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This page was generated on 2024-12-23 12:04 -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 nebbiolo2

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: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:HiCBricks.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings HiCBricks_1.24.0.tar.gz
StartedAt: 2024-12-20 01:01:35 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 01:08:03 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 387.3 seconds
RetCode: 0
Status:   OK  
CheckDir: HiCBricks.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:HiCBricks.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings HiCBricks_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/HiCBricks.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* 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 ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 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 loading without being on the library search path ... 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 ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

HiCBricks.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL HiCBricks
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-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_name0.9550.0230.977
BrickContainer_change_output_directory0.7760.0050.781
BrickContainer_get_path_to_file0.6690.0120.680
BrickContainer_list_chromosomes0.6730.0080.680
BrickContainer_list_experiment_name0.6600.0120.672
BrickContainer_list_files0.6850.0090.694
BrickContainer_list_output_directory0.6720.0550.728
BrickContainer_list_resolutions0.6770.0090.686
BrickContainer_unlink_resolution1.4390.0521.491
Brick_add_ranges1.5780.0321.610
Brick_call_compartments1.1010.0721.173
Brick_export_to_sparse1.9920.0392.033
Brick_fetch_range_index0.8070.0530.861
Brick_fetch_row_vector1.2030.0231.226
Brick_get_bintable0.7020.0090.711
Brick_get_chrominfo0.6590.0110.670
Brick_get_entire_matrix0.9390.0300.969
Brick_get_matrix1.2010.0561.257
Brick_get_matrix_mcols0.9140.0290.943
Brick_get_matrix_within_coords1.3220.0121.334
Brick_get_ranges0.7050.0050.709
Brick_get_values_by_distance1.0300.0641.094
Brick_get_vector_values0.9520.0180.971
Brick_list_matrices0.6730.0100.683
Brick_list_matrix_mcols0.6620.0040.667
Brick_list_mcool_normalisations000
Brick_list_mcool_resolutions000
Brick_list_rangekeys0.6650.0070.673
Brick_list_ranges_mcols0.6720.0080.680
Brick_load_cis_matrix_till_distance0.8270.0170.844
Brick_load_data_from_mcool000
Brick_load_data_from_sparse000
Brick_load_matrix0.8950.0140.910
Brick_local_score_differentiator1.4170.0381.456
Brick_make_ranges0.0070.0000.006
Brick_matrix_dimensions0.9050.0150.921
Brick_matrix_exists0.9090.0170.927
Brick_matrix_filename0.9060.0260.933
Brick_matrix_isdone0.8890.0180.908
Brick_matrix_issparse0.9160.0130.930
Brick_matrix_maxdist0.9280.0150.944
Brick_matrix_minmax0.9000.0110.912
Brick_mcool_normalisation_exists000
Brick_rangekey_exists0.6620.0100.672
Brick_return_region_position0.7360.0120.749
Brick_vizart_plot_heatmap1.6770.0321.709
Create_many_Bricks0.6710.0130.685
Create_many_Bricks_from_mcool000
load_BrickContainer0.6980.0110.710