Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2024-11-20 12:06 -0500 (Wed, 20 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4481
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4479
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4359
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4539
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4493
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: 2024-11-19 13:40 -0500 (Tue, 19 Nov 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)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  


CHECK results for HiCBricks on lconway

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: /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_1.24.0.tar.gz
StartedAt: 2024-11-19 22:57:13 -0500 (Tue, 19 Nov 2024)
EndedAt: 2024-11-19 23:03:02 -0500 (Tue, 19 Nov 2024)
EllapsedTime: 349.7 seconds
RetCode: 0
Status:   OK  
CheckDir: HiCBricks.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running 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_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/HiCBricks.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* 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 ‘1.24.0’
* 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 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


Installation output

HiCBricks.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL HiCBricks
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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_name0.8630.0830.958
BrickContainer_change_output_directory0.6950.0600.755
BrickContainer_get_path_to_file0.6040.0530.659
BrickContainer_list_chromosomes0.5790.0550.637
BrickContainer_list_experiment_name0.6290.0610.695
BrickContainer_list_files0.6300.0550.692
BrickContainer_list_output_directory0.5930.0540.650
BrickContainer_list_resolutions0.5940.0520.650
BrickContainer_unlink_resolution1.2720.1161.399
Brick_add_ranges1.4000.0971.516
Brick_call_compartments1.0580.1631.230
Brick_export_to_sparse1.8320.1952.037
Brick_fetch_range_index0.7120.0560.772
Brick_fetch_row_vector1.1300.1461.282
Brick_get_bintable0.6250.0570.684
Brick_get_chrominfo0.6010.0570.662
Brick_get_entire_matrix0.9080.1181.033
Brick_get_matrix1.1230.1331.261
Brick_get_matrix_mcols0.8510.1010.958
Brick_get_matrix_within_coords1.2070.2041.416
Brick_get_ranges0.5990.0520.654
Brick_get_values_by_distance0.9810.2591.254
Brick_get_vector_values0.8750.1070.988
Brick_list_matrices0.5910.0590.653
Brick_list_matrix_mcols0.5690.0530.624
Brick_list_mcool_normalisations0.0000.0010.000
Brick_list_mcool_resolutions000
Brick_list_rangekeys0.5840.0560.644
Brick_list_ranges_mcols0.5790.0550.638
Brick_load_cis_matrix_till_distance0.7830.1030.889
Brick_load_data_from_mcool000
Brick_load_data_from_sparse000
Brick_load_matrix0.8420.1230.968
Brick_local_score_differentiator1.3870.1921.589
Brick_make_ranges0.0070.0010.008
Brick_matrix_dimensions0.8890.1171.012
Brick_matrix_exists0.8700.1931.070
Brick_matrix_filename0.8570.1180.982
Brick_matrix_isdone0.8690.1291.005
Brick_matrix_issparse0.8710.1160.993
Brick_matrix_maxdist0.9290.1751.124
Brick_matrix_minmax0.9010.2121.124
Brick_mcool_normalisation_exists000
Brick_rangekey_exists0.6290.0650.697
Brick_return_region_position0.7110.0690.823
Brick_vizart_plot_heatmap1.6380.2591.907
Create_many_Bricks0.6400.0750.720
Create_many_Bricks_from_mcool0.0000.0010.001
load_BrickContainer0.6890.0690.761