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CHECK report for Uniquorn on tokay1

This page was generated on 2018-04-12 13:27:37 -0400 (Thu, 12 Apr 2018).

Package 1439/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Uniquorn 1.6.0
'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)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: Uniquorn
Version: 1.6.0
Command: rm -rf Uniquorn.buildbin-libdir Uniquorn.Rcheck && mkdir Uniquorn.buildbin-libdir Uniquorn.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Uniquorn.buildbin-libdir Uniquorn_1.6.0.tar.gz >Uniquorn.Rcheck\00install.out 2>&1 && cp Uniquorn.Rcheck\00install.out Uniquorn-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=Uniquorn.buildbin-libdir --install="check:Uniquorn-install.out" --force-multiarch --no-vignettes --timings Uniquorn_1.6.0.tar.gz
StartedAt: 2018-04-12 03:45:40 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 03:49:57 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 257.1 seconds
RetCode: 0
Status:  OK  
CheckDir: Uniquorn.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf Uniquorn.buildbin-libdir Uniquorn.Rcheck && mkdir Uniquorn.buildbin-libdir Uniquorn.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Uniquorn.buildbin-libdir Uniquorn_1.6.0.tar.gz >Uniquorn.Rcheck\00install.out 2>&1 && cp Uniquorn.Rcheck\00install.out Uniquorn-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=Uniquorn.buildbin-libdir --install="check:Uniquorn-install.out" --force-multiarch --no-vignettes --timings Uniquorn_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/Uniquorn.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* 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
** checking loading without being on the library search path ... 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 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
add_custom_vcf_to_database 17.77   1.41   19.17
identify_vcf_file          14.95   1.20   16.16
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
add_custom_vcf_to_database 17.77   1.16   18.92
identify_vcf_file          16.00   1.23   17.24
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
  Running 'testthat.R'
  Running 'uniquorn-Tests.R'
 OK
** running tests for arch 'x64' ...
  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

Installation output

Uniquorn.Rcheck/00install.out


install for i386

* installing *source* package 'Uniquorn' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'Uniquorn'
    finding HTML links ... done
    add_custom_vcf_to_database              html  
    create_bed_file                         html  
    identify_vcf_file                       html  
    initiate_canonical_databases            html  
    initiate_db_and_load_data               html  
    parse_ccle_genotype_data                html  
    parse_cosmic_genotype_data              html  
    parse_vcf_file                          html  
    re_calculate_cl_weights                 html  
    remove_custom_vcf_from_database         html  
    show_contained_cls                      html  
    show_contained_mutations                html  
    show_contained_mutations_for_cl         html  
    show_which_cls_contain_mutation         html  
    split_add                               html  
    write_data_to_db                        html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'Uniquorn' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Uniquorn' as Uniquorn_1.6.0.zip
* DONE (Uniquorn)
In R CMD INSTALL
In R CMD INSTALL

Tests output

Uniquorn.Rcheck/tests_i386/runTests.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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: C:/Users/biocbuild/bbs-3.6-bioc/meat/Uniquorn.buildbin-libdir/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: C:/Users/biocbuild/bbs-3.6-bioc/meat/Uniquorn.buildbin-libdir/Uniquorn/extdata/HT29.vcf.gz_uniquorn_ident.tab"


RUNIT TEST PROTOCOL -- Thu Apr 12 03:48:07 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 
  16.70    1.31   18.01

Uniquorn.Rcheck/tests_x64/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-w64-mingw32/x64 (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: C:/Users/biocbuild/bbs-3.6-bioc/meat/Uniquorn.buildbin-libdir/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: C:/Users/biocbuild/bbs-3.6-bioc/meat/Uniquorn.buildbin-libdir/Uniquorn/extdata/HT29.vcf.gz_uniquorn_ident.tab"


RUNIT TEST PROTOCOL -- Thu Apr 12 03:49:09 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 
  20.43    1.70   22.12

Uniquorn.Rcheck/tests_i386/testthat.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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: C:/Users/biocbuild/bbs-3.6-bioc/meat/Uniquorn.buildbin-libdir/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: C:/Users/biocbuild/bbs-3.6-bioc/meat/Uniquorn.buildbin-libdir/Uniquorn/extdata/HT29.vcf.gz_uniquorn_ident.tab"
== testthat results  ===========================================================
OK: 6 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  19.40    1.68   22.15

Uniquorn.Rcheck/tests_x64/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-w64-mingw32/x64 (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: C:/Users/biocbuild/bbs-3.6-bioc/meat/Uniquorn.buildbin-libdir/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: C:/Users/biocbuild/bbs-3.6-bioc/meat/Uniquorn.buildbin-libdir/Uniquorn/extdata/HT29.vcf.gz_uniquorn_ident.tab"
== testthat results  ===========================================================
OK: 6 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  18.06    1.71   19.78

Uniquorn.Rcheck/tests_i386/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: i386-w64-mingw32/i386 (32-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: C:/Users/biocbuild/bbs-3.6-bioc/meat/Uniquorn.buildbin-libdir/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: C:/Users/biocbuild/bbs-3.6-bioc/meat/Uniquorn.buildbin-libdir/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 
  15.68    1.29   16.98

Uniquorn.Rcheck/tests_x64/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-w64-mingw32/x64 (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: C:/Users/biocbuild/bbs-3.6-bioc/meat/Uniquorn.buildbin-libdir/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: C:/Users/biocbuild/bbs-3.6-bioc/meat/Uniquorn.buildbin-libdir/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 
  22.17    1.78   23.95

Example timings

Uniquorn.Rcheck/examples_i386/Uniquorn-Ex.timings

nameusersystemelapsed
add_custom_vcf_to_database17.77 1.4119.17
identify_vcf_file14.95 1.2016.16
initiate_canonical_databases0.130.000.13
remove_custom_vcf_from_database1.060.001.06
show_contained_cls000
show_contained_mutations0.110.020.12
show_contained_mutations_for_cl0.090.030.13
show_which_cls_contain_mutation0.140.000.14

Uniquorn.Rcheck/examples_x64/Uniquorn-Ex.timings

nameusersystemelapsed
add_custom_vcf_to_database17.77 1.1618.92
identify_vcf_file16.00 1.2317.24
initiate_canonical_databases0.110.000.11
remove_custom_vcf_from_database1.160.071.22
show_contained_cls0.010.000.02
show_contained_mutations0.080.030.11
show_contained_mutations_for_cl0.080.030.11
show_which_cls_contain_mutation0.110.000.11