Back to Multiple platform build/check report for BioC 3.11
ABC[D]EFGHIJKLMNOPQRSTUVWXYZ

CHECK report for DeepBlueR on tokay2

This page was generated on 2020-10-17 11:56:25 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE DeepBlueR PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 439/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DeepBlueR 1.14.0
Felipe Albrecht , Markus List
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/DeepBlueR
Branch: RELEASE_3_11
Last Commit: 051d911
Last Changed Date: 2020-04-27 14:59:21 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: DeepBlueR
Version: 1.14.0
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DeepBlueR.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings DeepBlueR_1.14.0.tar.gz
StartedAt: 2020-10-17 03:15:27 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 03:23:45 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 498.7 seconds
RetCode: 0
Status:  OK  
CheckDir: DeepBlueR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DeepBlueR.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings DeepBlueR_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/DeepBlueR.Rcheck'
* using R version 4.0.3 (2020-10-10)
* 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 '1.14.0'
* 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
* 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 ... 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
deepblue_liftover 0.54   0.31   16.16
** running examples for arch 'x64' ... 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: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/DeepBlueR.Rcheck/00check.log'
for details.



Installation output

DeepBlueR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/DeepBlueR_1.14.0.tar.gz && rm -rf DeepBlueR.buildbin-libdir && mkdir DeepBlueR.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DeepBlueR.buildbin-libdir DeepBlueR_1.14.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL DeepBlueR_1.14.0.zip && rm DeepBlueR_1.14.0.tar.gz DeepBlueR_1.14.0.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
100  524k  100  524k    0     0  8210k      0 --:--:-- --:--:-- --:--:-- 9195k

install for i386

Warning in untar2(tarfile, files, list, exdir, restore_times) :
  restoring symbolic link as a file copy
* 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

install for x64

Warning in untar2(tarfile, files, list, exdir, restore_times) :
  restoring symbolic link as a file copy
* installing *source* package 'DeepBlueR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DeepBlueR' as DeepBlueR_1.14.0.zip
* DONE (DeepBlueR)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'DeepBlueR' successfully unpacked and MD5 sums checked

Tests output


Example timings

DeepBlueR.Rcheck/examples_i386/DeepBlueR-Ex.timings

nameusersystemelapsed
deepblue_aggregate0.050.000.67
deepblue_batch_export_results1.190.264.33
deepblue_binning0.060.000.47
deepblue_cache_status0.000.000.03
deepblue_cancel_request0.020.020.22
deepblue_chromosomes0.080.000.28
deepblue_clear_cache000
deepblue_collection_experiments_count0.140.000.61
deepblue_commands0.190.010.77
deepblue_count_gene_ontology_terms0.070.100.61
deepblue_count_regions0.050.010.46
deepblue_coverage0.060.000.45
deepblue_delete_request_from_cache000
deepblue_diff0.200.110.98
deepblue_distinct_column_values0.050.020.46
deepblue_download_request_data0.310.262.32
deepblue_echo0.020.000.21
deepblue_enrich_regions_go_terms0.060.000.67
deepblue_enrich_regions_overlap0.690.003.61
deepblue_export_bed0.360.322.78
deepblue_export_meta_data0.110.030.43
deepblue_export_tab0.150.020.97
deepblue_extend0.050.000.47
deepblue_extract_ids000
deepblue_extract_names000
deepblue_faceting_experiments0.060.000.48
deepblue_filter_regions0.030.000.22
deepblue_find_motif0.030.000.24
deepblue_flank0.070.000.45
deepblue_get_biosource_children0.010.000.22
deepblue_get_biosource_parents0.030.000.22
deepblue_get_biosource_related0.020.000.23
deepblue_get_biosource_synonyms0.030.000.22
deepblue_get_experiments_by_query0.020.000.22
deepblue_get_regions0.040.020.45
deepblue_get_request_data0.070.000.85
deepblue_info0.030.000.23
deepblue_input_regions0.020.000.37
deepblue_intersection0.080.001.22
deepblue_is_biosource0.030.000.22
deepblue_liftover 0.54 0.3116.16
deepblue_list_annotations0.020.000.86
deepblue_list_biosources0.030.000.79
deepblue_list_cached_requests000
deepblue_list_column_types0.090.000.96
deepblue_list_epigenetic_marks0.500.001.29
deepblue_list_experiments0.210.000.89
deepblue_list_expressions0.170.010.66
deepblue_list_gene_models0.030.020.30
deepblue_list_genes0.380.111.21
deepblue_list_genomes0.030.000.29
deepblue_list_in_use0.450.051.62
deepblue_list_projects0.030.000.25
deepblue_list_recent_experiments0.030.000.28
deepblue_list_requests0.030.000.22
deepblue_list_samples0.180.010.59
deepblue_list_similar_biosources0.030.000.41
deepblue_list_similar_epigenetic_marks0.030.000.24
deepblue_list_similar_experiments0.030.000.81
deepblue_list_similar_genomes0.030.000.22
deepblue_list_similar_projects0.030.000.22
deepblue_list_similar_techniques0.030.000.21
deepblue_list_techniques0.050.000.24
deepblue_merge_queries0.080.000.67
deepblue_meta_data_to_table0.120.000.64
deepblue_name_to_id0.070.000.66
deepblue_overlap0.090.001.17
deepblue_preview_experiment0.020.000.22
deepblue_query_cache0.10.01.0
deepblue_query_experiment_type0.070.000.45
deepblue_reset_options000
deepblue_score_matrix0.040.000.44
deepblue_search0.070.000.58
deepblue_select_annotations0.030.020.23
deepblue_select_column0.310.000.83
deepblue_select_experiments0.000.000.22
deepblue_select_expressions0.050.010.34
deepblue_select_genes0.030.000.31
deepblue_select_regions0.010.000.24
deepblue_tiling_regions0.040.000.22

DeepBlueR.Rcheck/examples_x64/DeepBlueR-Ex.timings

nameusersystemelapsed
deepblue_aggregate0.100.000.68
deepblue_batch_export_results0.340.233.40
deepblue_binning0.040.000.45
deepblue_cache_status0.000.000.04
deepblue_cancel_request0.040.000.21
deepblue_chromosomes0.090.000.29
deepblue_clear_cache000
deepblue_collection_experiments_count0.140.000.64
deepblue_commands0.130.000.70
deepblue_count_gene_ontology_terms0.150.020.56
deepblue_count_regions0.050.000.45
deepblue_coverage0.060.000.44
deepblue_delete_request_from_cache000
deepblue_diff0.170.040.61
deepblue_distinct_column_values0.070.000.45
deepblue_download_request_data0.370.172.27
deepblue_echo0.030.000.22
deepblue_enrich_regions_go_terms0.060.000.67
deepblue_enrich_regions_overlap0.740.023.75
deepblue_export_bed0.280.162.58
deepblue_export_meta_data0.090.000.41
deepblue_export_tab0.140.010.98
deepblue_extend0.050.000.44
deepblue_extract_ids000
deepblue_extract_names000
deepblue_faceting_experiments0.030.000.45
deepblue_filter_regions0.030.000.23
deepblue_find_motif0.050.000.24
deepblue_flank0.060.000.44
deepblue_get_biosource_children0.030.000.25
deepblue_get_biosource_parents0.040.000.22
deepblue_get_biosource_related0.030.000.23
deepblue_get_biosource_synonyms0.030.000.22
deepblue_get_experiments_by_query0.010.000.22
deepblue_get_regions0.050.000.93
deepblue_get_request_data0.060.000.99
deepblue_info0.030.000.28
deepblue_input_regions0.040.000.23
deepblue_intersection0.070.000.66
deepblue_is_biosource0.020.000.22
deepblue_liftover1.480.174.80
deepblue_list_annotations0.050.000.23
deepblue_list_biosources0.030.000.22
deepblue_list_cached_requests000
deepblue_list_column_types0.110.000.37
deepblue_list_epigenetic_marks0.560.021.08
deepblue_list_experiments0.210.030.63
deepblue_list_expressions0.200.020.51
deepblue_list_gene_models0.020.010.22
deepblue_list_genes0.260.030.88
deepblue_list_genomes0.030.000.22
deepblue_list_in_use0.530.001.53
deepblue_list_projects0.020.000.22
deepblue_list_recent_experiments0.050.000.23
deepblue_list_requests0.030.000.22
deepblue_list_samples0.170.020.59
deepblue_list_similar_biosources0.050.000.41
deepblue_list_similar_epigenetic_marks0.040.000.25
deepblue_list_similar_experiments0.030.000.81
deepblue_list_similar_genomes0.040.000.22
deepblue_list_similar_projects0.030.000.22
deepblue_list_similar_techniques0.030.000.28
deepblue_list_techniques0.030.000.22
deepblue_merge_queries0.070.000.66
deepblue_meta_data_to_table0.140.000.63
deepblue_name_to_id0.080.000.65
deepblue_overlap0.070.000.69
deepblue_preview_experiment0.020.000.22
deepblue_query_cache0.110.000.89
deepblue_query_experiment_type0.080.000.45
deepblue_reset_options000
deepblue_score_matrix0.040.000.92
deepblue_search0.070.001.38
deepblue_select_annotations0.040.000.23
deepblue_select_column0.530.001.03
deepblue_select_experiments0.040.000.22
deepblue_select_expressions0.030.000.33
deepblue_select_genes0.040.000.41
deepblue_select_regions0.020.000.23
deepblue_tiling_regions0.020.000.24