundancy_elements_through_correlation
html
rename html
right_join html
rotate_dimensions-methods html
rowwise html
run_llsr html
scale_abundance-methods html
scale_design html
se html
se_mini html
select_closest_pairs html
summarise html
symbol_to_entrez html
test_differential_abundance-methods html
test_gene_enrichment-methods html
test_gene_enrichment_bulk_EGSEA html
test_gene_overrepresentation-methods html
tidybulk-methods html
tidybulk_SAM_BAM-methods html
tidybulk_to_SummarizedExperiment html
tidyr-methods html
** 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_1.0.2.zip
* DONE (tidybulk)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'tidybulk' successfully unpacked and MD5 sums checked