Back to Multiple platform build/check report for BioC 3.17:   simplified   long
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This page was generated on 2023-03-27 11:05:49 -0400 (Mon, 27 Mar 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2023-03-16 r83996) -- "Unsuffered Consequences" 4547
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2023-03-15 r83984 ucrt) -- "Unsuffered Consequences" 4308
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2023-03-16 r83985) -- "Unsuffered Consequences" 4300
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

CHECK results for HiCBricks on palomino3


To the developers/maintainers of the HiCBricks package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 911/2195HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HiCBricks 1.17.0  (landing page)
Koustav Pal
Snapshot Date: 2023-03-26 14:00:09 -0400 (Sun, 26 Mar 2023)
git_url: https://git.bioconductor.org/packages/HiCBricks
git_branch: devel
git_last_commit: d85dbc7
git_last_commit_date: 2022-11-01 11:18:41 -0400 (Tue, 01 Nov 2022)
nebbiolo1Linux (Ubuntu 22.04.1 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 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: HiCBricks
Version: 1.17.0
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_1.17.0.tar.gz
StartedAt: 2023-03-27 02:45:20 -0400 (Mon, 27 Mar 2023)
EndedAt: 2023-03-27 02:49:26 -0400 (Mon, 27 Mar 2023)
EllapsedTime: 245.9 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_1.17.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.17-bioc/meat/HiCBricks.Rcheck'
* using R Under development (unstable) (2023-03-15 r83984 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 '1.17.0'
* 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  2.63   0.38    5.06
Brick_get_vector_values 1.30   0.20    5.92
* 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_name1.150.232.54
BrickContainer_change_output_directory1.030.222.41
BrickContainer_get_path_to_file0.860.142.15
BrickContainer_list_chromosomes0.970.162.21
BrickContainer_list_experiment_name0.780.172.08
BrickContainer_list_files0.940.152.16
BrickContainer_list_output_directory0.920.191.95
BrickContainer_list_resolutions0.890.202.14
BrickContainer_unlink_resolution2.290.494.86
Brick_add_ranges2.270.304.28
Brick_call_compartments1.560.293.83
Brick_export_to_sparse2.630.385.06
Brick_fetch_range_index1.170.152.39
Brick_fetch_row_vector1.730.353.50
Brick_get_bintable1.520.222.72
Brick_get_chrominfo0.920.142.32
Brick_get_entire_matrix1.440.203.43
Brick_get_matrix1.450.163.02
Brick_get_matrix_mcols1.210.253.87
Brick_get_matrix_within_coords1.870.293.99
Brick_get_ranges1.030.102.23
Brick_get_values_by_distance1.700.173.63
Brick_get_vector_values1.300.205.92
Brick_list_matrices0.920.132.25
Brick_list_matrix_mcols1.000.112.51
Brick_list_mcool_normalisations000
Brick_list_mcool_resolutions000
Brick_list_rangekeys0.850.092.19
Brick_list_ranges_mcols0.950.192.50
Brick_load_cis_matrix_till_distance1.390.192.80
Brick_load_data_from_mcool000
Brick_load_data_from_sparse000
Brick_load_matrix1.250.313.16
Brick_local_score_differentiator1.970.284.30
Brick_make_ranges0.010.000.01
Brick_matrix_dimensions1.160.253.11
Brick_matrix_exists1.170.163.38
Brick_matrix_filename1.370.183.64
Brick_matrix_isdone1.080.333.36
Brick_matrix_issparse1.470.283.39
Brick_matrix_maxdist1.170.193.00
Brick_matrix_minmax1.390.163.84
Brick_mcool_normalisation_exists000
Brick_rangekey_exists0.940.212.06
Brick_return_region_position1.130.152.57
Brick_vizart_plot_heatmap2.570.264.89
Create_many_Bricks0.890.242.19
Create_many_Bricks_from_mcool000
load_BrickContainer1.100.152.35