Multiple platform build/check report for BioC 3.6 - CHECK report for DeepBlueR on tokay1

CHECK report for DeepBlueR on tokay1

This page was generated on 2018-04-12 13:28:23 -0400 (Thu, 12 Apr 2018).

DeepBlueR 1.4.1
Felipe Albrecht , Markus List

Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)

URL: https://git.bioconductor.org/packages/DeepBlueR

Branch: RELEASE_3_6

Last Commit: cfa73c1

Last Changed Date: 2017-11-14 04:33:35 -0400 (Tue, 14 Nov 2017)

malbec1

Linux (Ubuntu 16.04.1 LTS) / x86_64

NotNeeded

tokay1

Windows Server 2012 R2 Standard / x64

NotNeeded

[ OK ]

veracruz1

OS X 10.11.6 El Capitan / x86_64

NotNeeded

Summary

Package: DeepBlueR

Version: 1.4.1

Command: rm -rf DeepBlueR.buildbin-libdir DeepBlueR.Rcheck && mkdir DeepBlueR.buildbin-libdir DeepBlueR.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=DeepBlueR.buildbin-libdir DeepBlueR_1.4.1.tar.gz >DeepBlueR.Rcheck\00install.out 2>&1 && cp DeepBlueR.Rcheck\00install.out DeepBlueR-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=DeepBlueR.buildbin-libdir --install="check:DeepBlueR-install.out" --force-multiarch --no-vignettes --timings DeepBlueR_1.4.1.tar.gz

StartedAt: 2018-04-11 23:23:52 -0400 (Wed, 11 Apr 2018)

EndedAt: 2018-04-11 23:30:53 -0400 (Wed, 11 Apr 2018)

EllapsedTime: 421.4 seconds

RetCode: 0

Status: OK

CheckDir: DeepBlueR.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf DeepBlueR.buildbin-libdir DeepBlueR.Rcheck && mkdir DeepBlueR.buildbin-libdir DeepBlueR.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=DeepBlueR.buildbin-libdir DeepBlueR_1.4.1.tar.gz >DeepBlueR.Rcheck\00install.out 2>&1 && cp DeepBlueR.Rcheck\00install.out DeepBlueR-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=DeepBlueR.buildbin-libdir --install="check:DeepBlueR-install.out" --force-multiarch --no-vignettes --timings DeepBlueR_1.4.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/DeepBlueR.Rcheck'
* using R version 3.4.4 (2018-03-15)
* 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 '1.4.1'
* 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
* 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                              user system elapsed
deepblue_batch_export_results 1.02   0.15    5.08
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                              user system elapsed
deepblue_batch_export_results 1.51   0.14    5.58
* 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
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/DeepBlueR.Rcheck/00check.log'
for details.

Installation output

DeepBlueR.Rcheck/00install.out


install for i386

* installing *source* package 'DeepBlueR' ...
** R
** demo
** inst
** preparing 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
In R CMD INSTALL

install for x64

* installing *source* package 'DeepBlueR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DeepBlueR' as DeepBlueR_1.4.1.zip
* DONE (DeepBlueR)
In R CMD INSTALL
In R CMD INSTALL

Tests output

Example timings

DeepBlueR.Rcheck/examples_i386/DeepBlueR-Ex.timings

name	user	system	elapsed
deepblue_aggregate	0.42	0.03	1.28
deepblue_batch_export_results	1.02	0.15	5.08
deepblue_binning	0.04	0.00	0.88
deepblue_cache_status	0	0	0
deepblue_cancel_request	0.00	0.00	0.23
deepblue_chromosomes	0.07	0.00	0.28
deepblue_clear_cache	0	0	0
deepblue_collection_experiments_count	0.07	0.00	0.58
deepblue_commands	0.08	0.00	0.81
deepblue_count_gene_ontology_terms	0.21	0.00	0.75
deepblue_count_regions	0.01	0.00	0.45
deepblue_coverage	0.02	0.00	0.86
deepblue_delete_request_from_cache	0.01	0.00	0.02
deepblue_diff	0.27	0.02	2.87
deepblue_distinct_column_values	0.03	0.02	0.88
deepblue_download_request_data	0.81	0.09	3.28
deepblue_echo	0.03	0.00	0.25
deepblue_enrich_regions_go_terms	0.05	0.00	1.20
deepblue_enrich_regions_overlap	0.75	0.02	4.49
deepblue_export_bed	0.33	0.10	3.34
deepblue_export_meta_data	0.30	0.02	0.63
deepblue_export_tab	0.12	0.02	1.62
deepblue_extend	0.03	0.00	0.48
deepblue_extract_ids	0	0	0
deepblue_extract_names	0	0	0
deepblue_faceting_experiments	0.05	0.00	0.65
deepblue_filter_regions	0.02	0.00	0.30
deepblue_find_motif	0.01	0.00	0.25
deepblue_flank	0.06	0.00	0.50
deepblue_get_biosource_children	0.01	0.00	0.25
deepblue_get_biosource_parents	0.02	0.00	0.25
deepblue_get_biosource_related	0.02	0.00	0.72
deepblue_get_biosource_synonyms	0.01	0.00	0.23
deepblue_get_experiments_by_query	0.06	0.00	0.37
deepblue_get_regions	0.05	0.00	0.93
deepblue_get_request_data	0.14	0.00	1.45
deepblue_info	0.05	0.00	0.27
deepblue_input_regions	0.01	0.00	0.51
deepblue_intersection	0.07	0.00	0.99
deepblue_is_biosource	0.01	0.00	0.23
deepblue_liftover	1.02	0.07	4.31
deepblue_list_annotations	0.01	0.00	0.24
deepblue_list_biosources	0.02	0.00	0.23
deepblue_list_cached_requests	0.00	0.02	0.02
deepblue_list_column_types	0.09	0.00	0.42
deepblue_list_epigenetic_marks	0.53	0.02	1.19
deepblue_list_experiments	0.19	0.00	0.64
deepblue_list_expressions	0.11	0.00	0.58
deepblue_list_gene_models	0.03	0.00	0.25
deepblue_list_genes	0.19	0.00	1.03
deepblue_list_genomes	0.01	0.00	0.25
deepblue_list_in_use	0.31	0.00	1.47
deepblue_list_projects	0.03	0.00	0.25
deepblue_list_recent_experiments	0.04	0.01	0.27
deepblue_list_requests	0.01	0.00	0.23
deepblue_list_samples	0.19	0.00	0.78
deepblue_list_similar_biosources	0.03	0.00	0.42
deepblue_list_similar_epigenetic_marks	0.05	0.00	0.27
deepblue_list_similar_experiments	0.01	0.00	0.84
deepblue_list_similar_genomes	0.00	0.00	0.24
deepblue_list_similar_projects	0.02	0.00	0.23
deepblue_list_similar_techniques	0.01	0.00	0.28
deepblue_list_techniques	0.04	0.00	0.24
deepblue_merge_queries	0.06	0.00	0.75
deepblue_meta_data_to_table	0.24	0.02	0.80
deepblue_name_to_id	0.09	0.00	0.80
deepblue_overlap	0.08	0.00	1.26
deepblue_preview_experiment	0.00	0.00	0.25
deepblue_query_cache	0.06	0.01	0.97
deepblue_query_experiment_type	0.03	0.00	1.47
deepblue_reset_options	0	0	0
deepblue_score_matrix	0.05	0.00	0.89
deepblue_search	0.03	0.00	0.58
deepblue_select_annotations	0.03	0.00	0.25
deepblue_select_column	0.27	0.00	0.95
deepblue_select_experiments	0.03	0.00	0.24
deepblue_select_expressions	0.03	0.00	0.36
deepblue_select_genes	0.02	0.00	0.35
deepblue_select_regions	0.03	0.00	1.21
deepblue_tiling_regions	0.01	0.00	0.23

DeepBlueR.Rcheck/examples_x64/DeepBlueR-Ex.timings

name	user	system	elapsed
deepblue_aggregate	1.08	0.02	1.91
deepblue_batch_export_results	1.51	0.14	5.58
deepblue_binning	0.08	0.00	0.89
deepblue_cache_status	0	0	0
deepblue_cancel_request	0.03	0.00	0.26
deepblue_chromosomes	0.07	0.00	0.29
deepblue_clear_cache	0	0	0
deepblue_collection_experiments_count	0.14	0.00	0.62
deepblue_commands	0.11	0.01	0.86
deepblue_count_gene_ontology_terms	0.37	0.00	0.89
deepblue_count_regions	0.03	0.00	0.48
deepblue_coverage	0.05	0.00	0.91
deepblue_delete_request_from_cache	0	0	0
deepblue_diff	0.48	0.01	1.24
deepblue_distinct_column_values	0.03	0.00	0.87
deepblue_download_request_data	1.19	0.10	3.58
deepblue_echo	0.00	0.00	0.25
deepblue_enrich_regions_go_terms	0.05	0.00	1.14
deepblue_enrich_regions_overlap	0.59	0.00	4.22
deepblue_export_bed	0.24	0.04	3.26
deepblue_export_meta_data	0.20	0.00	0.58
deepblue_export_tab	0.10	0.00	1.61
deepblue_extend	0.03	0.00	0.50
deepblue_extract_ids	0	0	0
deepblue_extract_names	0	0	0
deepblue_faceting_experiments	0.03	0.00	0.64
deepblue_filter_regions	0.01	0.00	0.30
deepblue_find_motif	0.02	0.02	0.25
deepblue_flank	0.06	0.00	0.50
deepblue_get_biosource_children	0.02	0.00	0.25
deepblue_get_biosource_parents	0.01	0.00	0.25
deepblue_get_biosource_related	0.02	0.00	0.31
deepblue_get_biosource_synonyms	0.01	0.00	0.25
deepblue_get_experiments_by_query	0.04	0.00	0.75
deepblue_get_regions	0.03	0.00	0.91
deepblue_get_request_data	0.14	0.00	1.44
deepblue_info	0.05	0.00	0.26
deepblue_input_regions	0.03	0.00	0.50
deepblue_intersection	0.08	0.00	1.00
deepblue_is_biosource	0.03	0.00	0.25
deepblue_liftover	0.59	0.11	3.78
deepblue_list_annotations	0.02	0.00	0.23
deepblue_list_biosources	0.03	0.00	0.24
deepblue_list_cached_requests	0	0	0
deepblue_list_column_types	0.08	0.00	0.41
deepblue_list_epigenetic_marks	0.43	0.00	1.09
deepblue_list_experiments	0.16	0.00	0.62
deepblue_list_expressions	0.16	0.00	0.60
deepblue_list_gene_models	0.01	0.00	0.23
deepblue_list_genes	0.24	0.00	1.21
deepblue_list_genomes	0.01	0.00	0.25
deepblue_list_in_use	0.66	0.00	1.76
deepblue_list_projects	0.01	0.00	0.25
deepblue_list_recent_experiments	0.03	0.00	0.25
deepblue_list_requests	0.04	0.00	0.25
deepblue_list_samples	0.20	0.00	0.75
deepblue_list_similar_biosources	0.05	0.00	0.44
deepblue_list_similar_epigenetic_marks	0.01	0.00	0.25
deepblue_list_similar_experiments	0.00	0.00	0.82
deepblue_list_similar_genomes	0.01	0.00	0.25
deepblue_list_similar_projects	0.02	0.00	0.24
deepblue_list_similar_techniques	0.02	0.00	0.25
deepblue_list_techniques	0.05	0.00	0.25
deepblue_merge_queries	0.11	0.00	0.77
deepblue_meta_data_to_table	0.34	0.02	1.08
deepblue_name_to_id	0.09	0.00	0.76
deepblue_overlap	0.07	0.00	0.72
deepblue_preview_experiment	0.01	0.00	0.25
deepblue_query_cache	0.13	0.00	1.02
deepblue_query_experiment_type	0.04	0.00	1.48
deepblue_reset_options	0	0	0
deepblue_score_matrix	0.10	0.00	0.89
deepblue_search	0.06	0.00	0.61
deepblue_select_annotations	0.03	0.00	0.25
deepblue_select_column	0.44	0.00	1.23
deepblue_select_experiments	0.03	0.00	0.27
deepblue_select_expressions	0.01	0.02	0.36
deepblue_select_genes	0.02	0.00	0.36
deepblue_select_regions	0.06	0.00	1.23
deepblue_tiling_regions	0.03	0.00	0.27