Back to Multiple platform build/check report for BioC 3.19:   simplified   long
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This page was generated on 2024-06-21 17:38 -0400 (Fri, 21 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4758
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4492
merida1macOS 12.7.4 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4506
kjohnson1macOS 13.6.6 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 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 962/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HiCBricks 1.22.0  (landing page)
Koustav Pal
Snapshot Date: 2024-06-19 14:00 -0400 (Wed, 19 Jun 2024)
git_url: https://git.bioconductor.org/packages/HiCBricks
git_branch: RELEASE_3_19
git_last_commit: dceb449
git_last_commit_date: 2024-04-30 11:10:16 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for HiCBricks on nebbiolo1

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: 1.22.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:HiCBricks.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings HiCBricks_1.22.0.tar.gz
StartedAt: 2024-06-20 00:02:03 -0400 (Thu, 20 Jun 2024)
EndedAt: 2024-06-20 00:05:08 -0400 (Thu, 20 Jun 2024)
EllapsedTime: 184.6 seconds
RetCode: 0
Status:   OK  
CheckDir: HiCBricks.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:HiCBricks.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings HiCBricks_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/HiCBricks.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘HiCBricks/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HiCBricks’ version ‘1.22.0’
* 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 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


Installation output

HiCBricks.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL HiCBricks
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/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)

Tests output


Example timings

HiCBricks.Rcheck/HiCBricks-Ex.timings

nameusersystemelapsed
BrickContainer_change_experiment_name1.0410.0451.108
BrickContainer_change_output_directory0.8320.0440.877
BrickContainer_get_path_to_file0.7270.0310.759
BrickContainer_list_chromosomes0.6890.0360.725
BrickContainer_list_experiment_name0.8300.0630.893
BrickContainer_list_files0.7220.0160.737
BrickContainer_list_output_directory0.7150.0240.739
BrickContainer_list_resolutions0.6970.0200.717
BrickContainer_unlink_resolution1.5550.0201.575
Brick_add_ranges1.6730.0721.744
Brick_call_compartments1.2840.0481.333
Brick_export_to_sparse2.1440.0882.231
Brick_fetch_range_index0.8580.0150.874
Brick_fetch_row_vector1.3140.0441.358
Brick_get_bintable0.7990.0040.803
Brick_get_chrominfo0.6700.0160.686
Brick_get_entire_matrix1.0110.0391.051
Brick_get_matrix1.3080.0601.368
Brick_get_matrix_mcols0.9740.0361.010
Brick_get_matrix_within_coords1.3790.0311.411
Brick_get_ranges0.7160.0080.724
Brick_get_values_by_distance1.0820.0121.094
Brick_get_vector_values1.1130.0521.164
Brick_list_matrices0.6890.0160.705
Brick_list_matrix_mcols0.6950.0040.700
Brick_list_mcool_normalisations0.0000.0000.001
Brick_list_mcool_resolutions000
Brick_list_rangekeys0.6820.0080.690
Brick_list_ranges_mcols0.6700.0200.689
Brick_load_cis_matrix_till_distance0.8770.0360.914
Brick_load_data_from_mcool0.0000.0000.001
Brick_load_data_from_sparse0.0000.0000.001
Brick_load_matrix1.0200.0121.032
Brick_local_score_differentiator1.5020.0401.542
Brick_make_ranges0.0070.0000.008
Brick_matrix_dimensions0.9950.0161.010
Brick_matrix_exists0.9600.0441.004
Brick_matrix_filename0.9630.0240.986
Brick_matrix_isdone0.9580.0240.983
Brick_matrix_issparse0.9660.0240.990
Brick_matrix_maxdist0.9780.0441.022
Brick_matrix_minmax0.9600.0601.019
Brick_mcool_normalisation_exists000
Brick_rangekey_exists0.6970.0080.705
Brick_return_region_position0.7910.0160.807
Brick_vizart_plot_heatmap1.7660.0321.798
Create_many_Bricks0.7740.0120.786
Create_many_Bricks_from_mcool000
load_BrickContainer0.7860.0160.803