Back to Multiple platform build/check report for BioC 3.17:   simplified   long
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This page was generated on 2023-09-25 11:36:22 -0400 (Mon, 25 Sep 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4625
palomino3Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4378
merida1macOS 12.6.4 Montereyx86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4394
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 925/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HiCBricks 1.18.0  (landing page)
Koustav Pal
Snapshot Date: 2023-09-24 14:00:11 -0400 (Sun, 24 Sep 2023)
git_url: https://git.bioconductor.org/packages/HiCBricks
git_branch: RELEASE_3_17
git_last_commit: b4ffe28
git_last_commit_date: 2023-04-25 11:05:30 -0400 (Tue, 25 Apr 2023)
nebbiolo1Linux (Ubuntu 22.04.2 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 12.6.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for HiCBricks on palomino3


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: 1.18.0
Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:HiCBricks.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings HiCBricks_1.18.0.tar.gz
StartedAt: 2023-09-25 03:15:00 -0400 (Mon, 25 Sep 2023)
EndedAt: 2023-09-25 03:19:04 -0400 (Mon, 25 Sep 2023)
EllapsedTime: 243.7 seconds
RetCode: 0
Status:   OK  
CheckDir: HiCBricks.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:HiCBricks.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings HiCBricks_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.17-bioc/meat/HiCBricks.Rcheck'
* using R version 4.3.1 (2023-06-16 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.2.0
    GNU Fortran (GCC) 12.2.0
* 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 '1.18.0'
* 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           3.01   0.47    5.61
BrickContainer_unlink_resolution 2.34   0.48    5.11
Brick_vizart_plot_heatmap        2.30   0.30    5.11
* 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-3.17-bioc\R\bin\R.exe CMD INSTALL HiCBricks
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.17-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_name1.640.193.87
BrickContainer_change_output_directory0.910.223.33
BrickContainer_get_path_to_file0.940.253.91
BrickContainer_list_chromosomes0.800.083.14
BrickContainer_list_experiment_name1.070.122.47
BrickContainer_list_files1.000.312.70
BrickContainer_list_output_directory0.570.182.33
BrickContainer_list_resolutions1.200.142.34
BrickContainer_unlink_resolution2.340.485.11
Brick_add_ranges2.140.284.50
Brick_call_compartments1.720.283.98
Brick_export_to_sparse3.010.475.61
Brick_fetch_range_index0.990.222.74
Brick_fetch_row_vector1.970.283.80
Brick_get_bintable1.370.122.86
Brick_get_chrominfo0.990.212.27
Brick_get_entire_matrix1.250.253.64
Brick_get_matrix1.420.293.59
Brick_get_matrix_mcols1.120.243.19
Brick_get_matrix_within_coords1.610.183.76
Brick_get_ranges1.030.132.33
Brick_get_values_by_distance1.130.264.02
Brick_get_vector_values1.270.223.78
Brick_list_matrices1.000.182.11
Brick_list_matrix_mcols1.050.142.50
Brick_list_mcool_normalisations000
Brick_list_mcool_resolutions000
Brick_list_rangekeys0.860.302.72
Brick_list_ranges_mcols1.010.172.47
Brick_load_cis_matrix_till_distance1.000.233.03
Brick_load_data_from_mcool000
Brick_load_data_from_sparse000
Brick_load_matrix0.940.273.34
Brick_local_score_differentiator1.870.284.61
Brick_make_ranges0.020.000.02
Brick_matrix_dimensions1.410.243.26
Brick_matrix_exists1.320.203.64
Brick_matrix_filename1.380.203.42
Brick_matrix_isdone1.190.254.44
Brick_matrix_issparse1.340.143.88
Brick_matrix_maxdist1.140.213.61
Brick_matrix_minmax1.330.203.64
Brick_mcool_normalisation_exists000
Brick_rangekey_exists0.950.202.57
Brick_return_region_position1.030.192.24
Brick_vizart_plot_heatmap2.300.305.11
Create_many_Bricks0.840.222.08
Create_many_Bricks_from_mcool000
load_BrickContainer1.090.142.53