Package: HiCBricks

Version: 1.2.0

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_1.2.0.tar.gz

StartedAt: 2019-10-16 03:36:58 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 03:39:54 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 176.0 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_1.2.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/HiCBricks.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.2.0’
* 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 ... NOTE
Brick_get_ranges: no visible global function definition for ‘FUN<-’
Undefined global functions or variables:
  FUN<-
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/HiCBricks.Rcheck/00check.log’
for details.

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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
Brick_add_ranges	0.317	0.077	0.428
Brick_fetch_range_index	0.397	0.065	0.470
Brick_fetch_row_vector	1.122	0.024	1.193
Brick_get_bintable	0.071	0.003	0.074
Brick_get_chrominfo	0.011	0.001	0.012
Brick_get_matrix	0.128	0.005	0.143
Brick_get_matrix_mcols	0.070	0.018	0.099
Brick_get_matrix_within_coords	1.433	0.054	1.596
Brick_get_ranges	0.063	0.003	0.075
Brick_get_values_by_distance	0.621	0.164	0.903
Brick_get_vector_values	0.096	0.005	0.130
Brick_list_matrices	0.028	0.002	0.030
Brick_list_matrix_mcols	0.002	0.001	0.002
Brick_list_mcool_normalisations	0.001	0.000	0.001
Brick_list_rangekeys	0.003	0.001	0.004
Brick_list_ranges_mcols	0.012	0.002	0.014
Brick_load_cis_matrix_till_distance	3.740	0.483	4.300
Brick_load_data_from_mcool	0.000	0.000	0.001
Brick_load_matrix	3.745	0.606	4.465
Brick_local_score_differentiator	2.476	0.090	2.567
Brick_make_ranges	0.011	0.000	0.012
Brick_matrix_dimensions	0.012	0.002	0.014
Brick_matrix_exists	0.014	0.001	0.014
Brick_matrix_filename	0.025	0.003	0.028
Brick_matrix_isdone	0.032	0.007	0.038
Brick_matrix_issparse	0.033	0.008	0.041
Brick_matrix_maxdist	0.054	0.002	0.055
Brick_matrix_minmax	0.027	0.003	0.030
Brick_mcool_normalisation_exists	0.000	0.000	0.001
Brick_rangekey_exists	0.004	0.000	0.004
Brick_return_region_position	0.186	0.007	0.193
Brick_vizart_plot_heatmap	1.921	0.061	1.982
CreateBrick	0.113	0.041	0.159
CreateBrick_from_mcool	0.001	0.001	0.001