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This page was generated on 2024-03-29 11:36:01 -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 nebbiolo2


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: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:HiCBricks.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings HiCBricks_1.20.0.tar.gz
StartedAt: 2024-03-27 23:16:51 -0400 (Wed, 27 Mar 2024)
EndedAt: 2024-03-27 23:20:01 -0400 (Wed, 27 Mar 2024)
EllapsedTime: 189.6 seconds
RetCode: 0
Status:   OK  
CheckDir: HiCBricks.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:HiCBricks.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings HiCBricks_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/HiCBricks.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* 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 ‘1.20.0’
* 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 ...
  ‘IntroductionToHiCBricks.rmd’ using ‘UTF-8’... OK
 NONE
* 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-3.18-bioc/R/bin/R CMD INSTALL HiCBricks
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.18-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_name1.1210.0461.188
BrickContainer_change_output_directory0.7750.0560.831
BrickContainer_get_path_to_file0.7510.0280.780
BrickContainer_list_chromosomes0.7270.0240.751
BrickContainer_list_experiment_name0.8040.0160.819
BrickContainer_list_files0.7910.0400.830
BrickContainer_list_output_directory0.7620.0080.770
BrickContainer_list_resolutions0.7600.0200.781
BrickContainer_unlink_resolution1.6040.0601.665
Brick_add_ranges1.8030.0481.868
Brick_call_compartments1.1740.0401.215
Brick_export_to_sparse2.3380.0882.426
Brick_fetch_range_index0.9320.0160.948
Brick_fetch_row_vector1.6660.0561.723
Brick_get_bintable0.7970.0080.805
Brick_get_chrominfo1.0660.0481.115
Brick_get_entire_matrix1.0340.0561.090
Brick_get_matrix1.0190.0121.032
Brick_get_matrix_mcols1.1070.0121.119
Brick_get_matrix_within_coords1.4530.0521.505
Brick_get_ranges0.7680.0200.788
Brick_get_values_by_distance1.1400.0081.148
Brick_get_vector_values1.040.041.08
Brick_list_matrices0.7510.0040.756
Brick_list_matrix_mcols0.7290.0120.740
Brick_list_mcool_normalisations000
Brick_list_mcool_resolutions0.0000.0000.001
Brick_list_rangekeys0.8380.0160.854
Brick_list_ranges_mcols0.7390.0080.748
Brick_load_cis_matrix_till_distance0.9270.0200.948
Brick_load_data_from_mcool000
Brick_load_data_from_sparse0.0010.0000.000
Brick_load_matrix1.0250.0441.068
Brick_local_score_differentiator1.5630.0521.615
Brick_make_ranges0.0080.0000.008
Brick_matrix_dimensions1.0920.0201.111
Brick_matrix_exists1.0390.0481.087
Brick_matrix_filename1.0270.0201.046
Brick_matrix_isdone1.0340.0081.042
Brick_matrix_issparse1.0060.0081.013
Brick_matrix_maxdist1.0050.0201.024
Brick_matrix_minmax1.1060.0641.170
Brick_mcool_normalisation_exists000
Brick_rangekey_exists0.7820.0080.790
Brick_return_region_position0.8420.0160.859
Brick_vizart_plot_heatmap1.9070.0241.932
Create_many_Bricks0.7860.0120.798
Create_many_Bricks_from_mcool000
load_BrickContainer0.9770.0200.998