| Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-10-24 12:03 -0400 (Fri, 24 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4898 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4688 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4634 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4658 |
| 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 977/2359 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| HiCBricks 1.27.1 (landing page) Koustav Pal
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | |||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | NA | ||||||||||
|
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. |
| Package: HiCBricks |
| Version: 1.27.1 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:HiCBricks.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings HiCBricks_1.27.1.tar.gz |
| StartedAt: 2025-10-24 00:22:40 -0400 (Fri, 24 Oct 2025) |
| EndedAt: 2025-10-24 00:26:09 -0400 (Fri, 24 Oct 2025) |
| EllapsedTime: 209.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: HiCBricks.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:HiCBricks.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings HiCBricks_1.27.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/HiCBricks.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘HiCBricks/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HiCBricks’ version ‘1.27.1’
* 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 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
HiCBricks.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL HiCBricks ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘HiCBricks’ ... ** this is package ‘HiCBricks’ version ‘1.27.1’ ** 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)
HiCBricks.Rcheck/HiCBricks-Ex.timings
| name | user | system | elapsed | |
| BrickContainer_change_experiment_name | 1.518 | 0.028 | 1.552 | |
| BrickContainer_change_output_directory | 0.929 | 0.019 | 0.950 | |
| BrickContainer_get_path_to_file | 0.911 | 0.014 | 0.928 | |
| BrickContainer_list_chromosomes | 0.996 | 0.018 | 1.017 | |
| BrickContainer_list_experiment_name | 0.952 | 0.014 | 0.968 | |
| BrickContainer_list_files | 1.063 | 0.019 | 1.085 | |
| BrickContainer_list_output_directory | 0.944 | 0.012 | 0.960 | |
| BrickContainer_list_resolutions | 0.952 | 0.015 | 0.971 | |
| BrickContainer_unlink_resolution | 2.112 | 0.027 | 2.147 | |
| Brick_add_ranges | 2.489 | 0.017 | 2.509 | |
| Brick_call_compartments | 1.354 | 0.044 | 1.402 | |
| Brick_export_to_sparse | 2.761 | 0.110 | 2.874 | |
| Brick_fetch_range_index | 1.055 | 0.030 | 1.089 | |
| Brick_fetch_row_vector | 1.616 | 0.039 | 1.658 | |
| Brick_get_bintable | 1.483 | 0.068 | 1.554 | |
| Brick_get_chrominfo | 0.831 | 0.020 | 0.854 | |
| Brick_get_entire_matrix | 1.304 | 0.097 | 1.407 | |
| Brick_get_matrix | 1.152 | 0.043 | 1.199 | |
| Brick_get_matrix_mcols | 1.121 | 0.019 | 1.143 | |
| Brick_get_matrix_within_coords | 1.725 | 0.029 | 1.757 | |
| Brick_get_ranges | 0.862 | 0.012 | 0.877 | |
| Brick_get_values_by_distance | 1.362 | 0.033 | 1.399 | |
| Brick_get_vector_values | 1.198 | 0.020 | 1.224 | |
| Brick_list_matrices | 0.769 | 0.016 | 0.788 | |
| Brick_list_matrix_mcols | 0.816 | 0.013 | 0.838 | |
| Brick_list_mcool_normalisations | 0.001 | 0.000 | 0.001 | |
| Brick_list_mcool_resolutions | 0.001 | 0.000 | 0.000 | |
| Brick_list_rangekeys | 0.820 | 0.018 | 0.843 | |
| Brick_list_ranges_mcols | 0.790 | 0.016 | 0.809 | |
| Brick_load_cis_matrix_till_distance | 1.006 | 0.019 | 1.029 | |
| Brick_load_data_from_mcool | 0 | 0 | 0 | |
| Brick_load_data_from_sparse | 0 | 0 | 0 | |
| Brick_load_matrix | 1.119 | 0.027 | 1.149 | |
| Brick_local_score_differentiator | 1.772 | 0.038 | 1.815 | |
| Brick_make_ranges | 0.01 | 0.00 | 0.01 | |
| Brick_matrix_dimensions | 1.156 | 0.045 | 1.205 | |
| Brick_matrix_exists | 1.167 | 0.049 | 1.220 | |
| Brick_matrix_filename | 1.120 | 0.026 | 1.150 | |
| Brick_matrix_isdone | 1.144 | 0.031 | 1.179 | |
| Brick_matrix_issparse | 1.139 | 0.028 | 1.170 | |
| Brick_matrix_maxdist | 1.070 | 0.035 | 1.108 | |
| Brick_matrix_minmax | 1.107 | 0.026 | 1.137 | |
| Brick_mcool_normalisation_exists | 0 | 0 | 0 | |
| Brick_rangekey_exists | 0.832 | 0.012 | 0.846 | |
| Brick_return_region_position | 0.881 | 0.019 | 0.903 | |
| Brick_vizart_plot_heatmap | 2.223 | 0.041 | 2.266 | |
| Create_many_Bricks | 0.761 | 0.014 | 0.781 | |
| Create_many_Bricks_from_mcool | 0 | 0 | 0 | |
| load_BrickContainer | 0.819 | 0.015 | 0.837 | |