Back to Multiple platform build/check report for BioC 3.18:   simplified   long
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This page was generated on 2024-03-29 11:36:51 -0400 (Fri, 29 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4669
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4404
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4427
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 948/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HiCBricks 1.20.0  (landing page)
Koustav Pal
Snapshot Date: 2024-03-27 14:05:05 -0400 (Wed, 27 Mar 2024)
git_url: https://git.bioconductor.org/packages/HiCBricks
git_branch: RELEASE_3_18
git_last_commit: 011eda1
git_last_commit_date: 2023-10-24 11:08:46 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for HiCBricks on palomino4


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: 1.20.0
Command: F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:HiCBricks.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings HiCBricks_1.20.0.tar.gz
StartedAt: 2024-03-28 01:41:08 -0400 (Thu, 28 Mar 2024)
EndedAt: 2024-03-28 01:45:17 -0400 (Thu, 28 Mar 2024)
EllapsedTime: 248.8 seconds
RetCode: 0
Status:   OK  
CheckDir: HiCBricks.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:HiCBricks.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings HiCBricks_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.18-bioc/meat/HiCBricks.Rcheck'
* using R version 4.3.3 (2024-02-29 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.3.0
    GNU Fortran (GCC) 12.3.0
* running under: Windows Server 2022 x64 (build 20348)
* 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 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 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
Examples with CPU (user + system) or elapsed time > 5s
                                 user system elapsed
Brick_export_to_sparse           3.36   0.39    5.35
BrickContainer_unlink_resolution 2.50   0.41    5.34
* 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


Installation output

HiCBricks.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL HiCBricks
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.18-bioc/R/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_name1.590.212.97
BrickContainer_change_output_directory1.200.222.55
BrickContainer_get_path_to_file1.210.122.35
BrickContainer_list_chromosomes1.030.142.33
BrickContainer_list_experiment_name1.020.312.37
BrickContainer_list_files1.230.192.74
BrickContainer_list_output_directory1.110.222.17
BrickContainer_list_resolutions1.220.222.75
BrickContainer_unlink_resolution2.500.415.34
Brick_add_ranges2.170.234.52
Brick_call_compartments1.490.283.48
Brick_export_to_sparse3.360.395.35
Brick_fetch_range_index1.060.172.37
Brick_fetch_row_vector2.020.304.03
Brick_get_bintable1.470.132.72
Brick_get_chrominfo1.020.132.60
Brick_get_entire_matrix1.540.253.25
Brick_get_matrix1.550.313.45
Brick_get_matrix_mcols1.560.223.25
Brick_get_matrix_within_coords1.860.223.86
Brick_get_ranges0.990.262.53
Brick_get_values_by_distance1.700.273.45
Brick_get_vector_values1.500.283.57
Brick_list_matrices0.950.062.36
Brick_list_matrix_mcols0.960.132.23
Brick_list_mcool_normalisations000
Brick_list_mcool_resolutions000
Brick_list_rangekeys0.960.182.53
Brick_list_ranges_mcols1.100.182.24
Brick_load_cis_matrix_till_distance1.230.173.03
Brick_load_data_from_mcool000
Brick_load_data_from_sparse000
Brick_load_matrix1.360.292.98
Brick_local_score_differentiator2.440.474.39
Brick_make_ranges0.020.000.02
Brick_matrix_dimensions1.390.173.22
Brick_matrix_exists1.340.183.01
Brick_matrix_filename1.530.152.88
Brick_matrix_isdone1.410.213.28
Brick_matrix_issparse1.580.183.26
Brick_matrix_maxdist1.340.273.04
Brick_matrix_minmax1.610.253.35
Brick_mcool_normalisation_exists000
Brick_rangekey_exists0.970.142.29
Brick_return_region_position1.330.252.67
Brick_vizart_plot_heatmap2.780.334.84
Create_many_Bricks1.110.252.25
Create_many_Bricks_from_mcool000
load_BrickContainer0.980.222.42