| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-28 12:04 -0400 (Tue, 28 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" | 4901 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4691 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4637 |
| 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 978/2361 | 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 | |||||||||
|
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: /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_1.27.1.tar.gz |
| StartedAt: 2025-10-27 22:15:07 -0400 (Mon, 27 Oct 2025) |
| EndedAt: 2025-10-27 22:18:52 -0400 (Mon, 27 Oct 2025) |
| EllapsedTime: 225.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: HiCBricks.Rcheck |
| Warnings: 0 |
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### Running command:
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### /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_1.27.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/HiCBricks.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HiCBricks/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HiCBricks’ version ‘1.27.1’
* 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 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
HiCBricks.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL HiCBricks ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/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 | 1.297 | 0.145 | 4.222 | |
| BrickContainer_change_output_directory | 1.049 | 0.098 | 1.339 | |
| BrickContainer_get_path_to_file | 0.875 | 0.078 | 1.040 | |
| BrickContainer_list_chromosomes | 0.876 | 0.080 | 1.418 | |
| BrickContainer_list_experiment_name | 0.889 | 0.086 | 2.003 | |
| BrickContainer_list_files | 0.911 | 0.086 | 1.879 | |
| BrickContainer_list_output_directory | 0.879 | 0.087 | 1.457 | |
| BrickContainer_list_resolutions | 0.867 | 0.084 | 1.685 | |
| BrickContainer_unlink_resolution | 1.886 | 0.181 | 2.475 | |
| Brick_add_ranges | 1.986 | 0.135 | 2.144 | |
| Brick_call_compartments | 1.428 | 0.307 | 2.070 | |
| Brick_export_to_sparse | 2.572 | 0.426 | 3.222 | |
| Brick_fetch_range_index | 0.974 | 0.083 | 1.252 | |
| Brick_fetch_row_vector | 1.911 | 0.327 | 2.582 | |
| Brick_get_bintable | 0.961 | 0.086 | 1.180 | |
| Brick_get_chrominfo | 0.948 | 0.087 | 1.061 | |
| Brick_get_entire_matrix | 1.437 | 0.325 | 1.775 | |
| Brick_get_matrix | 1.411 | 0.329 | 1.778 | |
| Brick_get_matrix_mcols | 1.327 | 0.330 | 1.773 | |
| Brick_get_matrix_within_coords | 1.899 | 0.331 | 2.239 | |
| Brick_get_ranges | 0.957 | 0.086 | 1.046 | |
| Brick_get_values_by_distance | 1.485 | 0.368 | 1.866 | |
| Brick_get_vector_values | 1.352 | 0.329 | 1.691 | |
| Brick_list_matrices | 0.958 | 0.099 | 1.066 | |
| Brick_list_matrix_mcols | 0.973 | 0.092 | 1.071 | |
| Brick_list_mcool_normalisations | 0.001 | 0.000 | 0.001 | |
| Brick_list_mcool_resolutions | 0.000 | 0.001 | 0.000 | |
| Brick_list_rangekeys | 0.972 | 0.092 | 1.070 | |
| Brick_list_ranges_mcols | 0.980 | 0.097 | 1.084 | |
| Brick_load_cis_matrix_till_distance | 1.269 | 0.216 | 1.503 | |
| Brick_load_data_from_mcool | 0.001 | 0.000 | 0.001 | |
| Brick_load_data_from_sparse | 0.000 | 0.000 | 0.001 | |
| Brick_load_matrix | 1.364 | 0.342 | 1.734 | |
| Brick_local_score_differentiator | 2.200 | 0.632 | 2.883 | |
| Brick_make_ranges | 0.012 | 0.000 | 0.012 | |
| Brick_matrix_dimensions | 1.337 | 0.403 | 1.749 | |
| Brick_matrix_exists | 1.333 | 0.331 | 1.674 | |
| Brick_matrix_filename | 1.249 | 0.391 | 1.682 | |
| Brick_matrix_isdone | 1.175 | 0.277 | 1.462 | |
| Brick_matrix_issparse | 1.223 | 0.405 | 1.643 | |
| Brick_matrix_maxdist | 1.165 | 0.265 | 1.438 | |
| Brick_matrix_minmax | 1.142 | 0.248 | 1.396 | |
| Brick_mcool_normalisation_exists | 0.000 | 0.001 | 0.001 | |
| Brick_rangekey_exists | 0.799 | 0.082 | 0.885 | |
| Brick_return_region_position | 0.902 | 0.081 | 0.989 | |
| Brick_vizart_plot_heatmap | 2.408 | 0.344 | 2.775 | |
| Create_many_Bricks | 0.895 | 0.090 | 0.991 | |
| Create_many_Bricks_from_mcool | 0.000 | 0.001 | 0.000 | |
| load_BrickContainer | 0.928 | 0.095 | 1.028 | |