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This page was generated on 2024-12-23 12:05 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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 953/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HiCBricks 1.24.0  (landing page)
Koustav Pal
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/HiCBricks
git_branch: RELEASE_3_20
git_last_commit: 989054d
git_last_commit_date: 2024-10-29 10:32:24 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for HiCBricks on palomino8

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: 1.24.0
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:HiCBricks.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings HiCBricks_1.24.0.tar.gz
StartedAt: 2024-12-20 02:24:43 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 02:29:34 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 290.8 seconds
RetCode: 0
Status:   OK  
CheckDir: HiCBricks.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:HiCBricks.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings HiCBricks_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/HiCBricks.Rcheck'
* using R version 4.4.2 (2024-10-31 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'HiCBricks/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'HiCBricks' version '1.24.0'
* 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 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 code 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
Examples with CPU (user + system) or elapsed time > 5s
                                 user system elapsed
Brick_export_to_sparse           3.58   0.40    5.67
Brick_vizart_plot_heatmap        2.82   0.28    5.33
BrickContainer_unlink_resolution 2.34   0.26    6.57
Brick_add_ranges                 2.46   0.13    5.93
Brick_get_matrix_within_coords   1.89   0.28    5.46
Brick_matrix_minmax              1.48   0.25    6.10
Brick_get_matrix_mcols           1.43   0.14    5.21
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL HiCBricks
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/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_name1.690.163.25
BrickContainer_change_output_directory1.160.112.86
BrickContainer_get_path_to_file1.100.152.73
BrickContainer_list_chromosomes1.060.173.64
BrickContainer_list_experiment_name1.090.072.85
BrickContainer_list_files1.160.093.23
BrickContainer_list_output_directory1.110.113.05
BrickContainer_list_resolutions1.060.114.33
BrickContainer_unlink_resolution2.340.266.57
Brick_add_ranges2.460.135.93
Brick_call_compartments1.640.334.04
Brick_export_to_sparse3.580.405.67
Brick_fetch_range_index1.320.133.44
Brick_fetch_row_vector2.070.174.85
Brick_get_bintable1.170.093.18
Brick_get_chrominfo1.110.083.30
Brick_get_entire_matrix1.660.274.50
Brick_get_matrix1.880.204.68
Brick_get_matrix_mcols1.430.145.21
Brick_get_matrix_within_coords1.890.285.46
Brick_get_ranges1.220.163.38
Brick_get_values_by_distance1.520.233.97
Brick_get_vector_values1.480.284.00
Brick_list_matrices0.890.102.53
Brick_list_matrix_mcols0.920.192.86
Brick_list_mcool_normalisations000
Brick_list_mcool_resolutions000
Brick_list_rangekeys1.130.032.84
Brick_list_ranges_mcols1.020.202.89
Brick_load_cis_matrix_till_distance1.320.273.14
Brick_load_data_from_mcool000
Brick_load_data_from_sparse000
Brick_load_matrix1.280.173.85
Brick_local_score_differentiator1.960.314.61
Brick_make_ranges000
Brick_matrix_dimensions1.440.133.70
Brick_matrix_exists1.370.203.75
Brick_matrix_filename1.200.183.37
Brick_matrix_isdone1.350.254.52
Brick_matrix_issparse1.370.253.47
Brick_matrix_maxdist1.210.344.96
Brick_matrix_minmax1.480.256.10
Brick_mcool_normalisation_exists000
Brick_rangekey_exists1.050.123.29
Brick_return_region_position0.970.162.83
Brick_vizart_plot_heatmap2.820.285.33
Create_many_Bricks1.250.162.86
Create_many_Bricks_from_mcool000
load_BrickContainer1.190.123.58