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lisat

Longitudinal Integration Site Analysis Toolkit

v0.1.2 · Mar 27, 2026 · MIT + file LICENSE
CRAN GitHub Mirror

Description

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>.

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CRAN Check Status

3 ERROR
10 OK
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r-devel-linux-x86_64-debian-clang OK
r-devel-linux-x86_64-debian-gcc OK
r-devel-linux-x86_64-fedora-clang OK
r-devel-linux-x86_64-fedora-gcc OK
r-devel-macos-arm64 OK
r-devel-windows-x86_64 OK
r-oldrel-macos-x86_64 ERROR
r-oldrel-windows-x86_64 OK
r-patched-linux-x86_64 OK
r-release-linux-x86_64 OK
r-release-macos-arm64 ERROR
r-release-macos-x86_64 ERROR
r-release-windows-x86_64 OK
Check details (7 non-OK)
NOTE r-oldrel-macos-x86_64

package dependencies

Package suggested but not available for checking: ‘TxDb.Hsapiens.UCSC.hg38.knownGene’
ERROR r-oldrel-macos-x86_64

re-building of vignette outputs

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
ERROR r-oldrel-macos-x86_64

tests

Running ‘testthat.R’ [11s/12s]
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
ERROR r-release-macos-arm64

re-building of vignette outputs

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
ERROR r-release-macos-arm64

tests

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
ERROR r-release-macos-x86_64

re-building of vignette outputs

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
ERROR r-release-macos-x86_64

tests

Running ‘testthat.R’ [9s/9s]
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

Check History

ERROR 3 OK · 0 NOTE · 0 WARNING · 2 ERROR · 0 FAILURE Mar 27, 2026
ERROR r-release-macos-x86_64

tests

Running ‘testthat.R’ [8s/8s]
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 ]
  
...[truncated]...
piens.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
ERROR r-oldrel-macos-x86_64

package dependencies

Package suggested but not available for checking: ‘TxDb.Hsapiens.UCSC.hg38.knownGene’

Dependency Network

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

Version History

new 0.1.2 Mar 27, 2026