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This page was generated on 2023-10-20 09:38:04 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 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)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for HiCBricks on kjohnson2


To the developers/maintainers of the HiCBricks package:
- 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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:HiCBricks.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings HiCBricks_1.18.0.tar.gz
StartedAt: 2023-10-18 00:31:52 -0400 (Wed, 18 Oct 2023)
EndedAt: 2023-10-18 00:36:20 -0400 (Wed, 18 Oct 2023)
EllapsedTime: 268.5 seconds
RetCode: 0
Status:   OK  
CheckDir: HiCBricks.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:HiCBricks.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings HiCBricks_1.18.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/HiCBricks.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* 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 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 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:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL HiCBricks
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/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_name1.4220.1342.416
BrickContainer_change_output_directory1.0160.0941.678
BrickContainer_get_path_to_file0.9340.0961.563
BrickContainer_list_chromosomes0.9430.0981.596
BrickContainer_list_experiment_name0.9320.0961.570
BrickContainer_list_files0.9490.0981.617
BrickContainer_list_output_directory0.9360.0991.573
BrickContainer_list_resolutions0.9590.1031.634
BrickContainer_unlink_resolution2.0490.1973.433
Brick_add_ranges2.0880.1343.369
Brick_call_compartments1.5400.1812.611
Brick_export_to_sparse2.9760.2864.945
Brick_fetch_range_index1.1490.1011.907
Brick_fetch_row_vector2.0140.1793.326
Brick_get_bintable0.9740.0971.631
Brick_get_chrominfo0.9600.0991.621
Brick_get_entire_matrix1.3410.2032.356
Brick_get_matrix1.3280.1582.260
Brick_get_matrix_mcols1.2890.1882.270
Brick_get_matrix_within_coords1.8640.1743.073
Brick_get_ranges0.9920.1051.667
Brick_get_values_by_distance1.4140.1762.415
Brick_get_vector_values1.3700.1732.358
Brick_list_matrices0.9710.0991.640
Brick_list_matrix_mcols0.9540.1001.599
Brick_list_mcool_normalisations0.0000.0010.001
Brick_list_mcool_resolutions0.0000.0000.001
Brick_list_rangekeys0.9410.0981.584
Brick_list_ranges_mcols0.9240.0951.506
Brick_load_cis_matrix_till_distance1.1970.1482.058
Brick_load_data_from_mcool0.0000.0010.000
Brick_load_data_from_sparse0.0000.0010.000
Brick_load_matrix1.2820.1772.209
Brick_local_score_differentiator2.0120.2253.398
Brick_make_ranges0.0110.0010.015
Brick_matrix_dimensions1.3140.1632.248
Brick_matrix_exists1.2720.1632.183
Brick_matrix_filename1.3270.1592.275
Brick_matrix_isdone1.2860.1582.199
Brick_matrix_issparse1.2690.1552.169
Brick_matrix_maxdist1.3350.1622.276
Brick_matrix_minmax1.3030.1562.231
Brick_mcool_normalisation_exists0.0000.0000.001
Brick_rangekey_exists0.9380.0951.604
Brick_return_region_position1.0870.1001.793
Brick_vizart_plot_heatmap2.4120.2274.069
Create_many_Bricks0.9480.0941.589
Create_many_Bricks_from_mcool0.0000.0000.001
load_BrickContainer1.0030.0951.664