'Raik Otto'
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/Uniquorn |
| Branch: RELEASE_3_6 |
| Last Commit: 831cb9d |
| Last Changed Date: 2017-10-30 12:41:13 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:42:26 -0400 (Thu, 12 Apr 2018).
| Package 1439/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| Uniquorn 1.6.0 'Raik Otto'
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | [ OK ] | OK | |
| Package: Uniquorn |
| Version: 1.6.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Uniquorn_1.6.0.tar.gz |
| StartedAt: 2018-04-12 10:37:08 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 10:39:22 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 133.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Uniquorn.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Uniquorn_1.6.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/Uniquorn.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Uniquorn/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Uniquorn’ version ‘1.6.0’
* 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 ‘Uniquorn’ 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 loading without being on the library search path ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
add_custom_vcf_to_database 17.024 0.389 17.620
identify_vcf_file 14.880 0.326 15.342
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’
Running ‘testthat.R’
Running ‘uniquorn-Tests.R’
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
Uniquorn.Rcheck/00install.out
* installing *source* package ‘Uniquorn’ ... ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (Uniquorn)
Uniquorn.Rcheck/tests/runTests.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> BiocGenerics:::testPackage("Uniquorn")
[1] "Assuming reference genome GRCH37"
[1] "Reading VCF file: /Users/biocbuild/bbs-3.6-bioc/meat/Uniquorn.Rcheck/Uniquorn/extdata/HT29.vcf.gz"
[1] "Finished reading the VCF file, loading database"
[1] "Found 60 many CLs for reference genome GRCH37"
[1] "Finished reading database, identifying CL"
[1] "Adjusted mutational inclusion weight, \n only using mutations that are have a weight higher than 0.5"
[1] "Found 57126 many mutations with mutational weight of at least 0.5"
Correcting the background due to traces of random, scale-freeness amounts of matches,
requiring at least 50 variants to match.
[1] "Candidate(s): HT29"
[1] "Storing information in table: /Users/biocbuild/bbs-3.6-bioc/meat/Uniquorn.Rcheck/Uniquorn/extdata/HT29.vcf.gz_uniquorn_ident.tab"
RUNIT TEST PROTOCOL -- Thu Apr 12 10:38:43 2018
***********************************************
Number of test functions: 1
Number of errors: 0
Number of failures: 0
1 Test Suite :
Uniquorn RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1
Number of errors: 0
Number of failures: 0
Warning message:
In identify_vcf_file(HT29_vcf_file, ref_gen = "GRCH37", verbose = TRUE) :
CCLE & CoSMIC CLP cancer cell line fingerprint NOT
found, defaulting to 60 CellMiner cancer cell lines!
It is strongly advised to add ˜1900 CCLE & CoSMIC CLs, see readme.
>
> proc.time()
user system elapsed
15.950 0.414 16.435
Uniquorn.Rcheck/tests/testthat.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library("testthat")
> library("Uniquorn")
>
> test_check("Uniquorn")
[1] "Assuming reference genome GRCH37"
[1] "Reading VCF file: /Users/biocbuild/bbs-3.6-bioc/meat/Uniquorn.Rcheck/Uniquorn/extdata/HT29.vcf.gz"
[1] "Finished reading the VCF file, loading database"
[1] "Found 60 many CLs for reference genome GRCH37"
[1] "Finished reading database, identifying CL"
[1] "Adjusted mutational inclusion weight, \n only using mutations that are have a weight higher than 0.5"
[1] "Found 57126 many mutations with mutational weight of at least 0.5"
[1] "Candidate(s): HT29"
[1] "Storing information in table: /Users/biocbuild/bbs-3.6-bioc/meat/Uniquorn.Rcheck/Uniquorn/extdata/HT29.vcf.gz_uniquorn_ident.tab"
══ testthat results ═══════════════════════════════════════════════════════════
OK: 6 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
16.933 0.421 17.489
Uniquorn.Rcheck/tests/uniquorn-Tests.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library("Uniquorn")
> library("testthat")
>
> HT29_vcf_file = system.file("extdata/HT29.vcf.gz", package="Uniquorn")
>
> ident_result = identify_vcf_file( HT29_vcf_file, ref_gen = "GRCH37", verbose = TRUE )
[1] "Assuming reference genome GRCH37"
[1] "Reading VCF file: /Users/biocbuild/bbs-3.6-bioc/meat/Uniquorn.Rcheck/Uniquorn/extdata/HT29.vcf.gz"
[1] "Finished reading the VCF file, loading database"
[1] "Found 60 many CLs for reference genome GRCH37"
[1] "Finished reading database, identifying CL"
[1] "Adjusted mutational inclusion weight, \n only using mutations that are have a weight higher than 0.5"
[1] "Found 57126 many mutations with mutational weight of at least 0.5"
Correcting the background due to traces of random, scale-freeness amounts of matches,
requiring at least 50 variants to match.
[1] "Candidate(s): HT29"
[1] "Storing information in table: /Users/biocbuild/bbs-3.6-bioc/meat/Uniquorn.Rcheck/Uniquorn/extdata/HT29.vcf.gz_uniquorn_ident.tab"
Warning message:
In identify_vcf_file(HT29_vcf_file, ref_gen = "GRCH37", verbose = TRUE) :
CCLE & CoSMIC CLP cancer cell line fingerprint NOT
found, defaulting to 60 CellMiner cancer cell lines!
It is strongly advised to add ˜1900 CCLE & CoSMIC CLs, see readme.
>
> expect_that( ident_result, is_a("data.frame") )
>
> expect_that( dim(ident_result)[1], equals( 60 ) )
> expect_that( dim(ident_result)[2], equals( 10 ) )
>
> expect_that( as.logical( ident_result$Conf_score_sig[1] ), equals( rep(TRUE,1) ) )
> expect_that( as.logical( ident_result$Conf_score_sig[2:60] ), equals( rep(FALSE,60-1) ) )
>
> proc.time()
user system elapsed
16.866 0.426 17.362
Uniquorn.Rcheck/Uniquorn-Ex.timings
| name | user | system | elapsed | |
| add_custom_vcf_to_database | 17.024 | 0.389 | 17.620 | |
| identify_vcf_file | 14.880 | 0.326 | 15.342 | |
| initiate_canonical_databases | 0.139 | 0.008 | 0.147 | |
| remove_custom_vcf_from_database | 0.990 | 0.047 | 1.052 | |
| show_contained_cls | 0.004 | 0.001 | 0.005 | |
| show_contained_mutations | 0.141 | 0.009 | 0.149 | |
| show_contained_mutations_for_cl | 0.161 | 0.010 | 0.170 | |
| show_which_cls_contain_mutation | 0.153 | 0.012 | 0.165 | |