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This page was generated on 2024-03-04 11:37:26 -0500 (Mon, 04 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" 4692
palomino4Windows Server 2022 Datacenterx644.3.2 (2023-10-31 ucrt) -- "Eye Holes" 4445
lconwaymacOS 12.7.1 Montereyx86_644.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" 4466
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: 2024-03-03 14:05:05 -0500 (Sun, 03 Mar 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 -0500 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for HiCBricks on lconway


To the developers/maintainers of the HiCBricks package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/HiCBricks.git to reflect on this report. See Troubleshooting Build Report for more information.
- 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: 2024-03-03 21:07:22 -0500 (Sun, 03 Mar 2024)
EndedAt: 2024-03-03 21:10:24 -0500 (Sun, 03 Mar 2024)
EllapsedTime: 181.9 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
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/HiCBricks.Rcheck’
* using R version 4.3.2 Patched (2023-11-01 r85457)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* 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

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL HiCBricks
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/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_name1.3810.1371.558
BrickContainer_change_output_directory0.9790.0991.107
BrickContainer_get_path_to_file0.8910.0830.988
BrickContainer_list_chromosomes0.9070.0881.009
BrickContainer_list_experiment_name0.9130.0921.023
BrickContainer_list_files0.9380.0891.045
BrickContainer_list_output_directory0.9170.0891.019
BrickContainer_list_resolutions0.8860.0870.985
BrickContainer_unlink_resolution1.9370.1872.146
Brick_add_ranges1.9480.1342.102
Brick_call_compartments1.4260.2521.700
Brick_export_to_sparse2.6880.3463.068
Brick_fetch_range_index1.0520.0911.154
Brick_fetch_row_vector1.6710.2631.968
Brick_get_bintable1.2720.0971.385
Brick_get_chrominfo0.8890.0910.992
Brick_get_entire_matrix1.3560.2781.669
Brick_get_matrix1.3030.2411.579
Brick_get_matrix_mcols1.2540.2441.518
Brick_get_matrix_within_coords1.7670.2852.095
Brick_get_ranges0.9010.0901.005
Brick_get_values_by_distance1.4340.3101.831
Brick_get_vector_values1.3610.2301.614
Brick_list_matrices0.8970.0890.997
Brick_list_matrix_mcols0.9010.0880.999
Brick_list_mcool_normalisations0.0010.0000.001
Brick_list_mcool_resolutions000
Brick_list_rangekeys0.8900.0880.986
Brick_list_ranges_mcols0.8650.0900.972
Brick_load_cis_matrix_till_distance1.1290.2051.357
Brick_load_data_from_mcool0.0000.0010.001
Brick_load_data_from_sparse0.0000.0010.000
Brick_load_matrix1.2270.2501.509
Brick_local_score_differentiator1.8680.3312.251
Brick_make_ranges0.0070.0000.007
Brick_matrix_dimensions1.2380.2021.459
Brick_matrix_exists1.2120.2031.434
Brick_matrix_filename1.1990.2211.443
Brick_matrix_isdone1.2120.1811.418
Brick_matrix_issparse1.2650.2041.502
Brick_matrix_maxdist1.2170.2491.490
Brick_matrix_minmax1.2500.2091.478
Brick_mcool_normalisation_exists0.0000.0000.001
Brick_rangekey_exists0.8800.0970.994
Brick_return_region_position1.0250.0951.140
Brick_vizart_plot_heatmap2.2840.3242.632
Create_many_Bricks0.9070.0921.014
Create_many_Bricks_from_mcool000
load_BrickContainer0.9520.0911.053