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CHECK report for HiCBricks on merida2

This page was generated on 2019-04-09 13:37:47 -0400 (Tue, 09 Apr 2019).

Package 741/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HiCBricks 1.1.21
Koustav Pal
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/HiCBricks
Branch: master
Last Commit: 4d7426e
Last Changed Date: 2019-03-27 13:36:19 -0400 (Wed, 27 Mar 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK 

Summary

Package: HiCBricks
Version: 1.1.21
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:HiCBricks.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings HiCBricks_1.1.21.tar.gz
StartedAt: 2019-04-09 01:28:31 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 01:30:35 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 124.6 seconds
RetCode: 0
Status:  OK 
CheckDir: HiCBricks.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:HiCBricks.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings HiCBricks_1.1.21.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/HiCBricks.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HiCBricks/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HiCBricks’ version ‘1.1.21’
* 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 ... NOTE
Brick_get_ranges: no visible global function definition for ‘FUN<-’
Undefined global functions or variables:
  FUN<-
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/HiCBricks.Rcheck/00check.log’
for details.



Installation output

HiCBricks.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL HiCBricks
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘HiCBricks’ ...
** 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
* DONE (HiCBricks)

Tests output


Example timings

HiCBricks.Rcheck/HiCBricks-Ex.timings

nameusersystemelapsed
Brick_add_ranges0.2330.0430.280
Brick_fetch_range_index0.2930.0320.329
Brick_fetch_row_vector0.7400.0190.765
Brick_get_bintable0.0360.0010.037
Brick_get_chrominfo0.0060.0000.007
Brick_get_matrix0.0990.0040.103
Brick_get_matrix_mcols0.0560.0100.067
Brick_get_matrix_within_coords1.1560.0351.203
Brick_get_ranges0.0450.0020.047
Brick_get_values_by_distance0.4260.0700.507
Brick_get_vector_values0.0820.0020.084
Brick_list_matrices0.0180.0010.019
Brick_list_matrix_mcols0.0010.0000.001
Brick_list_mcool_normalisations0.0010.0010.001
Brick_list_rangekeys0.0030.0000.003
Brick_list_ranges_mcols0.0080.0010.008
Brick_load_cis_matrix_till_distance2.9470.3293.314
Brick_load_data_from_mcool0.0000.0000.001
Brick_load_matrix3.0170.4503.564
Brick_local_score_differentiator1.9290.0522.002
Brick_make_ranges0.0090.0000.010
Brick_matrix_dimensions0.0110.0010.011
Brick_matrix_exists0.0140.0010.014
Brick_matrix_filename0.0200.0000.021
Brick_matrix_isdone0.0190.0010.020
Brick_matrix_issparse0.0150.0000.016
Brick_matrix_maxdist0.0470.0010.048
Brick_matrix_minmax0.0190.0010.021
Brick_mcool_normalisation_exists000
Brick_rangekey_exists0.0020.0000.002
Brick_return_region_position0.1310.0050.137
Brick_vizart_plot_heatmap1.4330.0491.500
CreateBrick0.0780.0170.098
CreateBrick_from_mcool0.0010.0000.001