| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-21 12:07 -0400 (Tue, 21 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" | 4887 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4677 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4622 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4642 |
| 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 974/2353 | 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 | 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: HiCBricks |
| Version: 1.27.1 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:HiCBricks.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings HiCBricks_1.27.1.tar.gz |
| StartedAt: 2025-10-17 10:03:01 -0000 (Fri, 17 Oct 2025) |
| EndedAt: 2025-10-17 10:06:32 -0000 (Fri, 17 Oct 2025) |
| EllapsedTime: 211.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: HiCBricks.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:HiCBricks.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings HiCBricks_1.27.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/HiCBricks.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* 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 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 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: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL HiCBricks ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0/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 | 1.813 | 0.089 | 1.911 | |
| BrickContainer_change_output_directory | 1.288 | 0.028 | 1.324 | |
| BrickContainer_get_path_to_file | 1.200 | 0.072 | 1.276 | |
| BrickContainer_list_chromosomes | 1.200 | 0.060 | 1.265 | |
| BrickContainer_list_experiment_name | 1.243 | 0.028 | 1.280 | |
| BrickContainer_list_files | 1.202 | 0.051 | 1.259 | |
| BrickContainer_list_output_directory | 1.196 | 0.048 | 1.249 | |
| BrickContainer_list_resolutions | 1.190 | 0.044 | 1.238 | |
| BrickContainer_unlink_resolution | 2.515 | 0.084 | 2.612 | |
| Brick_add_ranges | 2.589 | 0.135 | 2.734 | |
| Brick_call_compartments | 2.215 | 0.063 | 2.295 | |
| Brick_export_to_sparse | 3.441 | 0.116 | 3.570 | |
| Brick_fetch_range_index | 1.405 | 0.040 | 1.450 | |
| Brick_fetch_row_vector | 1.988 | 0.047 | 2.043 | |
| Brick_get_bintable | 1.608 | 0.088 | 1.706 | |
| Brick_get_chrominfo | 1.165 | 0.016 | 1.186 | |
| Brick_get_entire_matrix | 1.605 | 0.079 | 1.691 | |
| Brick_get_matrix | 1.510 | 0.020 | 1.535 | |
| Brick_get_matrix_mcols | 1.486 | 0.028 | 1.520 | |
| Brick_get_matrix_within_coords | 2.196 | 0.087 | 2.292 | |
| Brick_get_ranges | 1.221 | 0.028 | 1.253 | |
| Brick_get_values_by_distance | 1.707 | 0.080 | 1.796 | |
| Brick_get_vector_values | 1.559 | 0.028 | 1.592 | |
| Brick_list_matrices | 1.198 | 0.032 | 1.234 | |
| Brick_list_matrix_mcols | 1.169 | 0.035 | 1.211 | |
| Brick_list_mcool_normalisations | 0.000 | 0.000 | 0.001 | |
| Brick_list_mcool_resolutions | 0 | 0 | 0 | |
| Brick_list_rangekeys | 1.184 | 0.059 | 1.247 | |
| Brick_list_ranges_mcols | 1.154 | 0.016 | 1.175 | |
| Brick_load_cis_matrix_till_distance | 1.414 | 0.028 | 1.448 | |
| Brick_load_data_from_mcool | 0 | 0 | 0 | |
| Brick_load_data_from_sparse | 0.001 | 0.000 | 0.001 | |
| Brick_load_matrix | 1.486 | 0.040 | 1.535 | |
| Brick_local_score_differentiator | 2.363 | 0.075 | 2.450 | |
| Brick_make_ranges | 0.013 | 0.000 | 0.013 | |
| Brick_matrix_dimensions | 1.493 | 0.055 | 1.556 | |
| Brick_matrix_exists | 1.505 | 0.032 | 1.543 | |
| Brick_matrix_filename | 1.470 | 0.052 | 1.528 | |
| Brick_matrix_isdone | 1.545 | 0.060 | 1.611 | |
| Brick_matrix_issparse | 1.510 | 0.040 | 1.559 | |
| Brick_matrix_maxdist | 1.502 | 0.032 | 1.541 | |
| Brick_matrix_minmax | 1.510 | 0.020 | 1.536 | |
| Brick_mcool_normalisation_exists | 0 | 0 | 0 | |
| Brick_rangekey_exists | 1.196 | 0.015 | 1.217 | |
| Brick_return_region_position | 1.329 | 0.040 | 1.374 | |
| Brick_vizart_plot_heatmap | 3.004 | 0.072 | 3.090 | |
| Create_many_Bricks | 1.234 | 0.020 | 1.258 | |
| Create_many_Bricks_from_mcool | 0 | 0 | 0 | |
| load_BrickContainer | 1.222 | 0.012 | 1.239 | |