R Observatory: Metrics for lisat version 0.1.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

lisat

0.1.2Package record

Longitudinal Integration Site Analysis Toolkit

0packages depend

2.2Kdownloads / year

–test coverage

11/13flavors OK

Overview

About

Maintained by Shuai NiCRAN page ↗

A comprehensive toolkit for the analysis of longitudinal integration site data, including data cleaning, quality control, statistical modeling, and visualization. It streamlines the entire workflow of integration site analysis, supports simple input formats, and provides user-friendly functions for researchers in virus integration site analysis. Ni et al. (2025) doi:10.64898/2025.12.20.695672.

Install

R (CRAN)Ubuntu (r2u)

install.packages("lisat", 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-lisat

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

ERRORre-building of vignette outputsr-oldrel-macos-arm64, r-oldrel-macos-x86_64

Error(s) in re-building vignettes:
--- re-building ‘lisat-intro.Rmd’ using rmarkdown

Quitting from lisat-intro.Rmd:107-111 [cis_analysis]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.frame`:
! undefined columns selected
---
Backtrace:
    ▆
 1. └─lisat::CIS(IS_raw = IS_raw, connect_distance = 50000)
 2.   ├─IS_raw[, c("Locus", "Chr", "nearest_gene_name")]
 3.   └─base::`[.data.frame`(IS_raw, , c("Locus", "Chr", "nearest_gene_name"))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'lisat-intro.Rmd' failed with diagnostics:
undefined columns selected
--- failed re-building ‘lisat-intro.Rmd’

SUMMARY: processing the following file failed:
  ‘lisat-intro.Rmd’

Error: Vignette re-building failed.
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(lisat)
  > testthat::test_check("lisat")
  Saving _problems/test-functions-71.R
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-functions.R:71:1'): (code run outside of `test_that()`) ────────
  Error: Package "TxDb.Hsapiens.UCSC.hg38.knownGene" needed for this function to work. Please install it.
  Backtrace:
      ▆
   1. └─lisat::get_feature(IS_raw) at test-functions.R:71:1
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
  Error:
  ! Test failures.
  Execution halted

r-oldrel-macos-x86_64

Running ‘testthat.R’ [11s/30s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(lisat)
  > testthat::test_check("lisat")
  Saving _problems/test-functions-71.R
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-functions.R:71:1'): (code run outside of `test_that()`) ────────
  Error: Package "TxDb.Hsapiens.UCSC.hg38.knownGene" needed for this function to work. Please install it.
  Backtrace:
      ▆
   1. └─lisat::get_feature(IS_raw) at test-functions.R:71:1
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
  Error:
  ! Test failures.
  Execution halted

CRAN check page ↗

Slowest check: 12.7 min · r-oldrel-macos-x86_64

Status changes

ERROR11 OK, 2 ERRORNow
ERROR3 OK, 2 ERROR2026-03-28

Advisories

none known

How this is measured·How advisories are found

Documentation

Documentation signals are not tracked yet for this package.

Websitenot tracked

Vignettes (1)

Introduction to LISAT HTML

How these are measured

Downloads

2.2K

CRAN downloads in the past year

Rank #18,805 · ~6/day · ~181/mo

lisat Releases R versions

Daily download trend is not available in this view yet.

27130 days

68890 days

2.2K1 year

Compare downloads with other packages →

Also on44 r2u

How downloads are counted

Dependencies

Declared dependencies

33 external dependencies (excludes base and recommended)

Installing lisat adds 31 packages (16 with compiled code, 29 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, isoband 1.5 MB. 5 more not on CRAN are not measured.

Depends (1)

R >= 3.5

Imports (11)

GenomicRanges IRanges tidyr (>= 1.3.0)dplyr AnnotationDbi S4Vectors GenomicFeatures magrittr ggplot2 purrr broom

LinkingTo (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (1)

Shuai Ni

Author, Maintainer since 0.1.2 (2026)

Releases (1)

R
R 4.6.0 released · 2026-04-24
0.1.2Latest
record
2026-03-27 · current release
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2026-03-27
Total releases: 1 / 1 yrs
License: MIT + file LICENSE OSI
Download size: 527 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("lisat")

Format

Ni, S. (2026). lisat: Longitudinal Integration Site Analysis Toolkit (Version 0.1.2) [Computer software]. https://doi.org/10.32614/CRAN.package.lisat

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

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 lisat version 0.1.2 [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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