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CHECK report for HiCBricks on machv2

This page was generated on 2020-10-17 11:58:41 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE HiCBricks PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 814/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HiCBricks 1.6.0
Koustav Pal
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/HiCBricks
Branch: RELEASE_3_11
Last Commit: 853214f
Last Changed Date: 2020-04-27 15:20:41 -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: HiCBricks
Version: 1.6.0
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_1.6.0.tar.gz
StartedAt: 2020-10-17 02:00:02 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 02:03:59 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 236.3 seconds
RetCode: 0
Status:  OK 
CheckDir: HiCBricks.Rcheck
Warnings: 0

Command output

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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_1.6.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/HiCBricks.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.6.0’
* 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


Installation output

HiCBricks.Rcheck/00install.out

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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/4.0/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)

Tests output


Example timings

HiCBricks.Rcheck/HiCBricks-Ex.timings

nameusersystemelapsed
BrickContainer_change_experiment_name1.3980.1011.502
BrickContainer_change_output_directory1.2080.0731.282
BrickContainer_get_path_to_file1.1540.0711.227
BrickContainer_list_chromosomes1.0480.0701.119
BrickContainer_list_experiment_name1.0650.0711.138
BrickContainer_list_files1.1120.0711.186
BrickContainer_list_output_directory1.1140.0741.189
BrickContainer_list_resolutions1.0580.0701.128
BrickContainer_unlink_resolution2.3370.1482.489
Brick_add_ranges2.0250.1262.267
Brick_call_compartments2.0790.2312.315
Brick_export_to_sparse3.8550.2764.137
Brick_fetch_range_index1.4140.0761.495
Brick_fetch_row_vector2.5870.1942.787
Brick_get_bintable1.1180.0791.240
Brick_get_chrominfo1.0530.0651.161
Brick_get_entire_matrix1.7350.2051.943
Brick_get_matrix1.6490.1841.835
Brick_get_matrix_mcols1.7060.1881.896
Brick_get_matrix_within_coords2.3890.1812.677
Brick_get_ranges1.1120.0771.190
Brick_get_values_by_distance1.9380.2182.265
Brick_get_vector_values1.6000.1731.778
Brick_list_matrices1.0660.0691.137
Brick_list_matrix_mcols1.0010.0641.124
Brick_list_mcool_normalisations0.0010.0000.001
Brick_list_mcool_resolutions0.0000.0010.001
Brick_list_rangekeys1.0050.0651.112
Brick_list_ranges_mcols1.0660.0701.137
Brick_load_cis_matrix_till_distance1.4430.1561.601
Brick_load_data_from_mcool0.0010.0010.001
Brick_load_data_from_sparse0.0010.0010.001
Brick_load_matrix1.5830.1751.762
Brick_local_score_differentiator2.7050.2473.039
Brick_make_ranges0.0150.0010.016
Brick_matrix_dimensions1.5860.1761.766
Brick_matrix_exists1.6450.1841.873
Brick_matrix_filename1.6160.1781.798
Brick_matrix_isdone1.6650.1831.850
Brick_matrix_issparse1.6930.1851.880
Brick_matrix_maxdist1.7070.1801.889
Brick_matrix_minmax1.6840.1801.866
Brick_mcool_normalisation_exists000
Brick_rangekey_exists1.1330.0751.209
Brick_return_region_position1.2960.0701.366
Brick_vizart_plot_heatmap3.1780.2543.472
Create_many_Bricks1.0090.0731.084
Create_many_Bricks_from_mcool0.0000.0000.001
load_BrickContainer1.0690.0621.133