R Observatory: Metrics for SATS version 1.0.11

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

SATS

1.0.11Package record

Signature Analyzer for Targeted Sequencing (SATS)

0packages depend

1.1Kdownloads / year

–test coverage

11/13flavors OK

Overview

About

Maintained by Bill WheelerCRAN page ↗

Performs mutational signature analysis for tumors profiled by targeted sequencing. Unlike the canonical analysis of mutational signatures, SATS factorizes the mutation count matrix into a panel-context matrix (measuring the number of mutation opportunities per million base pairs for each tumor), a signature profile matrix, and a signature activity matrix. SATS also calculates the expected number of mutations attributed to each signature, namely the signature burden, for each tumor profiled by targeted sequencing. For more details see Lee et al. (2024) doi:10.1101/2023.05.18.23290188.

Install

R (CRAN)Ubuntu (r2u)

install.packages("SATS", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-sats

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

bspm (used by r2u) also needs make: sudo apt install make

Health

CRAN checks

2ERROR11OK

Check messages

ERRORexamplesr-oldrel-macos-arm64, r-oldrel-macos-x86_64

Running examples in ‘SATS-Ex.R’ failed
The error most likely occurred in:

> ### Name: GenerateLMatrix
> ### Title: Generate a sample-level panel-context matrix
> ### Aliases: GenerateLMatrix
> 
> ### ** Examples
> 
> data(SimData, package="SATS")
> 
> keep <- match(SimData$PatientInfo$SEQ_ASSAY_ID,
+               unique(SimData$PanelEx$SEQ_ASSAY_ID), nomatch=0) > 0
> PatientInfo <- SimData$PatientInfo[keep, ]
> 
> L_mat <- GenerateLMatrix(SimData$PanelEx, PatientInfo, Class="SBS",
+                          SBS_order="COSMIC", ref.genome="hg19")
Error in (function (cond)  : 
  error in evaluating the argument 'x' in selecting a method for function 'getSeq': there is no package called ‘BSgenome.Hsapiens.UCSC.hg19’
Calls: GenerateLMatrix ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted

ERRORtestsr-oldrel-macos-arm64, r-oldrel-macos-x86_64

r-oldrel-macos-arm64

Running ‘testthat.R’ [4s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(SATS)
  > 
  > test_check("SATS")
  Saving _problems/test-GeneratePanelSize-14.R
  Saving _problems/test-GenerateVMatrix-18.R
  Saving _problems/test-GenerateVMatrix-27.R
  Saving _problems/test-GenerateVMatrix-42.R
  Saving _problems/test-GenerateVMatrix-62.R
  Saving _problems/test-GenerateVMatrix-78.R
  Saving _problems/test-input-conversion-63.R
  [ FAIL 7 | WARN 0 | SKIP 0 | PASS 45 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-GeneratePanelSize.R:14:1'): (code run outside of `test_that()`) ──
  Error in `(function (cond)  .Internal(C_tryCatchHelper(addr, 1L, cond)))(structure(list(message = "there is no package called 'BSgenome.Hsapiens.UCSC.hg19'", call = loadNamespace(x), package = "BSgenome.Hsapiens.UCSC.hg19", lib.loc = NULL), class = c("packageNotFoundError", "error", "condition")))`: error
...[truncated]...
 │ └─SATS:::GeneratePanelSize_SBS(...)
   3. │   └─Biostrings::getSeq(BSgenome.Hsapiens.UCSC.hg19::Hsapiens, Seq_assay_GRanges)
   4. ├─base::loadNamespace(x)
   5. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   6. │ │ └─base (local) withOneRestart(expr, restarts[[1L]])
   7. │ │   └─base (local) doWithOneRestart(return(expr), restart)
   8. │ └─base::stop(cond)
   9. └─base (local) `<fn>`(`<pckgNtFE>`)
  ── Error ('test-input-conversion.R:63:3'): VCF and BED converters feed GenerateVMatrix and GenerateLMatrix ──
  Error in `get_reference_genome(ref.genome)`: Make sure package BSgenome.Hsapiens.UCSC.hg19 is loaded
  Backtrace:
      ▆
   1. └─SATS::GenerateVMatrix(mut, Class = "SBS", ref.genome = "hg19") at test-input-conversion.R:63:3
   2.   └─SATS:::GenerateVMatrix_SBS(mutation_record, ref.genome, mutation_order)
   3.     └─SATS:::get_reference_genome(ref.genome)
  
  [ FAIL 7 | WARN 0 | SKIP 0 | PASS 45 ]
  Error:
  ! Test failures.
  Execution halted

r-oldrel-macos-x86_64

Running ‘testthat.R’ [8s/10s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(SATS)
  > 
  > test_check("SATS")
  Saving _problems/test-GeneratePanelSize-14.R
  Saving _problems/test-GenerateVMatrix-18.R
  Saving _problems/test-GenerateVMatrix-27.R
  Saving _problems/test-GenerateVMatrix-42.R
  Saving _problems/test-GenerateVMatrix-62.R
  Saving _problems/test-GenerateVMatrix-78.R
  Saving _problems/test-input-conversion-63.R
  [ FAIL 7 | WARN 0 | SKIP 0 | PASS 45 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-GeneratePanelSize.R:14:1'): (code run outside of `test_that()`) ──
  Error in `(function (cond)  .Internal(C_tryCatchHelper(addr, 1L, cond)))(structure(list(message = "there is no package called 'BSgenome.Hsapiens.UCSC.hg19'", call = loadNamespace(x), package = "BSgenome.Hsapiens.UCSC.hg19", lib.loc = NULL), class = c("packageNotFoundError", "error", "condition")))`: erro
...[truncated]...
 │ └─SATS:::GeneratePanelSize_SBS(...)
   3. │   └─Biostrings::getSeq(BSgenome.Hsapiens.UCSC.hg19::Hsapiens, Seq_assay_GRanges)
   4. ├─base::loadNamespace(x)
   5. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   6. │ │ └─base (local) withOneRestart(expr, restarts[[1L]])
   7. │ │   └─base (local) doWithOneRestart(return(expr), restart)
   8. │ └─base::stop(cond)
   9. └─base (local) `<fn>`(`<pckgNtFE>`)
  ── Error ('test-input-conversion.R:63:3'): VCF and BED converters feed GenerateVMatrix and GenerateLMatrix ──
  Error in `get_reference_genome(ref.genome)`: Make sure package BSgenome.Hsapiens.UCSC.hg19 is loaded
  Backtrace:
      ▆
   1. └─SATS::GenerateVMatrix(mut, Class = "SBS", ref.genome = "hg19") at test-input-conversion.R:63:3
   2.   └─SATS:::GenerateVMatrix_SBS(mutation_record, ref.genome, mutation_order)
   3.     └─SATS:::get_reference_genome(ref.genome)
  
  [ FAIL 7 | WARN 0 | SKIP 0 | PASS 45 ]
  Error:
  ! Test failures.
  Execution halted

CRAN check page ↗

Slowest check: 5.4 min · r-devel-windows-x86_64

Status changes

ERROR11 OK, 2 ERRORNow
ERROR5 OK, 2 ERROR2026-07-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.0.11

READMENoVignettesNoNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 12includes a package overview page
Examples that run: 100%8 run in a plain check
Exported functions with examples: 89%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 50%

How these are measured

Downloads

1.1K

CRAN downloads in the past year

Rank #9,438 · ~3/day · ~93/mo

Releases R versions

Daily download trend is not available in this view yet.

44130 days

1K90 days

1.1K1 year

Compare downloads with other packages →

Also on317 r2u

How downloads are counted

Dependencies

Declared dependencies

8 external dependencies (excludes base and recommended)

Installing SATS adds 21 packages (12 with compiled code, 12 MB of source tarballs). Heaviest: glmnet 2.7 MB, Rcpp 1.8 MB, RcppEigen 1.7 MB. 3 more not on CRAN are not measured.

Depends (1)

R >= 4.1.0

Imports (6)

statsglmnet GenomicRanges IRanges Biostrings dplyr

LinkingTo (0)

none

Suggests (3)

testthat BSgenome.Hsapiens.UCSC.hg19 BSgenome.Hsapiens.UCSC.hg38

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (3)

Bill Wheeler

Maintainer since 1.0.4 (2025)

DongHyuk Lee

Author

Bin Zhu

Author

Releases (4)

Pick two releases to compare their code metrics.

1.0.11Latest
record
2026-09-15 · current release · diff ↗ ·
added 4 exports
GenerateVMatrix, ReadVCFAsMutationRecord, ReadBEDAsPanelInfo, ValidateSATSInputs
unarchivedReturned to CRAN
2026-07-09
1.0.10
record
2026-07-09 · diff ↗
R
R 4.6.0 released · 2026-04-24
archivedRemoved from CRAN
2026-02-21
issues were not corrected despite reminders
1.0.6
record
2025-08-18 · diff ↗ ·
added 1 export
GenerateLMatrix
1.0.4
record
2025-07-05
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2025-07-05
Total releases: 4 / 1 yrs
License: GPL-2 OSI
Minimum R: ≥ 4.1.0
Bundled data: 688 KB / 2 files
Download size: 1.2 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("SATS")

Format

Wheeler, B., Lee, D., & Zhu, B. (2026). SATS: Signature Analyzer for Targeted Sequencing (SATS) (Version 1.0.11) [Computer software]. https://doi.org/10.32614/CRAN.package.SATS

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for SATS version 1.0.11 [Data set]. HJJB, LLC. Data release v2026-10-19. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-19, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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