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This page was generated on 2023-06-02 11:02:11 -0400 (Fri, 02 Jun 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.0 RC (2023-04-13 r84266) -- "Already Tomorrow" 4269
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CHECK results for DeepBlueR on kjohnson2


To the developers/maintainers of the DeepBlueR package:
Use the following Renviron settings to reproduce errors and warnings.

Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details.

raw results

Package 511/2229HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DeepBlueR 1.26.0  (landing page)
Felipe Albrecht , Markus List , Quirin Manz
Snapshot Date: 2023-05-28 13:00:06 -0400 (Sun, 28 May 2023)
git_url: https://git.bioconductor.org/packages/DeepBlueR
git_branch: RELEASE_3_17
git_last_commit: 422a55a
git_last_commit_date: 2023-04-25 10:48:12 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    OK    ERROR  

Summary

Package: DeepBlueR
Version: 1.26.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:DeepBlueR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings DeepBlueR_1.26.0.tar.gz
StartedAt: 2023-05-30 11:10:07 -0400 (Tue, 30 May 2023)
EndedAt: 2023-05-30 11:17:51 -0400 (Tue, 30 May 2023)
EllapsedTime: 463.6 seconds
RetCode: 0
Status:   OK  
CheckDir: DeepBlueR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:DeepBlueR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings DeepBlueR_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/DeepBlueR.Rcheck’
* using R version 4.3.0 RC (2023-04-13 r84266)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DeepBlueR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DeepBlueR’ version ‘1.26.0’
* 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 for sufficient/correct file permissions ... 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 ... NOTE
Problems with news in ‘NEWS’:
  Cannot process chunk/lines:
    v0.99.0 Initial Bioconductor submission
  Cannot process chunk/lines:
    v1.0.0 Bioconductor 3.4 release
  Cannot process chunk/lines:
    v1.2.0 Bioconductor 3.5 release
  Cannot process chunk/lines:
    v1.4.0 Bioconductor 3.6 release
  Cannot process chunk/lines:
    v1.4.1 Bugfixes following changes in the DeepBlue API
* 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 startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... 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 0.476  0.081    9.47
* 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
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/DeepBlueR.Rcheck/00check.log’
for details.



Installation output

DeepBlueR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL DeepBlueR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/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
** 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)

Tests output


Example timings

DeepBlueR.Rcheck/DeepBlueR-Ex.timings

nameusersystemelapsed
deepblue_aggregate0.0680.0100.817
deepblue_batch_export_results0.3580.0533.094
deepblue_binning0.0430.0050.537
deepblue_cache_status0.0020.0020.006
deepblue_cancel_request0.0160.0020.258
deepblue_chromosomes0.0530.0050.319
deepblue_clear_cache0.0010.0010.003
deepblue_collection_experiments_count0.0840.0040.643
deepblue_commands0.1090.0120.750
deepblue_count_gene_ontology_terms0.0970.0060.501
deepblue_count_regions0.0320.0050.551
deepblue_coverage0.0360.0060.536
deepblue_delete_request_from_cache0.0020.0020.009
deepblue_diff0.1300.0450.735
deepblue_distinct_column_values0.0350.0060.545
deepblue_download_request_data0.2290.0311.721
deepblue_echo0.0130.0020.257
deepblue_enrich_regions_go_terms0.0520.0050.787
deepblue_enrich_regions_overlap0.4830.0193.610
deepblue_export_bed0.8560.0403.125
deepblue_export_meta_data0.2790.0060.776
deepblue_export_tab0.1190.0111.135
deepblue_extend0.0390.0030.530
deepblue_extract_ids0.0000.0000.003
deepblue_extract_names0.0010.0000.001
deepblue_faceting_experiments0.0260.0020.552
deepblue_filter_regions0.0210.0020.268
deepblue_find_motif0.0240.0020.271
deepblue_flank0.0400.0030.546
deepblue_get_biosource_children0.0160.0020.273
deepblue_get_biosource_parents0.0150.0020.260
deepblue_get_biosource_related0.0170.0030.274
deepblue_get_biosource_synonyms0.0160.0020.258
deepblue_get_experiments_by_query0.0140.0020.437
deepblue_get_regions0.0320.0040.536
deepblue_get_request_data0.0580.0061.015
deepblue_info0.0330.0060.295
deepblue_input_regions0.0170.0020.274
deepblue_intersection0.0560.0060.794
deepblue_is_biosource0.0140.0030.256
deepblue_liftover0.4760.0819.470
deepblue_list_annotations0.0200.0020.272
deepblue_list_biosources0.0170.0020.255
deepblue_list_cached_requests0.0020.0020.004
deepblue_list_column_types0.0570.0040.434
deepblue_list_epigenetic_marks0.3900.0131.184
deepblue_list_experiments0.1350.0100.695
deepblue_list_expressions0.1550.0100.610
deepblue_list_gene_models0.0160.0020.262
deepblue_list_genes0.2580.0081.085
deepblue_list_genomes0.0160.0020.257
deepblue_list_in_use0.3200.0071.566
deepblue_list_projects0.0160.0020.285
deepblue_list_recent_experiments0.0290.0020.284
deepblue_list_requests0.0160.0030.261
deepblue_list_samples0.1230.0220.714
deepblue_list_similar_biosources0.0210.0020.448
deepblue_list_similar_epigenetic_marks0.0610.0050.360
deepblue_list_similar_experiments0.0160.0020.843
deepblue_list_similar_genomes0.0150.0020.257
deepblue_list_similar_projects0.0170.0020.264
deepblue_list_similar_techniques0.0170.0020.606
deepblue_list_techniques0.0260.0030.275
deepblue_merge_queries0.0560.0050.874
deepblue_meta_data_to_table0.2710.0101.002
deepblue_name_to_id0.0510.0050.784
deepblue_overlap0.0590.0050.804
deepblue_preview_experiment0.0130.0010.254
deepblue_query_cache0.0700.0071.044
deepblue_query_experiment_type0.0450.0040.548
deepblue_reset_options0.0000.0010.003
deepblue_score_matrix0.0360.0040.519
deepblue_search0.0380.0040.615
deepblue_select_annotations0.0210.0020.268
deepblue_select_column0.3410.0111.128
deepblue_select_experiments0.0190.0020.263
deepblue_select_expressions0.0220.0020.276
deepblue_select_genes0.0230.0020.270
deepblue_select_regions0.0240.0020.272
deepblue_tiling_regions0.0170.0020.255