Verena Körber
| Snapshot Date: 2025-11-13 13:40 -0500 (Thu, 13 Nov 2025) |
| git_url: https://git.bioconductor.org/packages/LACHESIS |
| git_branch: devel |
| git_last_commit: 0cbd1e4 |
| git_last_commit_date: 2025-11-03 10:21:55 -0500 (Mon, 03 Nov 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-11-14 11:35 -0500 (Fri, 14 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4825 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4547 |
| 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 1108/2325 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| LACHESIS 0.99.4 (landing page) Verena Körber
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the LACHESIS package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/LACHESIS.git to reflect on this report. See Troubleshooting Build Report for more information. - 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. |
| Package: LACHESIS |
| Version: 0.99.4 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:LACHESIS.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings LACHESIS_0.99.4.tar.gz |
| StartedAt: 2025-11-14 00:51:13 -0500 (Fri, 14 Nov 2025) |
| EndedAt: 2025-11-14 01:04:25 -0500 (Fri, 14 Nov 2025) |
| EllapsedTime: 792.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: LACHESIS.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:LACHESIS.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings LACHESIS_0.99.4.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/LACHESIS.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘LACHESIS/DESCRIPTION’ ... OK
* this is package ‘LACHESIS’ version ‘0.99.4’
* 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 ‘LACHESIS’ 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 code 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
LACHESIS 37.881 1.704 39.311
plotNB 22.134 0.334 22.293
plotSurvival 18.098 0.168 18.121
plotClonality 16.924 0.280 17.102
estimateClonality 16.579 0.444 16.958
plotLachesis 16.292 0.152 16.315
classifyLACHESIS 16.089 0.247 16.217
plotClinicalCorrelations 15.987 0.198 16.059
nbImport 8.892 0.459 9.263
MRCA 5.523 0.143 5.641
normalizeCounts 5.368 0.084 5.420
plotMutationDensities 5.297 0.044 5.298
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘tinytest.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
LACHESIS.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL LACHESIS ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’ * installing *source* package ‘LACHESIS’ ... ** this is package ‘LACHESIS’ version ‘0.99.4’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (LACHESIS)
LACHESIS.Rcheck/tests/tinytest.Rout
R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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.
> if (requireNamespace("tinytest", quietly = TRUE)) {
+ tinytest::test_package("LACHESIS")
+ }
test_examples.R............... 0 tests
test_examples.R............... 0 tests
test_examples.R............... 0 tests
test_examples.R............... 0 tests
test_examples.R............... 0 tests
test_examples.R............... 0 tests
test_examples.R............... 0 tests
test_examples.R............... 0 tests
test_examples.R............... 0 tests
test_examples.R............... 0 tests
test_examples.R............... 0 tests
test_examples.R............... 0 tests
test_examples.R............... 0 tests
test_examples.R............... 0 tests
test_examples.R............... 0 tests
test_examples.R............... 0 tests
test_examples.R............... 0 tests Computing SNV density for sample NBE11
Total copy number computed as A + B.
Read in 721 segments with copy number information on 23 chromosomes.
Removing 0 segments without copy number information...
Removing 8 segments with copy number > 4...
Removing 9 segments on allosomes...
Removing 0 segments without B allele information...
Merging adjacent segments with equal copy number...
Retaining 116 segments with copy number information on 21 chromosomes.
Assuming TUMOR as tumor
Importing VCF..
Total variants : 4819
Variants passing filter: 4819
Bi-allelic variants : 4819
single nucl. variants : 4819
Primary contig vars. : 4819
Autosomal variants : 4819
Filtering for min.depth and VAF..
Filtering 3 segments below the minimal segment size and 0 segments on excluded chromosomes.
Computing mutation density at MRCA...
Computing mutation densities at ECA...
Assuming TUMOR as tumor
Importing VCF..
Total variants : 4819
Variants passing filter: 4819
Bi-allelic variants : 4819
single nucl. variants : 4819
Primary contig vars. : 4819
Autosomal variants : 4819
Filtering for min.depth and VAF..
Assuming TUMOR as tumor
Importing VCF..
Total variants : 4819
Variants passing filter: 4819
Bi-allelic variants : 4819
single nucl. variants : 4819
Primary contig vars. : 4819
Autosomal variants : 4819
Filtering for min.depth and VAF..
Total copy number computed as A + B.
Read in 721 segments with copy number information on 23 chromosomes.
Removing 0 segments without copy number information...
Removing 8 segments with copy number > 4...
Removing 9 segments on allosomes...
Removing 0 segments without B allele information...
Merging adjacent segments with equal copy number...
Retaining 116 segments with copy number information on 21 chromosomes.
Total copy number computed as A + B.
Read in 721 segments with copy number information on 23 chromosomes.
Removing 0 segments without copy number information...
Removing 8 segments with copy number > 4...
Removing 9 segments on allosomes...
Removing 0 segments without B allele information...
Merging adjacent segments with equal copy number...
Retaining 116 segments with copy number information on 21 chromosomes.
Assuming NBE15 as tumor
Primary contig vars. : 2701
Autosomal variants : 2631
Filtering for min.depth and VAF..
Total copy number computed as A + B.
Read in 1770 segments with copy number information on 24 chromosomes.
Removing 0 segments without copy number information...
Removing 0 segments with copy number > 4...
Removing 0 segments on allosomes...
Removing 0 segments without B allele information...
Merging adjacent segments with equal copy number...
Retaining 241 segments with copy number information on 22 chromosomes.
Assuming NBE15 as tumor
Primary contig vars. : 2701
Autosomal variants : 2631
Filtering for min.depth and VAF..
Total copy number computed as A + B.
Read in 1770 segments with copy number information on 24 chromosomes.
Removing 0 segments without copy number information...
Removing 0 segments with copy number > 4...
Removing 0 segments on allosomes...
Removing 0 segments without B allele information...
Merging adjacent segments with equal copy number...
Retaining 241 segments with copy number information on 22 chromosomes.
Assuming NBE15 as tumor
Primary contig vars. : 2701
Autosomal variants : 2631
Filtering for min.depth and VAF..
Total copy number computed as A + B.
Read in 1770 segments with copy number information on 24 chromosomes.
Removing 0 segments without copy number information...
Removing 0 segments with copy number > 4...
Removing 0 segments on allosomes...
Removing 0 segments without B allele information...
Merging adjacent segments with equal copy number...
Retaining 241 segments with copy number information on 22 chromosomes.
Filtering 1 segments below the minimal segment size and 0 segments on excluded chromosomes.
Computing mutation density at MRCA...
Computing mutation densities at ECA...
Assuming NBE15 as tumor
Primary contig vars. : 2701
Autosomal variants : 2631
Filtering for min.depth and VAF..
Total copy number computed as A + B.
Read in 1770 segments with copy number information on 24 chromosomes.
Removing 0 segments without copy number information...
Removing 0 segments with copy number > 4...
Removing 0 segments on allosomes...
Removing 0 segments without B allele information...
Merging adjacent segments with equal copy number...
Retaining 241 segments with copy number information on 22 chromosomes.
Filtering 1 segments below the minimal segment size and 0 segments on excluded chromosomes.
Computing mutation density at MRCA...
Computing mutation densities at ECA...
Assuming TUMOR as tumor
Importing VCF..
Total variants : 4819
Variants passing filter: 4819
Bi-allelic variants : 4819
single nucl. variants : 4819
Primary contig vars. : 4819
Autosomal variants : 4819
Filtering for min.depth and VAF..
Total copy number computed as A + B.
Read in 721 segments with copy number information on 23 chromosomes.
Removing 0 segments without copy number information...
Removing 8 segments with copy number > 4...
Removing 9 segments on allosomes...
Removing 0 segments without B allele information...
Merging adjacent segments with equal copy number...
Retaining 116 segments with copy number information on 21 chromosomes.
Total copy number computed as A + B.
Read in 25 segments with copy number information on 23 chromosomes.
Removing 0 segments without copy number information...
Removing 0 segments with copy number > 4...
Removing 1 segments on allosomes...
Removing 0 segments without B allele information...
Merging adjacent segments with equal copy number...
Retaining 24 segments with copy number information on 22 chromosomes.
Total copy number computed as A + B.
Read in 690 segments with copy number information on 24 chromosomes.
Removing 0 segments without copy number information...
Removing 254 segments with copy number > 4...
Change chromosome names to 1, 2, 3, ...
Removing 4 segments on allosomes...
Removing 0 segments without B allele information...
Merging adjacent segments with equal copy number...
Retaining 44 segments with copy number information on 21 chromosomes.
Assuming NBE15 as tumor
Primary contig vars. : 2701
Autosomal variants : 2631
Filtering for min.depth and VAF..
Assuming sample_tumor_XI003_10023 as tumor
Importing VCF..
Total variants : 167
Variants passing filter: 167
Bi-allelic variants : 142
single nucl. variants : 47
Primary contig vars. : 47
Autosomal variants : 11
Filtering for min.depth and VAF..
Assuming TUMOR as tumor
Importing VCF..
Total variants : 4819
Variants passing filter: 4819
Bi-allelic variants : 4819
single nucl. variants : 4819
Primary contig vars. : 4819
Autosomal variants : 4819
Filtering for min.depth and VAF..
test_examples.R............... 30 tests [0;32mOK[0m [0;34m37.8s[0m
test_integration.R............ 0 tests
test_integration.R............ 0 tests
test_integration.R............ 0 tests
test_integration.R............ 0 tests
test_integration.R............ 0 tests
test_integration.R............ 0 tests
test_integration.R............ 0 tests
test_integration.R............ 0 tests
test_integration.R............ 0 tests
test_integration.R............ 0 tests
test_integration.R............ 0 tests
test_integration.R............ 0 tests
test_integration.R............ 0 tests
test_integration.R............ 0 tests
test_integration.R............ 0 tests
test_integration.R............ 0 tests
test_integration.R............ 0 tests Total copy number computed as A + B.
Read in 1770 segments with copy number information on 24 chromosomes.
Removing 0 segments without copy number information...
Removing 0 segments with copy number > 4...
Removing 0 segments on allosomes...
Removing 0 segments without B allele information...
Merging adjacent segments with equal copy number...
Retaining 241 segments with copy number information on 22 chromosomes.
Assuming NBE15 as tumor
Primary contig vars. : 2701
Autosomal variants : 2631
Filtering for min.depth and VAF..
Total copy number computed as A + B.
Read in 1770 segments with copy number information on 24 chromosomes.
Removing 0 segments without copy number information...
Removing 0 segments with copy number > 4...
Removing 0 segments on allosomes...
Removing 0 segments without B allele information...
Merging adjacent segments with equal copy number...
Retaining 241 segments with copy number information on 22 chromosomes.
Assuming NBE15 as tumor
Primary contig vars. : 2701
Autosomal variants : 2631
Filtering for min.depth and VAF..
Total copy number computed as A + B.
Read in 1770 segments with copy number information on 24 chromosomes.
Removing 0 segments without copy number information...
Removing 0 segments with copy number > 4...
Removing 0 segments on allosomes...
Removing 0 segments without B allele information...
Merging adjacent segments with equal copy number...
Retaining 241 segments with copy number information on 22 chromosomes.
Assuming NBE15 as tumor
Primary contig vars. : 2701
Autosomal variants : 2631
Filtering for min.depth and VAF..
Total copy number computed as A + B.
Read in 721 segments with copy number information on 23 chromosomes.
Removing 0 segments without copy number information...
Removing 8 segments with copy number > 4...
Removing 9 segments on allosomes...
Removing 0 segments without B allele information...
Merging adjacent segments with equal copy number...
Retaining 116 segments with copy number information on 21 chromosomes.
Total copy number computed as A + B.
Read in 25 segments with copy number information on 23 chromosomes.
Removing 0 segments without copy number information...
Removing 0 segments with copy number > 4...
Removing 1 segments on allosomes...
Removing 0 segments without B allele information...
Merging adjacent segments with equal copy number...
Retaining 24 segments with copy number information on 22 chromosomes.
Total copy number computed as A + B.
Read in 690 segments with copy number information on 24 chromosomes.
Removing 0 segments without copy number information...
Removing 254 segments with copy number > 4...
Change chromosome names to 1, 2, 3, ...
Removing 4 segments on allosomes...
Removing 0 segments without B allele information...
Merging adjacent segments with equal copy number...
Retaining 44 segments with copy number information on 21 chromosomes.
Total copy number computed as A + B.
Read in 1770 segments with copy number information on 24 chromosomes.
Removing 0 segments without copy number information...
Removing 0 segments with copy number > 4...
Removing 0 segments on allosomes...
Removing 0 segments without B allele information...
Merging adjacent segments with equal copy number...
Retaining 241 segments with copy number information on 22 chromosomes.
Assuming NBE15 as tumor
Primary contig vars. : 2701
Autosomal variants : 2631
Filtering for min.depth and VAF..
Filtering 1 segments below the minimal segment size and 0 segments on excluded chromosomes.
Computing mutation density at MRCA...
Computing mutation densities at ECA...
Filtering 1 segments below the minimal segment size and 0 segments on excluded chromosomes.
Computing mutation density at MRCA...
Computing mutation densities at ECA...
Assuming TUMOR as tumor
Importing VCF..
Total variants : 4819
Variants passing filter: 4819
Bi-allelic variants : 4819
single nucl. variants : 4819
Primary contig vars. : 4819
Autosomal variants : 4819
Filtering for min.depth and VAF..
Assuming sample_tumor_XI003_10023 as tumor
Importing VCF..
Total variants : 167
Variants passing filter: 167
Bi-allelic variants : 142
single nucl. variants : 47
Primary contig vars. : 47
Autosomal variants : 11
Filtering for min.depth and VAF..
Assuming NBE15 as tumor
Primary contig vars. : 2701
Autosomal variants : 2631
Filtering for min.depth and VAF..
Total copy number computed as A + B.
Read in 1770 segments with copy number information on 24 chromosomes.
Removing 0 segments without copy number information...
Removing 0 segments with copy number > 4...
Removing 0 segments on allosomes...
Removing 0 segments without B allele information...
Merging adjacent segments with equal copy number...
Retaining 241 segments with copy number information on 22 chromosomes.
Assuming NBE15 as tumor
Primary contig vars. : 2701
Autosomal variants : 2631
Filtering for min.depth and VAF..
Total copy number computed as A + B.
Read in 1770 segments with copy number information on 24 chromosomes.
Removing 0 segments without copy number information...
Removing 0 segments with copy number > 4...
Removing 0 segments on allosomes...
Removing 0 segments without B allele information...
Merging adjacent segments with equal copy number...
Retaining 241 segments with copy number information on 22 chromosomes.
Assuming NBE15 as tumor
Primary contig vars. : 2701
Autosomal variants : 2631
Filtering for min.depth and VAF..
Filtering 1 segments below the minimal segment size and 0 segments on excluded chromosomes.
Computing mutation density at MRCA...
Computing mutation densities at ECA...
Total copy number computed as A + B.
Read in 1770 segments with copy number information on 24 chromosomes.
Removing 0 segments without copy number information...
Removing 0 segments with copy number > 4...
Removing 0 segments on allosomes...
Removing 0 segments without B allele information...
Merging adjacent segments with equal copy number...
Retaining 241 segments with copy number information on 22 chromosomes.
Assuming NBE15 as tumor
Primary contig vars. : 2701
Autosomal variants : 2631
Filtering for min.depth and VAF..
Filtering 1 segments below the minimal segment size and 0 segments on excluded chromosomes.
Computing mutation density at MRCA...
Computing mutation densities at ECA...
Total copy number computed as A + B.
Read in 721 segments with copy number information on 23 chromosomes.
Removing 0 segments without copy number information...
Removing 8 segments with copy number > 4...
Removing 9 segments on allosomes...
Removing 0 segments without B allele information...
Merging adjacent segments with equal copy number...
Retaining 116 segments with copy number information on 21 chromosomes.
Assuming NBE11 as tumor
Primary contig vars. : 4827
Autosomal variants : 4718
Filtering for min.depth and VAF..
Filtering 5 segments below the minimal segment size and 0 segments on excluded chromosomes.
Computing mutation density at MRCA...
Computing mutation densities at ECA...
Total copy number computed as A + B.
Read in 1770 segments with copy number information on 24 chromosomes.
Removing 0 segments without copy number information...
Removing 0 segments with copy number > 4...
Removing 0 segments on allosomes...
Removing 0 segments without B allele information...
Merging adjacent segments with equal copy number...
Retaining 241 segments with copy number information on 22 chromosomes.
Assuming NBE15 as tumor
Primary contig vars. : 2701
Autosomal variants : 2631
Filtering for min.depth and VAF..
Filtering 1 segments below the minimal segment size and 0 segments on excluded chromosomes.
Computing mutation density at MRCA...
Computing mutation densities at ECA...
Total copy number computed as A + B.
Read in 160 segments with copy number information on 24 chromosomes.
Removing 0 segments without copy number information...
Removing 0 segments with copy number > 4...
Removing 0 segments on allosomes...
Removing 0 segments without B allele information...
Merging adjacent segments with equal copy number...
Retaining 69 segments with copy number information on 22 chromosomes.
Assuming NBE26 as tumor
Primary contig vars. : 308
Autosomal variants : 298
Filtering for min.depth and VAF..
Filtering 0 segments below the minimal segment size and 0 segments on excluded chromosomes.
Computing mutation density at MRCA...
Computing mutation densities at ECA...
Total copy number computed as A + B.
Read in 1770 segments with copy number information on 24 chromosomes.
Removing 0 segments without copy number information...
Removing 0 segments with copy number > 4...
Removing 0 segments on allosomes...
Removing 0 segments without B allele information...
Merging adjacent segments with equal copy number...
Retaining 241 segments with copy number information on 22 chromosomes.
Assuming NBE15 as tumor
Primary contig vars. : 2701
Autosomal variants : 2631
Filtering for min.depth and VAF..
Total copy number computed as A + B.
Read in 1770 segments with copy number information on 24 chromosomes.
Removing 0 segments without copy number information...
Removing 0 segments with copy number > 4...
Removing 0 segments on allosomes...
Removing 0 segments without B allele information...
Merging adjacent segments with equal copy number...
Retaining 241 segments with copy number information on 22 chromosomes.
Assuming NBE15 as tumor
Primary contig vars. : 2701
Autosomal variants : 2631
Filtering for min.depth and VAF..
Filtering 1 segments below the minimal segment size and 0 segments on excluded chromosomes.
Computing mutation density at MRCA...
Computing mutation densities at ECA...
Total copy number computed as A + B.
Read in 1770 segments with copy number information on 24 chromosomes.
Removing 0 segments without copy number information...
Removing 0 segments with copy number > 4...
Removing 0 segments on allosomes...
Removing 0 segments without B allele information...
Merging adjacent segments with equal copy number...
Retaining 241 segments with copy number information on 22 chromosomes.
Assuming NBE15 as tumor
Primary contig vars. : 2701
Autosomal variants : 2631
Filtering for min.depth and VAF..
Total copy number computed as A + B.
Read in 1770 segments with copy number information on 24 chromosomes.
Removing 0 segments without copy number information...
Removing 0 segments with copy number > 4...
Removing 0 segments on allosomes...
Removing 0 segments without B allele information...
Merging adjacent segments with equal copy number...
Retaining 241 segments with copy number information on 22 chromosomes.
Assuming NBE15 as tumor
Primary contig vars. : 2701
Autosomal variants : 2631
Filtering for min.depth and VAF..
Signature methods test skipped due to: some columns are not in the data.table: [chrom, TCN, A, B]
test_integration.R............ 34 tests [0;32mOK[0m [0;34m1.4s[0m
test_nbImport.R............... 0 tests
test_nbImport.R............... 0 tests
test_nbImport.R............... 0 tests
test_nbImport.R............... 0 tests
test_nbImport.R............... 0 tests
test_nbImport.R............... 0 tests
test_nbImport.R............... 0 tests
test_nbImport.R............... 0 tests
test_nbImport.R............... 0 tests
test_nbImport.R............... 0 tests
test_nbImport.R............... 0 tests
test_nbImport.R............... 0 tests
test_nbImport.R............... 0 tests
test_nbImport.R............... 0 tests
test_nbImport.R............... 0 tests
test_nbImport.R............... 0 tests
test_nbImport.R............... 0 tests
test_nbImport.R............... 0 tests
test_nbImport.R............... 0 tests
test_nbImport.R............... 0 tests
test_nbImport.R............... 0 tests Total copy number computed as A + B.
Read in 1770 segments with copy number information on 24 chromosomes.
Removing 0 segments without copy number information...
Removing 0 segments with copy number > 4...
Removing 0 segments on allosomes...
Removing 0 segments without B allele information...
Merging adjacent segments with equal copy number...
Retaining 241 segments with copy number information on 22 chromosomes.
Assuming NBE15 as tumor
Primary contig vars. : 2701
Autosomal variants : 2631
Filtering for min.depth and VAF..
Total copy number computed as A + B.
Read in 1770 segments with copy number information on 24 chromosomes.
Removing 0 segments without copy number information...
Removing 0 segments with copy number > 4...
Removing 0 segments on allosomes...
Removing 0 segments without B allele information...
Merging adjacent segments with equal copy number...
Retaining 241 segments with copy number information on 22 chromosomes.
Assuming NBE15 as tumor
Primary contig vars. : 2701
Autosomal variants : 2631
Filtering for min.depth and VAF..
Total copy number computed as A + B.
Read in 1770 segments with copy number information on 24 chromosomes.
Removing 0 segments without copy number information...
Removing 0 segments with copy number > 4...
Removing 0 segments on allosomes...
Removing 0 segments without B allele information...
Merging adjacent segments with equal copy number...
Retaining 241 segments with copy number information on 22 chromosomes.
Assuming NBE15 as tumor
Primary contig vars. : 2701
Autosomal variants : 2631
Filtering for min.depth and VAF..
Total copy number computed as A + B.
Read in 1770 segments with copy number information on 24 chromosomes.
Removing 0 segments without copy number information...
Removing 0 segments with copy number > 4...
Removing 0 segments on allosomes...
Removing 0 segments without B allele information...
Merging adjacent segments with equal copy number...
Retaining 241 segments with copy number information on 22 chromosomes.
Assuming NBE15 as tumor
Primary contig vars. : 2701
Autosomal variants : 2631
Filtering for min.depth and VAF..
Total copy number computed as A + B.
Read in 1770 segments with copy number information on 24 chromosomes.
Removing 0 segments without copy number information...
Removing 0 segments with copy number > 4...
Removing 0 segments on allosomes...
Removing 0 segments without B allele information...
Merging adjacent segments with equal copy number...
Retaining 241 segments with copy number information on 22 chromosomes.
Assuming NBE15 as tumor
Primary contig vars. : 2701
Autosomal variants : 2631
Filtering for min.depth and VAF..
Total copy number computed as A + B.
Read in 1770 segments with copy number information on 24 chromosomes.
Removing 0 segments without copy number information...
Removing 0 segments with copy number > 4...
Removing 0 segments on allosomes...
Removing 0 segments without B allele information...
Merging adjacent segments with equal copy number...
Retaining 241 segments with copy number information on 22 chromosomes.
Assuming NBE15 as tumor
Primary contig vars. : 2701
Autosomal variants : 2631
Filtering for min.depth and VAF..
Total copy number computed as A + B.
Read in 1770 segments with copy number information on 24 chromosomes.
Removing 0 segments without copy number information...
Removing 0 segments with copy number > 4...
Removing 0 segments on allosomes...
Removing 0 segments without B allele information...
Merging adjacent segments with equal copy number...
Retaining 241 segments with copy number information on 22 chromosomes.
Assuming NBE15 as tumor
Primary contig vars. : 2701
Autosomal variants : 2631
Filtering for min.depth and VAF..
Total copy number computed as A + B.
Read in 1770 segments with copy number information on 24 chromosomes.
Removing 0 segments without copy number information...
Removing 0 segments with copy number > 4...
Removing 0 segments on allosomes...
Removing 0 segments without B allele information...
Merging adjacent segments with equal copy number...
Retaining 241 segments with copy number information on 22 chromosomes.
Assuming NBE15 as tumor
Primary contig vars. : 2701
Autosomal variants : 2631
Filtering for min.depth and VAF..
Total copy number computed as A + B.
Read in 1770 segments with copy number information on 24 chromosomes.
Removing 0 segments without copy number information...
Removing 0 segments with copy number > 4...
Removing 0 segments on allosomes...
Removing 0 segments without B allele information...
Merging adjacent segments with equal copy number...
Retaining 241 segments with copy number information on 22 chromosomes.
Assuming NBE15 as tumor
Primary contig vars. : 2701
Autosomal variants : 2631
Filtering for min.depth and VAF..
Total copy number computed as A + B.
Read in 721 segments with copy number information on 23 chromosomes.
Removing 0 segments without copy number information...
Removing 8 segments with copy number > 4...
Removing 9 segments on allosomes...
Removing 0 segments without B allele information...
Merging adjacent segments with equal copy number...
Retaining 116 segments with copy number information on 21 chromosomes.
Assuming NBE11 as tumor
Primary contig vars. : 4827
Autosomal variants : 4718
Filtering for min.depth and VAF..
Total copy number computed as A + B.
Read in 1770 segments with copy number information on 24 chromosomes.
Removing 0 segments without copy number information...
Removing 0 segments with copy number > 4...
Removing 0 segments on allosomes...
Removing 0 segments without B allele information...
Merging adjacent segments with equal copy number...
Retaining 241 segments with copy number information on 22 chromosomes.
Assuming NBE15 as tumor
Primary contig vars. : 2701
Autosomal variants : 2631
Filtering for min.depth and VAF..
Total copy number computed as A + B.
Read in 1770 segments with copy number information on 24 chromosomes.
Removing 0 segments without copy number information...
Removing 0 segments with copy number > 4...
Removing 0 segments on allosomes...
Removing 0 segments without B allele information...
Merging adjacent segments with equal copy number...
Retaining 241 segments with copy number information on 22 chromosomes.
Assuming NBE15 as tumor
Primary contig vars. : 2701
Autosomal variants : 2631
Filtering for min.depth and VAF..
Total copy number computed as A + B.
Read in 1770 segments with copy number information on 24 chromosomes.
Removing 0 segments without copy number information...
Removing 0 segments with copy number > 4...
Removing 0 segments on allosomes...
Removing 0 segments without B allele information...
Merging adjacent segments with equal copy number...
Retaining 241 segments with copy number information on 22 chromosomes.
Assuming NBE15 as tumor
Primary contig vars. : 2701
Autosomal variants : 2631
Filtering for min.depth and VAF..
Total copy number computed as A + B.
Read in 1770 segments with copy number information on 24 chromosomes.
Removing 0 segments without copy number information...
Removing 0 segments with copy number > 4...
Removing 0 segments on allosomes...
Removing 0 segments without B allele information...
Merging adjacent segments with equal copy number...
Retaining 241 segments with copy number information on 22 chromosomes.
Assuming NBE15 as tumor
Primary contig vars. : 2701
Autosomal variants : 2631
Filtering for min.depth and VAF..
Total copy number computed as A + B.
Read in 1770 segments with copy number information on 24 chromosomes.
Removing 0 segments without copy number information...
Removing 0 segments with copy number > 4...
Removing 0 segments on allosomes...
Removing 0 segments without B allele information...
Merging adjacent segments with equal copy number...
Retaining 241 segments with copy number information on 22 chromosomes.
Assuming NBE15 as tumor
Primary contig vars. : 2701
Autosomal variants : 2631
Filtering for min.depth and VAF..
Total copy number computed as A + B.
Read in 1770 segments with copy number information on 24 chromosomes.
Removing 0 segments without copy number information...
Removing 0 segments with copy number > 4...
Removing 0 segments on allosomes...
Removing 0 segments without B allele information...
Merging adjacent segments with equal copy number...
Retaining 241 segments with copy number information on 22 chromosomes.
Assuming NBE15 as tumor
Primary contig vars. : 2701
Autosomal variants : 2631
Filtering for min.depth and VAF..
Total copy number computed as A + B.
Read in 1770 segments with copy number information on 24 chromosomes.
Removing 0 segments without copy number information...
Removing 0 segments with copy number > 4...
Removing 0 segments on allosomes...
Removing 0 segments without B allele information...
Merging adjacent segments with equal copy number...
Retaining 241 segments with copy number information on 22 chromosomes.
Assuming NBE15 as tumor
Primary contig vars. : 2701
Autosomal variants : 2631
Filtering for min.depth and VAF..
Total copy number computed as A + B.
Read in 1770 segments with copy number information on 24 chromosomes.
Removing 0 segments without copy number information...
Removing 0 segments with copy number > 4...
Removing 0 segments on allosomes...
Removing 0 segments without B allele information...
Merging adjacent segments with equal copy number...
Retaining 241 segments with copy number information on 22 chromosomes.
Assuming NBE15 as tumor
Primary contig vars. : 2701
Autosomal variants : 2631
Filtering for min.depth and VAF..
test_nbImport.R............... 33 tests [0;32mOK[0m [0;34m56.9s[0m
test_parameter_validation.R... 0 tests
test_parameter_validation.R... 0 tests
test_parameter_validation.R... 0 tests
test_parameter_validation.R... 0 tests
test_parameter_validation.R... 0 tests
test_parameter_validation.R... 0 tests
test_parameter_validation.R... 0 tests
test_parameter_validation.R... 0 tests
test_parameter_validation.R... 0 tests
test_parameter_validation.R... 0 tests
test_parameter_validation.R... 0 tests
test_parameter_validation.R... 0 tests
test_parameter_validation.R... 0 tests
test_parameter_validation.R... 0 tests
test_parameter_validation.R... 0 tests
test_parameter_validation.R... 0 tests
test_parameter_validation.R... 0 tests
test_parameter_validation.R... 0 tests Total copy number computed as A + B.
Read in 1770 segments with copy number information on 24 chromosomes.
Removing 0 segments without copy number information...
Removing 0 segments with copy number > 4...
Removing 0 segments on allosomes...
Removing 0 segments without B allele information...
Merging adjacent segments with equal copy number...
Retaining 241 segments with copy number information on 22 chromosomes.
Assuming NBE15 as tumor
Primary contig vars. : 2701
Autosomal variants : 2631
Filtering for min.depth and VAF..
Total copy number computed as A + B.
Read in 1770 segments with copy number information on 24 chromosomes.
Removing 0 segments without copy number information...
Removing 0 segments with copy number > 4...
Removing 0 segments on allosomes...
Removing 0 segments without B allele information...
Merging adjacent segments with equal copy number...
Retaining 241 segments with copy number information on 22 chromosomes.
Assuming NBE15 as tumor
Primary contig vars. : 2701
Autosomal variants : 2631
Filtering for min.depth and VAF..
Total copy number computed as A + B.
Read in 1770 segments with copy number information on 24 chromosomes.
Removing 0 segments without copy number information...
Removing 0 segments with copy number > 4...
Removing 0 segments on allosomes...
Removing 0 segments without B allele information...
Merging adjacent segments with equal copy number...
Retaining 241 segments with copy number information on 22 chromosomes.
Assuming NBE15 as tumor
Primary contig vars. : 2701
Autosomal variants : 2631
Filtering for min.depth and VAF..
Total copy number computed as A + B.
Read in 1770 segments with copy number information on 24 chromosomes.
Removing 0 segments without copy number information...
Removing 0 segments with copy number > 4...
Removing 0 segments on allosomes...
Removing 0 segments without B allele information...
Merging adjacent segments with equal copy number...
Retaining 241 segments with copy number information on 22 chromosomes.
Assuming NBE15 as tumor
Primary contig vars. : 2701
Autosomal variants : 2631
Filtering for min.depth and VAF..
Total copy number computed as A + B.
Read in 1770 segments with copy number information on 24 chromosomes.
Removing 0 segments without copy number information...
Removing 0 segments with copy number > 4...
Removing 0 segments on allosomes...
Removing 0 segments without B allele information...
Merging adjacent segments with equal copy number...
Retaining 241 segments with copy number information on 22 chromosomes.
Assuming NBE15 as tumor
Primary contig vars. : 2701
Autosomal variants : 2631
Filtering for min.depth and VAF..
Total copy number computed as A + B.
Read in 1770 segments with copy number information on 24 chromosomes.
Removing 0 segments without copy number information...
Removing 0 segments with copy number > 4...
Removing 0 segments on allosomes...
Removing 0 segments without B allele information...
Merging adjacent segments with equal copy number...
Retaining 241 segments with copy number information on 22 chromosomes.
Assuming NBE15 as tumor
Primary contig vars. : 2701
Autosomal variants : 2631
Filtering for min.depth and VAF..
Total copy number computed as A + B.
Read in 1770 segments with copy number information on 24 chromosomes.
Removing 0 segments without copy number information...
Removing 0 segments with copy number > 4...
Removing 0 segments on allosomes...
Removing 0 segments without B allele information...
Merging adjacent segments with equal copy number...
Retaining 241 segments with copy number information on 22 chromosomes.
Assuming NBE15 as tumor
Primary contig vars. : 2701
Autosomal variants : 2631
Filtering for min.depth and VAF..
Total copy number computed as A + B.
Read in 1770 segments with copy number information on 24 chromosomes.
Removing 0 segments without copy number information...
Removing 0 segments with copy number > 4...
Removing 0 segments on allosomes...
Removing 0 segments without B allele information...
Merging adjacent segments with equal copy number...
Retaining 241 segments with copy number information on 22 chromosomes.
Assuming NBE15 as tumor
Primary contig vars. : 2701
Autosomal variants : 2631
Filtering for min.depth and VAF..
Total copy number computed as A + B.
Read in 1770 segments with copy number information on 24 chromosomes.
Removing 0 segments without copy number information...
Removing 0 segments with copy number > 4...
Removing 0 segments on allosomes...
Removing 0 segments without B allele information...
Merging adjacent segments with equal copy number...
Retaining 241 segments with copy number information on 22 chromosomes.
Assuming NBE15 as tumor
Primary contig vars. : 2701
Autosomal variants : 2631
Filtering for min.depth and VAF..
Total copy number computed as A + B.
Read in 1770 segments with copy number information on 24 chromosomes.
Removing 0 segments without copy number information...
Removing 0 segments with copy number > 4...
Removing 0 segments on allosomes...
Removing 0 segments without B allele information...
Merging adjacent segments with equal copy number...
Retaining 241 segments with copy number information on 22 chromosomes.
Assuming NBE15 as tumor
Primary contig vars. : 2701
Autosomal variants : 2631
Filtering for min.depth and VAF..
Total copy number computed as A + B.
Read in 1770 segments with copy number information on 24 chromosomes.
Removing 0 segments without copy number information...
Removing 0 segments with copy number > 4...
Removing 0 segments on allosomes...
Removing 0 segments without B allele information...
Merging adjacent segments with equal copy number...
Retaining 241 segments with copy number information on 22 chromosomes.
Assuming NBE15 as tumor
Primary contig vars. : 2701
Autosomal variants : 2631
Filtering for min.depth and VAF..
Total copy number computed as A + B.
Read in 1770 segments with copy number information on 24 chromosomes.
Removing 0 segments without copy number information...
Removing 0 segments with copy number > 4...
Removing 0 segments on allosomes...
Removing 0 segments without B allele information...
Merging adjacent segments with equal copy number...
Retaining 241 segments with copy number information on 22 chromosomes.
Assuming NBE15 as tumor
Primary contig vars. : 2701
Autosomal variants : 2631
Filtering for min.depth and VAF..
Assuming TUMOR as tumor
Importing VCF..
Total variants : 4819
Variants passing filter: 4819
Bi-allelic variants : 4819
single nucl. variants : 4819
Primary contig vars. : 4819
Autosomal variants : 4819
Filtering for min.depth and VAF..
Assuming sample_tumor_XI003_10023 as tumor
Importing VCF..
Total variants : 167
Variants passing filter: 167
Bi-allelic variants : 142
single nucl. variants : 47
Primary contig vars. : 47
Autosomal variants : 11
Filtering for min.depth and VAF..
Assuming NBE15 as tumor
Primary contig vars. : 2701
Autosomal variants : 2631
Filtering for min.depth and VAF..
Total copy number computed as A + B.
Read in 1770 segments with copy number information on 24 chromosomes.
Removing 0 segments without copy number information...
Removing 0 segments with copy number > 4...
Removing 0 segments on allosomes...
Removing 0 segments without B allele information...
Merging adjacent segments with equal copy number...
Retaining 241 segments with copy number information on 22 chromosomes.
Assuming NBE15 as tumor
Primary contig vars. : 2701
Autosomal variants : 2631
Filtering for min.depth and VAF..
test_parameter_validation.R... 34 tests [0;32mOK[0m [0;34m42.7s[0m
test_readCNV.R................ 0 tests
test_readCNV.R................ 0 tests
test_readCNV.R................ 0 tests
test_readCNV.R................ 0 tests
test_readCNV.R................ 0 tests
test_readCNV.R................ 0 tests
test_readCNV.R................ 0 tests
test_readCNV.R................ 0 tests
test_readCNV.R................ 0 tests
test_readCNV.R................ 0 tests
test_readCNV.R................ 0 tests
test_readCNV.R................ 0 tests
test_readCNV.R................ 0 tests
test_readCNV.R................ 0 tests Total copy number computed as A + B.
Read in 721 segments with copy number information on 23 chromosomes.
Removing 0 segments without copy number information...
Removing 8 segments with copy number > 4...
Removing 9 segments on allosomes...
Removing 0 segments without B allele information...
Merging adjacent segments with equal copy number...
Retaining 116 segments with copy number information on 21 chromosomes.
Total copy number computed as A + B.
Read in 721 segments with copy number information on 23 chromosomes.
Removing 0 segments without copy number information...
Removing 8 segments with copy number > 4...
Removing 9 segments on allosomes...
Removing 0 segments without B allele information...
Merging adjacent segments with equal copy number...
Retaining 116 segments with copy number information on 21 chromosomes.
Total copy number computed as A + B.
Read in 25 segments with copy number information on 23 chromosomes.
Removing 0 segments without copy number information...
Removing 0 segments with copy number > 4...
Removing 1 segments on allosomes...
Removing 0 segments without B allele information...
Merging adjacent segments with equal copy number...
Retaining 24 segments with copy number information on 22 chromosomes.
Total copy number computed as A + B.
Read in 721 segments with copy number information on 23 chromosomes.
Removing 0 segments without copy number information...
Removing 25 segments with copy number > 3...
Removing 9 segments on allosomes...
Removing 0 segments without B allele information...
Merging adjacent segments with equal copy number...
Retaining 98 segments with copy number information on 20 chromosomes.
Total copy number computed as A + B.
Read in 721 segments with copy number information on 23 chromosomes.
Removing 0 segments without copy number information...
Removing 0 segments with copy number > 5...
Removing 9 segments on allosomes...
Removing 0 segments without B allele information...
Merging adjacent segments with equal copy number...
Retaining 123 segments with copy number information on 22 chromosomes.
Total copy number computed as A + B.
Read in 721 segments with copy number information on 23 chromosomes.
Removing 0 segments without copy number information...
Removing 8 segments with copy number > 4...
Removing 9 segments on allosomes...
Removing 0 segments without B allele information...
Merging adjacent segments with equal copy number...
Retaining 116 segments with copy number information on 21 chromosomes.
Total copy number computed as A + B.
Read in 721 segments with copy number information on 23 chromosomes.
Removing 0 segments without copy number information...
Removing 8 segments with copy number > 4...
Removing 0 segments without B allele information...
Merging adjacent segments with equal copy number...
Retaining 121 segments with copy number information on 22 chromosomes.
Total copy number computed as A + B.
Read in 721 segments with copy number information on 23 chromosomes.
Removing 0 segments without copy number information...
Removing 8 segments with copy number > 4...
Removing 9 segments on allosomes...
Removing 0 segments without B allele information...
Merging adjacent segments with equal copy number...
Retaining 116 segments with copy number information on 21 chromosomes.
Total copy number computed as A + B.
Read in 721 segments with copy number information on 23 chromosomes.
Removing 0 segments without copy number information...
Removing 8 segments with copy number > 4...
Removing 9 segments on allosomes...
Removing 0 segments without B allele information...
Merging adjacent segments with equal copy number...
Retaining 487 segments with copy number information on 21 chromosomes.
Total copy number computed as A + B.
Read in 721 segments with copy number information on 23 chromosomes.
Removing 0 segments without copy number information...
Removing 8 segments with copy number > 4...
Removing 9 segments on allosomes...
Removing 0 segments without B allele information...
Merging adjacent segments with equal copy number...
Retaining 81 segments with copy number information on 21 chromosomes.
Total copy number computed as A + B.
Read in 721 segments with copy number information on 23 chromosomes.
Removing 0 segments without copy number information...
Removing 8 segments with copy number > 4...
Removing 9 segments on allosomes...
Removing 0 segments without B allele information...
Merging adjacent segments with equal copy number...
Retaining 116 segments with copy number information on 21 chromosomes.
Total copy number computed as A + B.
Read in 25 segments with copy number information on 23 chromosomes.
Removing 0 segments without copy number information...
Removing 0 segments with copy number > 4...
Removing 1 segments on allosomes...
Removing 0 segments without B allele information...
Merging adjacent segments with equal copy number...
Retaining 24 segments with copy number information on 22 chromosomes.
Total copy number computed as A + B.
Read in 690 segments with copy number information on 24 chromosomes.
Removing 0 segments without copy number information...
Removing 254 segments with copy number > 4...
Change chromosome names to 1, 2, 3, ...
Removing 4 segments on allosomes...
Removing 0 segments without B allele information...
Merging adjacent segments with equal copy number...
Retaining 44 segments with copy number information on 21 chromosomes.
Total copy number computed as A + B.
Read in 721 segments with copy number information on 23 chromosomes.
Removing 0 segments without copy number information...
Removing 8 segments with copy number > 4...
Removing 9 segments on allosomes...
Removing 0 segments without B allele information...
Merging adjacent segments with equal copy number...
Retaining 116 segments with copy number information on 21 chromosomes.
Total copy number computed as A + B.
Read in 721 segments with copy number information on 23 chromosomes.
Removing 0 segments without copy number information...
Removing 8 segments with copy number > 4...
Removing 9 segments on allosomes...
Removing 0 segments without B allele information...
Merging adjacent segments with equal copy number...
Retaining 116 segments with copy number information on 21 chromosomes.
test_readCNV.R................ 24 tests [0;32mOK[0m [0;34m0.3s[0m
test_readVCF.R................ 0 tests
test_readVCF.R................ 0 tests
test_readVCF.R................ 0 tests
test_readVCF.R................ 0 tests
test_readVCF.R................ 0 tests
test_readVCF.R................ 0 tests
test_readVCF.R................ 0 tests
test_readVCF.R................ 0 tests
test_readVCF.R................ 0 tests
test_readVCF.R................ 0 tests
test_readVCF.R................ 0 tests
test_readVCF.R................ 0 tests Assuming TUMOR as tumor
Importing VCF..
Total variants : 4819
Variants passing filter: 4819
Bi-allelic variants : 4819
single nucl. variants : 4819
Primary contig vars. : 4819
Autosomal variants : 4819
Filtering for min.depth and VAF..
Assuming NBE15 as tumor
Primary contig vars. : 2701
Autosomal variants : 2631
Filtering for min.depth and VAF..
Assuming TUMOR as tumor
Importing VCF..
Total variants : 4819
Variants passing filter: 4819
Bi-allelic variants : 4819
single nucl. variants : 4819
Primary contig vars. : 4819
Filtering for min.depth and VAF..
Assuming TUMOR as tumor
Importing VCF..
Total variants : 4819
Variants passing filter: 4819
Bi-allelic variants : 4819
single nucl. variants : 4819
Primary contig vars. : 4819
Autosomal variants : 4819
Filtering for min.depth and VAF..
Assuming TUMOR as tumor
Importing VCF..
Total variants : 4819
Variants passing filter: 4819
Bi-allelic variants : 4819
single nucl. variants : 4819
Primary contig vars. : 4819
Autosomal variants : 4819
Filtering for min.depth and VAF..
Assuming sample_tumor_XI003_10023 as tumor
Importing VCF..
Total variants : 167
Variants passing filter: 167
Bi-allelic variants : 142
single nucl. variants : 47
Primary contig vars. : 47
Autosomal variants : 11
Filtering for min.depth and VAF..
Assuming TUMOR as tumor
Importing VCF..
Total variants : 4819
Variants passing filter: 4819
Bi-allelic variants : 4819
single nucl. variants : 4819
Primary contig vars. : 4819
Autosomal variants : 4819
Filtering for min.depth and VAF..
Assuming TUMOR as tumor
Importing VCF..
Total variants : 4819
Variants passing filter: 4819
Bi-allelic variants : 4819
single nucl. variants : 4819
Primary contig vars. : 4819
Autosomal variants : 4819
Filtering for min.depth and VAF..
Assuming TUMOR as tumor
Importing VCF..
Total variants : 4819
Variants passing filter: 4819
Bi-allelic variants : 4819
single nucl. variants : 4819
Primary contig vars. : 4819
Autosomal variants : 4819
Filtering for min.depth and VAF..
Assuming TUMOR as tumor
Importing VCF..
Total variants : 4819
Variants passing filter: 4819
Bi-allelic variants : 4819
single nucl. variants : 4819
Primary contig vars. : 4819
Autosomal variants : 4819
Filtering for min.depth and VAF..
test_readVCF.R................ 20 tests [0;32mOK[0m [0;34m4.2s[0m
test_signature_assignment.R... 0 tests
test_signature_assignment.R... 0 tests
test_signature_assignment.R... 0 tests
test_signature_assignment.R... 0 tests
test_signature_assignment.R... 0 tests
test_signature_assignment.R... 0 tests
test_signature_assignment.R... 0 tests
test_signature_assignment.R... 0 tests
test_signature_assignment.R... 0 tests
test_signature_assignment.R... 0 tests
test_signature_assignment.R... 0 tests
test_signature_assignment.R... 0 tests
test_signature_assignment.R... 0 tests
test_signature_assignment.R... 0 tests
test_signature_assignment.R... 0 tests
test_signature_assignment.R... 0 tests
test_signature_assignment.R... 0 tests
test_signature_assignment.R... 0 tests Total copy number computed as A + B.
Read in 1770 segments with copy number information on 24 chromosomes.
Removing 0 segments without copy number information...
Removing 0 segments with copy number > 4...
Removing 0 segments on allosomes...
Removing 0 segments without B allele information...
Merging adjacent segments with equal copy number...
Retaining 241 segments with copy number information on 22 chromosomes.
Assuming NBE15 as tumor
Primary contig vars. : 2701
Autosomal variants : 2631
Filtering for min.depth and VAF..
Total copy number computed as A + B.
Read in 1770 segments with copy number information on 24 chromosomes.
Removing 0 segments without copy number information...
Removing 0 segments with copy number > 4...
Removing 0 segments on allosomes...
Removing 0 segments without B allele information...
Merging adjacent segments with equal copy number...
Retaining 241 segments with copy number information on 22 chromosomes.
Assuming NBE15 as tumor
Primary contig vars. : 2701
Autosomal variants : 2631
Filtering for min.depth and VAF..
Total copy number computed as A + B.
Read in 1770 segments with copy number information on 24 chromosomes.
Removing 0 segments without copy number information...
Removing 0 segments with copy number > 4...
Removing 0 segments on allosomes...
Removing 0 segments without B allele information...
Merging adjacent segments with equal copy number...
Retaining 241 segments with copy number information on 22 chromosomes.
Assuming NBE15 as tumor
Primary contig vars. : 2701
Autosomal variants : 2631
Filtering for min.depth and VAF..
Total copy number computed as A + B.
Read in 1770 segments with copy number information on 24 chromosomes.
Removing 0 segments without copy number information...
Removing 0 segments with copy number > 4...
Removing 0 segments on allosomes...
Removing 0 segments without B allele information...
Merging adjacent segments with equal copy number...
Retaining 241 segments with copy number information on 22 chromosomes.
Assuming NBE15 as tumor
Primary contig vars. : 2701
Autosomal variants : 2631
Filtering for min.depth and VAF..
Total copy number computed as A + B.
Read in 1770 segments with copy number information on 24 chromosomes.
Removing 0 segments without copy number information...
Removing 0 segments with copy number > 4...
Removing 0 segments on allosomes...
Removing 0 segments without B allele information...
Merging adjacent segments with equal copy number...
Retaining 241 segments with copy number information on 22 chromosomes.
Assuming NBE15 as tumor
Primary contig vars. : 2701
Autosomal variants : 2631
Filtering for min.depth and VAF..
Total copy number computed as A + B.
Read in 1770 segments with copy number information on 24 chromosomes.
Removing 0 segments without copy number information...
Removing 0 segments with copy number > 4...
Removing 0 segments on allosomes...
Removing 0 segments without B allele information...
Merging adjacent segments with equal copy number...
Retaining 241 segments with copy number information on 22 chromosomes.
Assuming NBE15 as tumor
Primary contig vars. : 2701
Autosomal variants : 2631
Filtering for min.depth and VAF..
Total copy number computed as A + B.
Read in 1770 segments with copy number information on 24 chromosomes.
Removing 0 segments without copy number information...
Removing 0 segments with copy number > 4...
Removing 0 segments on allosomes...
Removing 0 segments without B allele information...
Merging adjacent segments with equal copy number...
Retaining 241 segments with copy number information on 22 chromosomes.
Assuming NBE15 as tumor
Primary contig vars. : 2701
Autosomal variants : 2631
Filtering for min.depth and VAF..
Total copy number computed as A + B.
Read in 1770 segments with copy number information on 24 chromosomes.
Removing 0 segments without copy number information...
Removing 0 segments with copy number > 4...
Removing 0 segments on allosomes...
Removing 0 segments without B allele information...
Merging adjacent segments with equal copy number...
Retaining 241 segments with copy number information on 22 chromosomes.
Assuming NBE15 as tumor
Primary contig vars. : 2701
Autosomal variants : 2631
Filtering for min.depth and VAF..
Total copy number computed as A + B.
Read in 1770 segments with copy number information on 24 chromosomes.
Removing 0 segments without copy number information...
Removing 0 segments with copy number > 4...
Removing 0 segments on allosomes...
Removing 0 segments without B allele information...
Merging adjacent segments with equal copy number...
Retaining 241 segments with copy number information on 22 chromosomes.
Assuming NBE15 as tumor
Primary contig vars. : 2701
Autosomal variants : 2631
Filtering for min.depth and VAF..
Total copy number computed as A + B.
Read in 1770 segments with copy number information on 24 chromosomes.
Removing 0 segments without copy number information...
Removing 0 segments with copy number > 4...
Removing 0 segments on allosomes...
Removing 0 segments without B allele information...
Merging adjacent segments with equal copy number...
Retaining 241 segments with copy number information on 22 chromosomes.
Assuming NBE15 as tumor
Primary contig vars. : 2701
Autosomal variants : 2631
Filtering for min.depth and VAF..
Total copy number computed as A + B.
Read in 1770 segments with copy number information on 24 chromosomes.
Removing 0 segments without copy number information...
Removing 0 segments with copy number > 4...
Removing 0 segments on allosomes...
Removing 0 segments without B allele information...
Merging adjacent segments with equal copy number...
Retaining 241 segments with copy number information on 22 chromosomes.
Assuming NBE15 as tumor
Primary contig vars. : 2701
Autosomal variants : 2631
Filtering for min.depth and VAF..
Total copy number computed as A + B.
Read in 1770 segments with copy number information on 24 chromosomes.
Removing 0 segments without copy number information...
Removing 0 segments with copy number > 4...
Removing 0 segments on allosomes...
Removing 0 segments without B allele information...
Merging adjacent segments with equal copy number...
Retaining 241 segments with copy number information on 22 chromosomes.
Assuming NBE15 as tumor
Primary contig vars. : 2701
Autosomal variants : 2631
Filtering for min.depth and VAF..
Total copy number computed as A + B.
Read in 1770 segments with copy number information on 24 chromosomes.
Removing 0 segments without copy number information...
Removing 0 segments with copy number > 4...
Removing 0 segments on allosomes...
Removing 0 segments without B allele information...
Merging adjacent segments with equal copy number...
Retaining 241 segments with copy number information on 22 chromosomes.
Assuming NBE15 as tumor
Primary contig vars. : 2701
Autosomal variants : 2631
Filtering for min.depth and VAF..
Total copy number computed as A + B.
Read in 1770 segments with copy number information on 24 chromosomes.
Removing 0 segments without copy number information...
Removing 0 segments with copy number > 4...
Removing 0 segments on allosomes...
Removing 0 segments without B allele information...
Merging adjacent segments with equal copy number...
Retaining 241 segments with copy number information on 22 chromosomes.
Assuming NBE15 as tumor
Primary contig vars. : 2701
Autosomal variants : 2631
Filtering for min.depth and VAF..
Total copy number computed as A + B.
Read in 1770 segments with copy number information on 24 chromosomes.
Removing 0 segments without copy number information...
Removing 0 segments with copy number > 4...
Removing 0 segments on allosomes...
Removing 0 segments without B allele information...
Merging adjacent segments with equal copy number...
Retaining 241 segments with copy number information on 22 chromosomes.
Assuming NBE15 as tumor
Primary contig vars. : 2701
Autosomal variants : 2631
Filtering for min.depth and VAF..
test_signature_assignment.R... 22 tests [0;32mOK[0m [0;34m1.0s[0m
All ok, 197 results (4m 46.4s)
There were 50 or more warnings (use warnings() to see the first 50)
>
> proc.time()
user system elapsed
286.580 6.791 292.348
LACHESIS.Rcheck/LACHESIS-Ex.timings
| name | user | system | elapsed | |
| LACHESIS | 37.881 | 1.704 | 39.311 | |
| MRCA | 5.523 | 0.143 | 5.641 | |
| classifyLACHESIS | 16.089 | 0.247 | 16.217 | |
| clonalMutationCounter | 4.372 | 0.065 | 4.410 | |
| estimateClonality | 16.579 | 0.444 | 16.958 | |
| nbImport | 8.892 | 0.459 | 9.263 | |
| normalizeCounts | 5.368 | 0.084 | 5.420 | |
| plotClinicalCorrelations | 15.987 | 0.198 | 16.059 | |
| plotClonality | 16.924 | 0.280 | 17.102 | |
| plotLachesis | 16.292 | 0.152 | 16.315 | |
| plotMutationDensities | 5.297 | 0.044 | 5.298 | |
| plotNB | 22.134 | 0.334 | 22.293 | |
| plotSurvival | 18.098 | 0.168 | 18.121 | |
| plotVAFdistr | 0.254 | 0.014 | 0.246 | |
| readCNV | 0.067 | 0.003 | 0.065 | |
| readVCF | 3.127 | 0.055 | 3.148 | |