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This page was generated on 2021-10-15 15:06:07 -0400 (Fri, 15 Oct 2021).

CHECK results for HiCBricks on tokay2

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? here 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 856/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HiCBricks 1.10.0  (landing page)
Koustav Pal
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/HiCBricks
git_branch: RELEASE_3_13
git_last_commit: f242bbd
git_last_commit_date: 2021-05-19 12:38:53 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: HiCBricks
Version: 1.10.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:HiCBricks.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings HiCBricks_1.10.0.tar.gz
StartedAt: 2021-10-15 00:21:45 -0400 (Fri, 15 Oct 2021)
EndedAt: 2021-10-15 00:30:19 -0400 (Fri, 15 Oct 2021)
EllapsedTime: 513.8 seconds
RetCode: 0
Status:   OK  
CheckDir: HiCBricks.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:HiCBricks.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings HiCBricks_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/HiCBricks.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'HiCBricks/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'HiCBricks' version '1.10.0'
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                       user system elapsed
Brick_vizart_plot_heatmap              3.64   0.55    5.80
Brick_export_to_sparse                 3.55   0.61    5.11
BrickContainer_unlink_resolution       3.05   0.45    5.73
Brick_get_matrix_within_coords         2.82   0.64    6.17
Brick_call_compartments                2.38   0.58    6.08
Brick_matrix_exists                    1.85   0.75    6.89
Brick_get_matrix                       2.00   0.57   13.92
BrickContainer_change_output_directory 1.48   0.32    6.11
BrickContainer_get_path_to_file        1.48   0.24    5.55
BrickContainer_list_resolutions        1.35   0.31    6.96
BrickContainer_list_chromosomes        1.39   0.23    8.41
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                               user system elapsed
Brick_export_to_sparse         4.00   0.71    5.48
Brick_get_matrix_within_coords 2.66   0.67    7.55
Brick_fetch_row_vector         2.37   0.72    5.09
Brick_get_entire_matrix        2.08   0.61    6.93
Brick_get_vector_values        2.14   0.53   12.96
Brick_get_matrix               1.98   0.60    6.72
Brick_get_matrix_mcols         1.86   0.58    6.05
Brick_matrix_isdone            1.95   0.47    8.45
Brick_list_rangekeys           1.49   0.27    7.88
* 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:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/HiCBricks_1.10.0.tar.gz && rm -rf HiCBricks.buildbin-libdir && mkdir HiCBricks.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=HiCBricks.buildbin-libdir HiCBricks_1.10.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL HiCBricks_1.10.0.zip && rm HiCBricks_1.10.0.tar.gz HiCBricks_1.10.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 47 2314k   47 1088k    0     0  2091k      0  0:00:01 --:--:--  0:00:01 2090k
100 2314k  100 2314k    0     0  2671k      0 --:--:-- --:--:-- --:--:-- 2672k

install for i386

* installing *source* package 'HiCBricks' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'HiCBricks'
    finding HTML links ... done
    BrickContainer_change_experiment_name   html  
    BrickContainer_change_output_directory
                                            html  
    BrickContainer_get_path_to_file         html  
    BrickContainer_list_chromosomes         html  
    BrickContainer_list_experiment_name     html  
    BrickContainer_list_files               html  
    BrickContainer_list_output_directory    html  
    BrickContainer_list_resolutions         html  
    BrickContainer_unlink_resolution        html  
    Brick_add_ranges                        html  
    Brick_call_compartments                 html  
    Brick_export_to_sparse                  html  
    Brick_fetch_range_index                 html  
    Brick_fetch_row_vector                  html  
    Brick_get_bintable                      html  
    Brick_get_chrominfo                     html  
    Brick_get_entire_matrix                 html  
    Brick_get_matrix                        html  
    Brick_get_matrix_mcols                  html  
    Brick_get_matrix_within_coords          html  
    Brick_get_ranges                        html  
    Brick_get_values_by_distance            html  
    Brick_get_vector_values                 html  
    Brick_list_matrices                     html  
    Brick_list_matrix_mcols                 html  
    Brick_list_mcool_normalisations         html  
    Brick_list_mcool_resolutions            html  
    Brick_list_rangekeys                    html  
    Brick_list_ranges_mcols                 html  
    Brick_load_cis_matrix_till_distance     html  
    Brick_load_data_from_mcool              html  
    Brick_load_data_from_sparse             html  
    Brick_load_matrix                       html  
    Brick_local_score_differentiator        html  
    Brick_make_ranges                       html  
    Brick_matrix_dimensions                 html  
    Brick_matrix_exists                     html  
    Brick_matrix_filename                   html  
    Brick_matrix_isdone                     html  
    Brick_matrix_issparse                   html  
    Brick_matrix_maxdist                    html  
    Brick_matrix_minmax                     html  
    Brick_mcool_normalisation_exists        html  
    Brick_rangekey_exists                   html  
    Brick_return_region_position            html  
    Brick_vizart_plot_heatmap               html  
    Create_many_Bricks                      html  
    Create_many_Bricks_from_mcool           html  
    HiCBricks                               html  
    load_BrickContainer                     html  
** 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

install for x64

* installing *source* package 'HiCBricks' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'HiCBricks' as HiCBricks_1.10.0.zip
* DONE (HiCBricks)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'HiCBricks' successfully unpacked and MD5 sums checked

Tests output


Example timings

HiCBricks.Rcheck/examples_i386/HiCBricks-Ex.timings

nameusersystemelapsed
BrickContainer_change_experiment_name1.850.403.75
BrickContainer_change_output_directory1.480.326.11
BrickContainer_get_path_to_file1.480.245.55
BrickContainer_list_chromosomes1.390.238.41
BrickContainer_list_experiment_name1.500.212.46
BrickContainer_list_files1.360.293.43
BrickContainer_list_output_directory1.340.303.71
BrickContainer_list_resolutions1.350.316.96
BrickContainer_unlink_resolution3.050.455.73
Brick_add_ranges2.460.273.69
Brick_call_compartments2.380.586.08
Brick_export_to_sparse3.550.615.11
Brick_fetch_range_index1.710.222.34
Brick_fetch_row_vector2.490.574.33
Brick_get_bintable1.480.221.98
Brick_get_chrominfo1.630.322.28
Brick_get_entire_matrix2.060.573.55
Brick_get_matrix 2.00 0.5713.92
Brick_get_matrix_mcols1.860.644.07
Brick_get_matrix_within_coords2.820.646.17
Brick_get_ranges1.520.233.11
Brick_get_values_by_distance2.140.714.77
Brick_get_vector_values2.200.514.22
Brick_list_matrices1.300.282.64
Brick_list_matrix_mcols1.310.332.61
Brick_list_mcool_normalisations000
Brick_list_mcool_resolutions000
Brick_list_rangekeys1.380.232.28
Brick_list_ranges_mcols1.390.272.72
Brick_load_cis_matrix_till_distance1.580.312.03
Brick_load_data_from_mcool000
Brick_load_data_from_sparse000
Brick_load_matrix1.810.644.45
Brick_local_score_differentiator2.580.695.00
Brick_make_ranges000
Brick_matrix_dimensions1.890.594.78
Brick_matrix_exists1.850.756.89
Brick_matrix_filename1.930.614.26
Brick_matrix_isdone2.100.503.94
Brick_matrix_issparse1.780.613.96
Brick_matrix_maxdist1.840.583.82
Brick_matrix_minmax1.720.533.63
Brick_mcool_normalisation_exists000
Brick_rangekey_exists1.390.172.22
Brick_return_region_position1.470.222.09
Brick_vizart_plot_heatmap3.640.555.80
Create_many_Bricks0.960.191.31
Create_many_Bricks_from_mcool000
load_BrickContainer1.140.281.69

HiCBricks.Rcheck/examples_x64/HiCBricks-Ex.timings

nameusersystemelapsed
BrickContainer_change_experiment_name1.950.142.95
BrickContainer_change_output_directory1.500.312.44
BrickContainer_get_path_to_file1.210.201.51
BrickContainer_list_chromosomes1.300.202.08
BrickContainer_list_experiment_name1.300.191.93
BrickContainer_list_files1.390.241.96
BrickContainer_list_output_directory1.140.141.42
BrickContainer_list_resolutions1.170.151.50
BrickContainer_unlink_resolution2.500.302.75
Brick_add_ranges1.670.231.91
Brick_call_compartments1.940.593.48
Brick_export_to_sparse4.000.715.48
Brick_fetch_range_index1.830.242.52
Brick_fetch_row_vector2.370.725.09
Brick_get_bintable1.520.263.17
Brick_get_chrominfo1.750.284.88
Brick_get_entire_matrix2.080.616.93
Brick_get_matrix1.980.606.72
Brick_get_matrix_mcols1.860.586.05
Brick_get_matrix_within_coords2.660.677.55
Brick_get_ranges1.480.182.08
Brick_get_values_by_distance2.000.553.35
Brick_get_vector_values 2.14 0.5312.96
Brick_list_matrices1.490.141.92
Brick_list_matrix_mcols1.370.222.23
Brick_list_mcool_normalisations000
Brick_list_mcool_resolutions000
Brick_list_rangekeys1.490.277.88
Brick_list_ranges_mcols1.250.313.78
Brick_load_cis_matrix_till_distance1.600.282.58
Brick_load_data_from_mcool000
Brick_load_data_from_sparse000
Brick_load_matrix1.690.614.34
Brick_local_score_differentiator2.580.553.89
Brick_make_ranges0.020.000.02
Brick_matrix_dimensions1.760.583.09
Brick_matrix_exists1.950.643.36
Brick_matrix_filename1.430.422.60
Brick_matrix_isdone1.950.478.45
Brick_matrix_issparse1.970.403.37
Brick_matrix_maxdist2.030.524.36
Brick_matrix_minmax1.690.482.94
Brick_mcool_normalisation_exists000
Brick_rangekey_exists0.900.141.08
Brick_return_region_position1.050.081.12
Brick_vizart_plot_heatmap2.770.604.08
Create_many_Bricks1.310.252.92
Create_many_Bricks_from_mcool000
load_BrickContainer1.450.281.96