ruv

Detect and Remove Unwanted Variation using Negative Controls

v0.9.7.1 · Aug 30, 2019 · GPL

Description

Implements the 'RUV' (Remove Unwanted Variation) algorithms. These algorithms attempt to adjust for systematic errors of unknown origin in high-dimensional data. The algorithms were originally developed for use with genomic data, especially microarray data, but may be useful with other types of high-dimensional data as well. These algorithms were proposed in Gagnon-Bartsch and Speed (2012) <doi:10.1093/nar/gkz433>, Gagnon-Bartsch, Jacob and Speed (2013), and Molania, et. al. (2019) <doi:10.1093/nar/gkz433>. The algorithms require the user to specify a set of negative control variables, as described in the references. The algorithms included in this package are 'RUV-2', 'RUV-4', 'RUV-inv', 'RUV-rinv', 'RUV-I', and RUV-III', along with various supporting algorithms.

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CRAN Check Status

14 NOTE

Show all 14 flavors

Flavor	Status	Time
r-devel-linux-x86_64-debian-clang	NOTE	81.8s
r-devel-linux-x86_64-debian-gcc	NOTE	56.8s
r-devel-linux-x86_64-fedora-clang	NOTE	129.3s
r-devel-linux-x86_64-fedora-gcc	NOTE	131.4s
r-devel-macos-arm64	NOTE	22s
r-devel-windows-x86_64	NOTE	101s
r-oldrel-macos-arm64	NOTE
r-oldrel-macos-x86_64	NOTE	47s
r-oldrel-windows-x86_64	NOTE	121s
r-patched-linux-x86_64	NOTE	77.5s
r-release-linux-x86_64	NOTE	76s
r-release-macos-arm64	NOTE
r-release-macos-x86_64	NOTE	56s
r-release-windows-x86_64	NOTE	100s

Check details (16 non-OK)

NOTE r-devel-linux-x86_64-debian-clang

CRAN incoming feasibility

Maintainer: ‘Johann Gagnon-Bartsch <johanngb@umich.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Johann",
                    family = "Gagnon-Bartsch",
                    role = c("aut", "cre"),
                    email = "johanngb@umich.edu")
as necessary.

NOTE r-devel-linux-x86_64-debian-clang

Rd files

checkRd: (-1) RUVIII.Rd:51: Lost braces
    51 | If code{return.info} is \code{TRUE}, a list is returned that contains:
       |        ^

NOTE r-devel-linux-x86_64-debian-gcc

CRAN incoming feasibility

Maintainer: ‘Johann Gagnon-Bartsch <johanngb@umich.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Johann",
                    family = "Gagnon-Bartsch",
                    role = c("aut", "cre"),
                    email = "johanngb@umich.edu")
as necessary.

NOTE r-devel-linux-x86_64-debian-gcc

Rd files

checkRd: (-1) RUVIII.Rd:51: Lost braces
    51 | If code{return.info} is \code{TRUE}, a list is returned that contains:
       |        ^

NOTE r-devel-linux-x86_64-fedora-clang

Rd files

checkRd: (-1) RUVIII.Rd:51: Lost braces
    51 | If code{return.info} is \code{TRUE}, a list is returned that contains:
       |        ^

NOTE r-devel-linux-x86_64-fedora-gcc

Rd files

checkRd: (-1) RUVIII.Rd:51: Lost braces
    51 | If code{return.info} is \code{TRUE}, a list is returned that contains:
       |        ^

NOTE r-devel-macos-arm64

Rd files

checkRd: (-1) RUVIII.Rd:51: Lost braces
    51 | If code{return.info} is \code{TRUE}, a list is returned that contains:
       |        ^

NOTE r-devel-windows-x86_64

Rd files

checkRd: (-1) RUVIII.Rd:51: Lost braces
    51 | If code{return.info} is \code{TRUE}, a list is returned that contains:
       |        ^

NOTE r-oldrel-macos-arm64

Rd files

checkRd: (-1) RUVIII.Rd:51: Lost braces
    51 | If code{return.info} is \code{TRUE}, a list is returned that contains:
       |        ^

NOTE r-oldrel-macos-x86_64

Rd files

checkRd: (-1) RUVIII.Rd:51: Lost braces
    51 | If code{return.info} is \code{TRUE}, a list is returned that contains:
       |        ^

NOTE r-oldrel-windows-x86_64

Rd files

checkRd: (-1) RUVIII.Rd:51: Lost braces
    51 | If code{return.info} is \code{TRUE}, a list is returned that contains:
       |        ^

NOTE r-patched-linux-x86_64

Rd files

checkRd: (-1) RUVIII.Rd:51: Lost braces
    51 | If code{return.info} is \code{TRUE}, a list is returned that contains:
       |        ^

NOTE r-release-linux-x86_64

Rd files

checkRd: (-1) RUVIII.Rd:51: Lost braces
    51 | If code{return.info} is \code{TRUE}, a list is returned that contains:
       |        ^

NOTE r-release-macos-arm64

Rd files

checkRd: (-1) RUVIII.Rd:51: Lost braces
    51 | If code{return.info} is \code{TRUE}, a list is returned that contains:
       |        ^

NOTE r-release-macos-x86_64

Rd files

checkRd: (-1) RUVIII.Rd:51: Lost braces
    51 | If code{return.info} is \code{TRUE}, a list is returned that contains:
       |        ^

NOTE r-release-windows-x86_64

Rd files

checkRd: (-1) RUVIII.Rd:51: Lost braces
    51 | If code{return.info} is \code{TRUE}, a list is returned that contains:
       |        ^

Check History

NOTE 0 OK · 14 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Mar 9, 2026

NOTE r-devel-linux-x86_64-debian-clang

CRAN incoming feasibility

Maintainer: ‘Johann Gagnon-Bartsch <johanngb@umich.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Johann",
                    family = "Gagnon-Bartsch",
                    role = c("aut", "cre"),
                    email = "johanngb@umich.edu")
as necessary.

NOTE r-devel-linux-x86_64-debian-gcc

CRAN incoming feasibility

Maintainer: ‘Johann Gagnon-Bartsch <johanngb@umich.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Johann",
                    family = "Gagnon-Bartsch",
                    role = c("aut", "cre"),
                    email = "johanngb@umich.edu")
as necessary.

NOTE r-devel-linux-x86_64-fedora-clang

Rd files

checkRd: (-1) RUVIII.Rd:51: Lost braces
    51 | If code{return.info} is \code{TRUE}, a list is returned that contains:
       |        ^

NOTE r-devel-linux-x86_64-fedora-gcc

Rd files

checkRd: (-1) RUVIII.Rd:51: Lost braces
    51 | If code{return.info} is \code{TRUE}, a list is returned that contains:
       |        ^

NOTE r-devel-macos-arm64

Rd files

checkRd: (-1) RUVIII.Rd:51: Lost braces
    51 | If code{return.info} is \code{TRUE}, a list is returned that contains:
       |        ^

NOTE r-devel-windows-x86_64

Rd files

checkRd: (-1) RUVIII.Rd:51: Lost braces
    51 | If code{return.info} is \code{TRUE}, a list is returned that contains:
       |        ^

NOTE r-patched-linux-x86_64

Rd files

checkRd: (-1) RUVIII.Rd:51: Lost braces
    51 | If code{return.info} is \code{TRUE}, a list is returned that contains:
       |        ^

NOTE r-release-linux-x86_64

Rd files

checkRd: (-1) RUVIII.Rd:51: Lost braces
    51 | If code{return.info} is \code{TRUE}, a list is returned that contains:
       |        ^

NOTE r-release-macos-arm64

Rd files

checkRd: (-1) RUVIII.Rd:51: Lost braces
    51 | If code{return.info} is \code{TRUE}, a list is returned that contains:
       |        ^

NOTE r-release-macos-x86_64

Rd files

checkRd: (-1) RUVIII.Rd:51: Lost braces
    51 | If code{return.info} is \code{TRUE}, a list is returned that contains:
       |        ^

NOTE r-release-windows-x86_64

Rd files

checkRd: (-1) RUVIII.Rd:51: Lost braces
    51 | If code{return.info} is \code{TRUE}, a list is returned that contains:
       |        ^

NOTE r-oldrel-macos-arm64

Rd files

checkRd: (-1) RUVIII.Rd:51: Lost braces
    51 | If code{return.info} is \code{TRUE}, a list is returned that contains:
       |        ^

NOTE r-oldrel-macos-x86_64

Rd files

checkRd: (-1) RUVIII.Rd:51: Lost braces
    51 | If code{return.info} is \code{TRUE}, a list is returned that contains:
       |        ^

NOTE r-oldrel-windows-x86_64

Rd files

checkRd: (-1) RUVIII.Rd:51: Lost braces
    51 | If code{return.info} is \code{TRUE}, a list is returned that contains:
       |        ^

Dependency Network

Version History

new 0.9.7.1 Mar 9, 2026