Felipe Albrecht
| Snapshot Date: 2022-03-01 13:55:23 -0500 (Tue, 01 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/DeepBlueR |
| git_branch: master |
| git_last_commit: 340e089 |
| git_last_commit_date: 2021-10-26 12:28:59 -0500 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-02 11:07:11 -0500 (Wed, 02 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4332 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4093 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4068 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" | 4143 |
| 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 DeepBlueR package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DeepBlueR.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 475/2088 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| DeepBlueR 1.21.0 (landing page) Felipe Albrecht
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: DeepBlueR |
| Version: 1.21.0 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:DeepBlueR.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings DeepBlueR_1.21.0.tar.gz |
| StartedAt: 2022-03-01 18:59:17 -0500 (Tue, 01 Mar 2022) |
| EndedAt: 2022-03-01 19:05:00 -0500 (Tue, 01 Mar 2022) |
| EllapsedTime: 343.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: DeepBlueR.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:DeepBlueR.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings DeepBlueR_1.21.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/DeepBlueR.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'DeepBlueR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'DeepBlueR' version '1.21.0'
* 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 'DeepBlueR' 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
* 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 ... OK
* checking Rd files ... NOTE
prepare_Rd: deepblue_enrich_regions_fast.Rd:35-38: Dropping empty section \examples
* 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 files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
deepblue_liftover 0.36 0.19 6.98
* 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: 1 NOTE
See
'D:/biocbuild/bbs-3.15-bioc/meat/DeepBlueR.Rcheck/00check.log'
for details.
DeepBlueR.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL DeepBlueR
###
##############################################################################
##############################################################################
* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'DeepBlueR' ...
** using staged installation
** R
** demo
** inst
** byte-compile and prepare package for lazy loading
Called method: deepblue_list_column_types
Reported status was: okay
Called method: deepblue_info
Reported status was: okay
** help
*** installing help indices
converting help for package 'DeepBlueR'
finding HTML links ... done
DeepBlueCommand-class html
deepblue_aggregate html
deepblue_batch_export_results html
deepblue_binning html
deepblue_cache_status html
deepblue_cancel_request html
deepblue_chromosomes html
deepblue_clear_cache html
deepblue_collection_experiments_count html
deepblue_column_types html
deepblue_commands html
deepblue_convert_to_df html
deepblue_convert_to_grange html
deepblue_count_gene_ontology_terms html
deepblue_count_regions html
deepblue_coverage html
deepblue_delete_request_from_cache html
deepblue_diff html
deepblue_distinct_column_values html
deepblue_download_request_data-DeepBlueCommand-method
html
deepblue_download_request_data html
deepblue_echo html
deepblue_enrich_regions_fast html
deepblue_enrich_regions_go_terms html
deepblue_enrich_regions_overlap html
deepblue_export_bed html
deepblue_export_meta_data html
deepblue_export_tab html
deepblue_extend html
deepblue_extract_ids html
deepblue_extract_names html
deepblue_faceting_experiments html
deepblue_filter_regions html
deepblue_find_motif html
deepblue_flank html
deepblue_format_object_size html
deepblue_get_biosource_children html
deepblue_get_biosource_parents html
deepblue_get_biosource_related html
deepblue_get_biosource_synonyms html
deepblue_get_db html
deepblue_get_experiments_by_query html
deepblue_get_regions html
deepblue_get_request_data html
deepblue_info html
deepblue_input_regions html
deepblue_intersection html
deepblue_is_biosource html
deepblue_liftover html
deepblue_list_annotations html
deepblue_list_biosources html
deepblue_list_cached_requests html
deepblue_list_column_types html
deepblue_list_epigenetic_marks html
deepblue_list_experiments html
deepblue_list_expressions html
deepblue_list_gene_models html
deepblue_list_genes html
deepblue_list_genomes html
deepblue_list_in_use html
deepblue_list_projects html
deepblue_list_recent_experiments html
deepblue_list_requests html
deepblue_list_samples html
deepblue_list_similar_biosources html
deepblue_list_similar_epigenetic_marks
html
deepblue_list_similar_experiments html
deepblue_list_similar_genomes html
deepblue_list_similar_projects html
deepblue_list_similar_techniques html
deepblue_list_techniques html
deepblue_merge_queries html
deepblue_meta_data_to_table html
deepblue_name_to_id html
deepblue_options html
deepblue_overlap html
deepblue_parse_gtf html
deepblue_preview_experiment html
deepblue_query_cache html
deepblue_query_experiment_type html
deepblue_reset_options html
deepblue_score_matrix html
deepblue_search html
deepblue_select_annotations html
deepblue_select_column html
deepblue_select_experiments html
deepblue_select_expressions html
deepblue_select_genes html
deepblue_select_regions html
deepblue_switch_get_request_data html
deepblue_tiling_regions html
deepblue_wait_request html
show-DeepBlueCommand-method html
xml.rpc 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
* DONE (DeepBlueR)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'r3Cseq' is missing or broken
done
DeepBlueR.Rcheck/DeepBlueR-Ex.timings
| name | user | system | elapsed | |
| deepblue_aggregate | 0.06 | 0.00 | 0.91 | |
| deepblue_batch_export_results | 0.41 | 0.16 | 4.44 | |
| deepblue_binning | 0.03 | 0.00 | 0.55 | |
| deepblue_cache_status | 0 | 0 | 0 | |
| deepblue_cancel_request | 0.02 | 0.00 | 0.28 | |
| deepblue_chromosomes | 0.05 | 0.00 | 0.30 | |
| deepblue_clear_cache | 0 | 0 | 0 | |
| deepblue_collection_experiments_count | 0.06 | 0.03 | 0.64 | |
| deepblue_commands | 0.06 | 0.06 | 0.75 | |
| deepblue_count_gene_ontology_terms | 0.13 | 0.00 | 0.61 | |
| deepblue_count_regions | 0.04 | 0.00 | 0.54 | |
| deepblue_coverage | 0.05 | 0.00 | 0.57 | |
| deepblue_delete_request_from_cache | 0 | 0 | 0 | |
| deepblue_diff | 0.70 | 0.02 | 1.46 | |
| deepblue_distinct_column_values | 0.02 | 0.00 | 0.52 | |
| deepblue_download_request_data | 0.12 | 0.17 | 2.50 | |
| deepblue_echo | 0.00 | 0.00 | 0.25 | |
| deepblue_enrich_regions_go_terms | 0.03 | 0.01 | 0.80 | |
| deepblue_enrich_regions_overlap | 0.36 | 0.08 | 3.97 | |
| deepblue_export_bed | 0.24 | 0.20 | 3.18 | |
| deepblue_export_meta_data | 0.03 | 0.00 | 0.41 | |
| deepblue_export_tab | 0.11 | 0.00 | 1.12 | |
| deepblue_extend | 0.05 | 0.02 | 0.57 | |
| deepblue_extract_ids | 0 | 0 | 0 | |
| deepblue_extract_names | 0 | 0 | 0 | |
| deepblue_faceting_experiments | 0.01 | 0.00 | 0.53 | |
| deepblue_filter_regions | 0.02 | 0.00 | 0.26 | |
| deepblue_find_motif | 0.01 | 0.00 | 0.29 | |
| deepblue_flank | 0.05 | 0.00 | 0.54 | |
| deepblue_get_biosource_children | 0.00 | 0.00 | 0.27 | |
| deepblue_get_biosource_parents | 0.00 | 0.00 | 0.26 | |
| deepblue_get_biosource_related | 0.02 | 0.00 | 0.28 | |
| deepblue_get_biosource_synonyms | 0.00 | 0.00 | 0.29 | |
| deepblue_get_experiments_by_query | 0.01 | 0.00 | 0.28 | |
| deepblue_get_regions | 0.02 | 0.00 | 0.51 | |
| deepblue_get_request_data | 0.03 | 0.00 | 1.03 | |
| deepblue_info | 0.04 | 0.00 | 0.30 | |
| deepblue_input_regions | 0.02 | 0.00 | 0.28 | |
| deepblue_intersection | 0.03 | 0.00 | 0.79 | |
| deepblue_is_biosource | 0.02 | 0.00 | 0.27 | |
| deepblue_liftover | 0.36 | 0.19 | 6.98 | |
| deepblue_list_annotations | 0.03 | 0.00 | 0.28 | |
| deepblue_list_biosources | 0.03 | 0.00 | 0.28 | |
| deepblue_list_cached_requests | 0 | 0 | 0 | |
| deepblue_list_column_types | 0.03 | 0.00 | 0.41 | |
| deepblue_list_epigenetic_marks | 0.23 | 0.00 | 0.86 | |
| deepblue_list_experiments | 0.13 | 0.00 | 0.66 | |
| deepblue_list_expressions | 0.14 | 0.00 | 0.53 | |
| deepblue_list_gene_models | 0.01 | 0.00 | 0.27 | |
| deepblue_list_genes | 0.25 | 0.03 | 1.03 | |
| deepblue_list_genomes | 0.02 | 0.00 | 0.26 | |
| deepblue_list_in_use | 0.26 | 0.03 | 1.46 | |
| deepblue_list_projects | 0.02 | 0.00 | 0.26 | |
| deepblue_list_recent_experiments | 0.03 | 0.00 | 0.28 | |
| deepblue_list_requests | 0.02 | 0.00 | 0.27 | |
| deepblue_list_samples | 0.09 | 0.02 | 0.62 | |
| deepblue_list_similar_biosources | 0.03 | 0.00 | 0.43 | |
| deepblue_list_similar_epigenetic_marks | 0.02 | 0.00 | 0.29 | |
| deepblue_list_similar_experiments | 0.00 | 0.00 | 0.83 | |
| deepblue_list_similar_genomes | 0.01 | 0.00 | 0.27 | |
| deepblue_list_similar_projects | 0.02 | 0.00 | 0.28 | |
| deepblue_list_similar_techniques | 0.03 | 0.00 | 0.28 | |
| deepblue_list_techniques | 0.01 | 0.00 | 0.27 | |
| deepblue_merge_queries | 0.07 | 0.00 | 0.82 | |
| deepblue_meta_data_to_table | 0.07 | 0.00 | 0.72 | |
| deepblue_name_to_id | 0.05 | 0.00 | 0.80 | |
| deepblue_overlap | 0.03 | 0.00 | 0.80 | |
| deepblue_preview_experiment | 0.01 | 0.00 | 0.28 | |
| deepblue_query_cache | 0.07 | 0.00 | 1.08 | |
| deepblue_query_experiment_type | 0.03 | 0.00 | 0.53 | |
| deepblue_reset_options | 0 | 0 | 0 | |
| deepblue_score_matrix | 0.03 | 0.00 | 0.63 | |
| deepblue_search | 0.03 | 0.00 | 0.61 | |
| deepblue_select_annotations | 0.01 | 0.00 | 0.30 | |
| deepblue_select_column | 0.35 | 0.00 | 0.98 | |
| deepblue_select_experiments | 0.03 | 0.00 | 0.29 | |
| deepblue_select_expressions | 0.01 | 0.00 | 0.39 | |
| deepblue_select_genes | 0.02 | 0.00 | 0.39 | |
| deepblue_select_regions | 0.05 | 0.00 | 0.29 | |
| deepblue_tiling_regions | 0.00 | 0.00 | 0.29 | |