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This page was generated on 2024-04-18 11:32:11 -0400 (Thu, 18 Apr 2024).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson1macOS 13.6.1 Venturaarm644.3.3 (2024-02-29) -- "Angel Food Cake" 4388
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 948/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HiCBricks 1.20.0  (landing page)
Koustav Pal
Snapshot Date: 2024-04-16 09:00:03 -0400 (Tue, 16 Apr 2024)
git_url: https://git.bioconductor.org/packages/HiCBricks
git_branch: RELEASE_3_18
git_last_commit: 011eda1
git_last_commit_date: 2023-10-24 11:08:46 -0400 (Tue, 24 Oct 2023)
kjohnson1macOS 13.6.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for HiCBricks on kjohnson1


To the developers/maintainers of the HiCBricks package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: HiCBricks
Version: 1.20.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:HiCBricks.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings HiCBricks_1.20.0.tar.gz
StartedAt: 2024-04-17 16:15:27 -0400 (Wed, 17 Apr 2024)
EndedAt: 2024-04-17 16:18:15 -0400 (Wed, 17 Apr 2024)
EllapsedTime: 167.5 seconds
RetCode: 0
Status:   OK  
CheckDir: HiCBricks.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:HiCBricks.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings HiCBricks_1.20.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/HiCBricks.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HiCBricks/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HiCBricks’ version ‘1.20.0’
* 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:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL HiCBricks
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/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_name1.1480.1051.261
BrickContainer_change_output_directory0.7300.0790.810
BrickContainer_get_path_to_file0.6880.0880.817
BrickContainer_list_chromosomes0.6850.0880.775
BrickContainer_list_experiment_name0.6740.0750.752
BrickContainer_list_files0.6950.0820.790
BrickContainer_list_output_directory0.6780.0740.753
BrickContainer_list_resolutions0.6730.0940.781
BrickContainer_unlink_resolution1.5370.2031.744
Brick_add_ranges1.6810.1301.813
Brick_call_compartments1.2820.1921.489
Brick_export_to_sparse2.3610.3512.750
Brick_fetch_range_index0.8920.1201.025
Brick_fetch_row_vector1.4020.2331.666
Brick_get_bintable1.1630.1061.278
Brick_get_chrominfo0.6930.0860.784
Brick_get_entire_matrix1.0830.1561.243
Brick_get_matrix1.0400.1441.185
Brick_get_matrix_mcols1.0600.1661.234
Brick_get_matrix_within_coords1.5230.1941.732
Brick_get_ranges0.7000.0920.796
Brick_get_values_by_distance1.1240.1731.300
Brick_get_vector_values1.0670.1491.227
Brick_list_matrices0.7170.0900.837
Brick_list_matrix_mcols0.6650.0790.746
Brick_list_mcool_normalisations0.0000.0000.001
Brick_list_mcool_resolutions0.0010.0000.000
Brick_list_rangekeys0.6750.0760.755
Brick_list_ranges_mcols0.6930.0970.791
Brick_load_cis_matrix_till_distance0.9400.1351.077
Brick_load_data_from_mcool0.0000.0000.001
Brick_load_data_from_sparse0.0000.0010.001
Brick_load_matrix1.0160.1441.202
Brick_local_score_differentiator1.5820.1961.784
Brick_make_ranges0.0100.0010.011
Brick_matrix_dimensions1.0360.1471.194
Brick_matrix_exists1.0200.3251.350
Brick_matrix_filename1.0070.2841.292
Brick_matrix_isdone1.0360.1741.242
Brick_matrix_issparse1.0510.2681.338
Brick_matrix_maxdist1.0520.1981.266
Brick_matrix_minmax1.0620.2451.319
Brick_mcool_normalisation_exists000
Brick_rangekey_exists0.7270.1280.863
Brick_return_region_position0.8140.1300.953
Brick_vizart_plot_heatmap2.0500.2882.374
Create_many_Bricks0.7370.1190.865
Create_many_Bricks_from_mcool0.0000.0010.001
load_BrickContainer0.7710.1110.903