Package: HiCBricks

Version: 1.4.0

Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:HiCBricks.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings HiCBricks_1.4.0.tar.gz

StartedAt: 2020-04-15 06:05:54 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 06:08:33 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 159.0 seconds

RetCode: 0

Status:  OK

CheckDir: HiCBricks.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:HiCBricks.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings HiCBricks_1.4.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/HiCBricks.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (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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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL HiCBricks
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/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	1.052	0.012	1.080
BrickContainer_change_output_directory	1.012	0.024	1.037
BrickContainer_get_path_to_file	0.880	0.012	0.895
BrickContainer_list_chromosomes	0.884	0.012	0.907
BrickContainer_list_experiment_name	0.900	0.012	0.920
BrickContainer_list_files	0.924	0.012	0.951
BrickContainer_list_output_directory	0.852	0.012	0.866
BrickContainer_list_resolutions	0.872	0.012	0.892
BrickContainer_unlink_resolution	1.600	0.020	1.628
Brick_add_ranges	1.700	0.028	1.731
Brick_call_compartments	1.264	0.056	1.339
Brick_export_to_sparse	2.896	0.052	2.954
Brick_fetch_range_index	1.264	0.016	1.280
Brick_fetch_row_vector	1.880	0.032	1.913
Brick_get_bintable	1.012	0.008	1.022
Brick_get_chrominfo	0.908	0.024	0.933
Brick_get_entire_matrix	1.384	0.096	1.486
Brick_get_matrix	1.368	0.028	1.394
Brick_get_matrix_mcols	1.072	0.012	1.092
Brick_get_matrix_within_coords	1.468	0.016	1.483
Brick_get_ranges	0.744	0.016	0.759
Brick_get_values_by_distance	1.292	0.048	1.344
Brick_get_vector_values	1.416	0.016	1.436
Brick_list_matrices	0.720	0.008	0.728
Brick_list_matrix_mcols	0.892	0.008	0.910
Brick_list_mcool_normalisations	0.000	0.000	0.001
Brick_list_mcool_resolutions	0	0	0
Brick_list_rangekeys	0.924	0.008	0.933
Brick_list_ranges_mcols	0.624	0.004	0.632
Brick_load_cis_matrix_till_distance	0.972	0.016	0.987
Brick_load_data_from_mcool	0	0	0
Brick_load_matrix	1.304	0.036	1.356
Brick_local_score_differentiator	2.104	0.052	2.247
Brick_make_ranges	0.020	0.000	0.022
Brick_matrix_dimensions	1.100	0.020	1.121
Brick_matrix_exists	1.092	0.024	1.117
Brick_matrix_filename	1.300	0.036	1.333
Brick_matrix_isdone	1.324	0.044	1.375
Brick_matrix_issparse	1.156	0.052	1.211
Brick_matrix_maxdist	1.280	0.028	1.311
Brick_matrix_minmax	1.248	0.032	1.281
Brick_mcool_normalisation_exists	0	0	0
Brick_rangekey_exists	0.648	0.016	0.666
Brick_return_region_position	1.004	0.000	1.006
Brick_vizart_plot_heatmap	2.556	0.052	2.618
Create_many_Bricks	0.764	0.004	0.768
Create_many_Bricks_from_mcool	0	0	0
load_BrickContainer	0.688	0.004	0.692