Package: HiCBricks

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:HiCBricks.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings HiCBricks_1.4.0.tar.gz

StartedAt: 2020-04-15 03:00:40 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 03:04:06 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 206.5 seconds

RetCode: 0

Status:  OK

CheckDir: HiCBricks.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:HiCBricks.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings HiCBricks_1.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/HiCBricks.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HiCBricks/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HiCBricks’ version ‘1.4.0’
* package encoding: UTF-8
* 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 ‘HiCBricks’ 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 ... OK
* 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
* 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: OK

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL HiCBricks
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘HiCBricks’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** 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 (HiCBricks)

name	user	system	elapsed
BrickContainer_change_experiment_name	1.460	0.067	1.543
BrickContainer_change_output_directory	1.173	0.045	1.254
BrickContainer_get_path_to_file	1.061	0.040	1.126
BrickContainer_list_chromosomes	1.094	0.040	1.153
BrickContainer_list_experiment_name	1.080	0.040	1.137
BrickContainer_list_files	1.120	0.040	1.185
BrickContainer_list_output_directory	1.079	0.039	1.137
BrickContainer_list_resolutions	1.068	0.038	1.121
BrickContainer_unlink_resolution	2.282	0.080	2.401
Brick_add_ranges	1.944	0.080	2.055
Brick_call_compartments	2.065	0.182	2.280
Brick_export_to_sparse	3.703	0.182	3.933
Brick_fetch_range_index	1.437	0.056	1.511
Brick_fetch_row_vector	2.424	0.130	2.601
Brick_get_bintable	1.230	0.054	1.295
Brick_get_chrominfo	1.158	0.044	1.228
Brick_get_entire_matrix	2.111	0.391	2.554
Brick_get_matrix	1.784	0.125	1.945
Brick_get_matrix_mcols	2.014	0.132	2.195
Brick_get_matrix_within_coords	2.544	0.146	2.752
Brick_get_ranges	1.042	0.042	1.099
Brick_get_values_by_distance	1.849	0.175	2.046
Brick_get_vector_values	1.488	0.124	1.634
Brick_list_matrices	0.950	0.047	1.010
Brick_list_matrix_mcols	1.187	0.046	1.245
Brick_list_mcool_normalisations	0.001	0.000	0.001
Brick_list_mcool_resolutions	0	0	0
Brick_list_rangekeys	0.890	0.031	0.931
Brick_list_ranges_mcols	0.882	0.032	0.922
Brick_load_cis_matrix_till_distance	1.35	0.09	1.45
Brick_load_data_from_mcool	0	0	0
Brick_load_matrix	1.438	0.103	1.572
Brick_local_score_differentiator	2.454	0.199	2.686
Brick_make_ranges	0.008	0.000	0.009
Brick_matrix_dimensions	1.464	0.104	1.585
Brick_matrix_exists	1.457	0.114	1.589
Brick_matrix_filename	1.434	0.117	1.573
Brick_matrix_isdone	1.411	0.103	1.534
Brick_matrix_issparse	1.414	0.112	1.542
Brick_matrix_maxdist	1.472	0.109	1.610
Brick_matrix_minmax	1.441	0.109	1.583
Brick_mcool_normalisation_exists	0	0	0
Brick_rangekey_exists	0.945	0.043	1.008
Brick_return_region_position	1.123	0.035	1.194
Brick_vizart_plot_heatmap	2.908	0.146	3.133
Create_many_Bricks	0.894	0.035	0.940
Create_many_Bricks_from_mcool	0.000	0.001	0.001
load_BrickContainer	0.967	0.031	1.010