Package: HiCBricks

Version: 1.0.0

Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:HiCBricks.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings HiCBricks_1.0.0.tar.gz

StartedAt: 2019-04-16 00:36:53 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 00:39:18 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 144.8 seconds

RetCode: 0

Status:  OK

CheckDir: HiCBricks.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:HiCBricks.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings HiCBricks_1.0.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/HiCBricks.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.0.0’
* 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
  ‘/home/biocbuild/bbs-3.8-bioc/meat/HiCBricks.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL HiCBricks
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘HiCBricks’ ...
** 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
* DONE (HiCBricks)

name	user	system	elapsed
Brick_add_ranges	3.084	0.116	3.492
Brick_fetch_range_index	0.228	0.004	0.256
Brick_fetch_row_vector	0.952	0.008	1.034
Brick_get_bintable	0.052	0.000	0.054
Brick_get_chrominfo	0.012	0.000	0.011
Brick_get_matrix	0.136	0.004	0.138
Brick_get_matrix_mcols	0.072	0.008	0.085
Brick_get_matrix_within_coords	1.344	0.008	1.370
Brick_get_ranges	0.056	0.000	0.057
Brick_get_values_by_distance	0.412	0.020	0.437
Brick_get_vector_values	0.104	0.000	0.103
Brick_is_tracked	0.276	0.000	0.278
Brick_list_matrices	0.020	0.000	0.023
Brick_list_matrix_mcols	0.000	0.000	0.001
Brick_list_mcool_normalisations	0	0	0
Brick_list_rangekeys	0.004	0.000	0.003
Brick_list_ranges_mcols	0.012	0.000	0.009
Brick_list_tracked_bricks	0.296	0.004	0.301
Brick_load_cis_matrix_till_distance	4.468	0.184	4.725
Brick_load_data_from_mcool	0	0	0
Brick_load_matrix	4.056	0.192	4.287
Brick_local_score_differentiator	1.932	0.044	1.976
Brick_make_ranges	0.008	0.000	0.008
Brick_matrix_dimensions	0.012	0.000	0.010
Brick_matrix_exists	0.012	0.000	0.013
Brick_matrix_filename	0.028	0.000	0.025
Brick_matrix_isdone	0.024	0.000	0.024
Brick_matrix_issparse	0.024	0.000	0.023
Brick_matrix_maxdist	0.048	0.000	0.047
Brick_matrix_minmax	0.032	0.000	0.032
Brick_mcool_normalisation_exists	0	0	0
Brick_path_to_file	2.692	0.076	2.804
Brick_rangekey_exists	0.004	0.000	0.005
Brick_return_region_position	0.120	0.000	0.118
Brick_track_bricks	0.820	0.008	0.831
Brick_untrack_brick	1.628	0.032	1.674
Brick_vizart_plot_heatmap	1.192	0.012	1.224
CreateBrick	2.476	0.052	2.550
CreateBrick_from_mcool	0	0	0