Back to Build/check report for BioC 3.17
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This page was generated on 2023-01-02 09:00:33 -0500 (Mon, 02 Jan 2023).

HostnameOSArch (*)R versionInstalled pkgs
palomino5Windows Server 2022 Datacenterx64R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" 4165
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 palomino5


To the developers/maintainers of the HiCBricks package:
Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 890/2158HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HiCBricks 1.17.0  (landing page)
Koustav Pal
Snapshot Date: 2022-12-28 11:00:06 -0500 (Wed, 28 Dec 2022)
git_url: https://git.bioconductor.org/packages/HiCBricks
git_branch: master
git_last_commit: d85dbc7
git_last_commit_date: 2022-11-01 11:18:41 -0500 (Tue, 01 Nov 2022)
palomino5Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  

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: 2022-12-29 00:28:58 -0500 (Thu, 29 Dec 2022)
EndedAt: 2022-12-29 00:32:09 -0500 (Thu, 29 Dec 2022)
EllapsedTime: 191.9 seconds
RetCode: 0
Status:   OK  
CheckDir: HiCBricks.Rcheck
Warnings: 0

Command output

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###
### 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
###
##############################################################################
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* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/HiCBricks.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 10.4.0
    GNU Fortran (GCC) 10.4.0
* running under: Windows Server 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
* 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

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###
### 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_name1.110.202.19
BrickContainer_change_output_directory0.790.192.50
BrickContainer_get_path_to_file0.880.092.06
BrickContainer_list_chromosomes0.810.161.60
BrickContainer_list_experiment_name0.770.171.76
BrickContainer_list_files0.780.162.22
BrickContainer_list_output_directory0.740.201.67
BrickContainer_list_resolutions0.660.201.87
BrickContainer_unlink_resolution1.890.363.96
Brick_add_ranges1.680.193.31
Brick_call_compartments1.190.222.75
Brick_export_to_sparse2.530.253.97
Brick_fetch_range_index0.810.111.64
Brick_fetch_row_vector1.440.292.92
Brick_get_bintable0.780.191.91
Brick_get_chrominfo0.770.081.57
Brick_get_entire_matrix1.110.192.57
Brick_get_matrix0.980.232.31
Brick_get_matrix_mcols1.070.332.36
Brick_get_matrix_within_coords1.280.172.83
Brick_get_ranges0.870.191.68
Brick_get_values_by_distance1.240.282.75
Brick_get_vector_values1.150.202.54
Brick_list_matrices0.740.081.96
Brick_list_matrix_mcols0.620.151.66
Brick_list_mcool_normalisations000
Brick_list_mcool_resolutions000
Brick_list_rangekeys0.780.161.79
Brick_list_ranges_mcols0.720.121.58
Brick_load_cis_matrix_till_distance1.060.182.28
Brick_load_data_from_mcool000
Brick_load_data_from_sparse0.020.000.02
Brick_load_matrix0.910.183.12
Brick_local_score_differentiator1.290.352.88
Brick_make_ranges000
Brick_matrix_dimensions0.940.182.25
Brick_matrix_exists0.860.142.08
Brick_matrix_filename0.920.162.13
Brick_matrix_isdone0.970.252.36
Brick_matrix_issparse0.940.252.20
Brick_matrix_maxdist0.780.182.20
Brick_matrix_minmax0.910.182.28
Brick_mcool_normalisation_exists000
Brick_rangekey_exists0.810.091.55
Brick_return_region_position0.810.172.14
Brick_vizart_plot_heatmap1.720.213.30
Create_many_Bricks0.720.071.67
Create_many_Bricks_from_mcool000
load_BrickContainer0.810.211.70