| Back to Multiple platform build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-11-02 11:40:47 -0400 (Thu, 02 Nov 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4729 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4463 |
| lconway | macOS 12.6.5 Monterey | x86_64 | 4.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" | 4478 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4464 |
| 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 948/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| HiCBricks 1.20.0 (landing page) Koustav Pal
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
| lconway | macOS 12.6.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / 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: 1.20.0 |
| Command: /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:HiCBricks.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings HiCBricks_1.20.0.tar.gz |
| StartedAt: 2023-11-02 11:15:41 -0000 (Thu, 02 Nov 2023) |
| EndedAt: 2023-11-02 11:18:53 -0000 (Thu, 02 Nov 2023) |
| EllapsedTime: 192.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: HiCBricks.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:HiCBricks.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings HiCBricks_1.20.0.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/HiCBricks.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HiCBricks/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HiCBricks’ version ‘1.20.0’
* 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 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 R 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 in ‘inst/doc’ ... 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-4.3.1/bin/R CMD INSTALL HiCBricks ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.1/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)
HiCBricks.Rcheck/HiCBricks-Ex.timings
| name | user | system | elapsed | |
| BrickContainer_change_experiment_name | 1.763 | 0.293 | 2.095 | |
| BrickContainer_change_output_directory | 1.342 | 0.264 | 1.607 | |
| BrickContainer_get_path_to_file | 1.210 | 0.016 | 1.228 | |
| BrickContainer_list_chromosomes | 1.231 | 0.000 | 1.235 | |
| BrickContainer_list_experiment_name | 1.206 | 0.024 | 1.233 | |
| BrickContainer_list_files | 1.244 | 0.036 | 1.283 | |
| BrickContainer_list_output_directory | 1.217 | 0.024 | 1.244 | |
| BrickContainer_list_resolutions | 1.221 | 0.016 | 1.239 | |
| BrickContainer_unlink_resolution | 2.508 | 0.040 | 2.552 | |
| Brick_add_ranges | 2.693 | 0.247 | 2.949 | |
| Brick_call_compartments | 2.403 | 0.100 | 2.511 | |
| Brick_export_to_sparse | 3.507 | 0.104 | 3.621 | |
| Brick_fetch_range_index | 1.426 | 0.015 | 1.450 | |
| Brick_fetch_row_vector | 2.418 | 0.032 | 2.464 | |
| Brick_get_bintable | 1.599 | 0.032 | 1.638 | |
| Brick_get_chrominfo | 1.149 | 0.016 | 1.169 | |
| Brick_get_entire_matrix | 1.620 | 0.024 | 1.648 | |
| Brick_get_matrix | 1.586 | 0.020 | 1.610 | |
| Brick_get_matrix_mcols | 1.509 | 0.032 | 1.546 | |
| Brick_get_matrix_within_coords | 2.233 | 0.012 | 2.250 | |
| Brick_get_ranges | 1.255 | 0.040 | 1.299 | |
| Brick_get_values_by_distance | 1.723 | 0.056 | 1.787 | |
| Brick_get_vector_values | 1.636 | 0.039 | 1.680 | |
| Brick_list_matrices | 1.221 | 0.016 | 1.239 | |
| Brick_list_matrix_mcols | 1.164 | 0.020 | 1.189 | |
| Brick_list_mcool_normalisations | 0 | 0 | 0 | |
| Brick_list_mcool_resolutions | 0 | 0 | 0 | |
| Brick_list_rangekeys | 1.168 | 0.020 | 1.193 | |
| Brick_list_ranges_mcols | 1.224 | 0.024 | 1.251 | |
| Brick_load_cis_matrix_till_distance | 1.468 | 0.048 | 1.521 | |
| Brick_load_data_from_mcool | 0 | 0 | 0 | |
| Brick_load_data_from_sparse | 0.001 | 0.000 | 0.000 | |
| Brick_load_matrix | 1.580 | 0.068 | 1.652 | |
| Brick_local_score_differentiator | 2.420 | 0.047 | 2.479 | |
| Brick_make_ranges | 0.012 | 0.000 | 0.013 | |
| Brick_matrix_dimensions | 1.553 | 0.040 | 1.597 | |
| Brick_matrix_exists | 1.520 | 0.012 | 1.536 | |
| Brick_matrix_filename | 1.626 | 0.047 | 1.678 | |
| Brick_matrix_isdone | 1.582 | 0.059 | 1.646 | |
| Brick_matrix_issparse | 1.562 | 0.028 | 1.593 | |
| Brick_matrix_maxdist | 1.606 | 0.028 | 1.637 | |
| Brick_matrix_minmax | 1.522 | 0.040 | 1.566 | |
| Brick_mcool_normalisation_exists | 0 | 0 | 0 | |
| Brick_rangekey_exists | 1.223 | 0.024 | 1.250 | |
| Brick_return_region_position | 1.341 | 0.008 | 1.352 | |
| Brick_vizart_plot_heatmap | 2.741 | 0.072 | 2.819 | |
| Create_many_Bricks | 1.193 | 0.064 | 1.259 | |
| Create_many_Bricks_from_mcool | 0 | 0 | 0 | |
| load_BrickContainer | 1.251 | 0.028 | 1.279 | |