leapp

Latent Effect Adjustment After Primary Projection

v1.3 · Jun 19, 2022 · GPL (>= 2)

Description

These functions take a gene expression value matrix, a primary covariate vector, an additional known covariates matrix. A two stage analysis is applied to counter the effects of latent variables on the rankings of hypotheses. The estimation and adjustment of latent effects are proposed by Sun, Zhang and Owen (2011). "leapp" is developed in the context of microarray experiments, but may be used as a general tool for high throughput data sets where dependence may be involved.

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CRAN Check Status

14 NOTE

Show all 14 flavors

Flavor	Status	Time
r-devel-linux-x86_64-debian-clang	NOTE	228.7s
r-devel-linux-x86_64-debian-gcc	NOTE	162.1s
r-devel-linux-x86_64-fedora-clang	NOTE	363.7s
r-devel-linux-x86_64-fedora-gcc	NOTE	342.4s
r-devel-macos-arm64	NOTE	55s
r-devel-windows-x86_64	NOTE	206s
r-oldrel-macos-arm64	NOTE
r-oldrel-macos-x86_64	NOTE	149s
r-oldrel-windows-x86_64	NOTE	249s
r-patched-linux-x86_64	NOTE	215.5s
r-release-linux-x86_64	NOTE	214.2s
r-release-macos-arm64	NOTE
r-release-macos-x86_64	NOTE	186s
r-release-windows-x86_64	NOTE	206s

Check details (16 non-OK)

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

CRAN incoming feasibility

Maintainer: ‘Yunting Sun <yunting.sun@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Yunting",
                      family = "Sun",
                      role = c("aut", "cre"),
                      email = "yunting.sun@gmail.com"),
               person(given = "Nancy",
                      family = "R.Zhang",
                      role = "aut",
                      email = "nzhang@stanford.edu"),
               person(given = "Art",
                      family = "B.Owen",
                      role = "aut",
                      email = "owen@stanford.edu"))
as necessary.

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

Rd files

checkRd: (-1) IPODFUN.Rd:18: Lost braces; missing escapes or markup?
    18 |   \item{H}{an N by N projection matrix X(X'X)^{-1}X' }
       |                                               ^

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

CRAN incoming feasibility

Maintainer: ‘Yunting Sun <yunting.sun@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Yunting",
                      family = "Sun",
                      role = c("aut", "cre"),
                      email = "yunting.sun@gmail.com"),
               person(given = "Nancy",
                      family = "R.Zhang",
                      role = "aut",
                      email = "nzhang@stanford.edu"),
               person(given = "Art",
                      family = "B.Owen",
                      role = "aut",
                      email = "owen@stanford.edu"))
as necessary.

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

Rd files

checkRd: (-1) IPODFUN.Rd:18: Lost braces; missing escapes or markup?
    18 |   \item{H}{an N by N projection matrix X(X'X)^{-1}X' }
       |                                               ^

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

Rd files

checkRd: (-1) IPODFUN.Rd:18: Lost braces; missing escapes or markup?
    18 |   \item{H}{an N by N projection matrix X(X'X)^{-1}X' }
       |                                               ^

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

Rd files

checkRd: (-1) IPODFUN.Rd:18: Lost braces; missing escapes or markup?
    18 |   \item{H}{an N by N projection matrix X(X'X)^{-1}X' }
       |                                               ^

NOTE r-devel-macos-arm64

Rd files

checkRd: (-1) IPODFUN.Rd:18: Lost braces; missing escapes or markup?
    18 |   \item{H}{an N by N projection matrix X(X'X)^{-1}X' }
       |                                               ^

NOTE r-devel-windows-x86_64

Rd files

checkRd: (-1) IPODFUN.Rd:18: Lost braces; missing escapes or markup?
    18 |   \item{H}{an N by N projection matrix X(X'X)^{-1}X' }
       |                                               ^

NOTE r-oldrel-macos-arm64

Rd files

checkRd: (-1) IPODFUN.Rd:18: Lost braces; missing escapes or markup?
    18 |   \item{H}{an N by N projection matrix X(X'X)^{-1}X' }
       |                                               ^

NOTE r-oldrel-macos-x86_64

Rd files

checkRd: (-1) IPODFUN.Rd:18: Lost braces; missing escapes or markup?
    18 |   \item{H}{an N by N projection matrix X(X'X)^{-1}X' }
       |                                               ^

NOTE r-oldrel-windows-x86_64

Rd files

checkRd: (-1) IPODFUN.Rd:18: Lost braces; missing escapes or markup?
    18 |   \item{H}{an N by N projection matrix X(X'X)^{-1}X' }
       |                                               ^

NOTE r-patched-linux-x86_64

Rd files

checkRd: (-1) IPODFUN.Rd:18: Lost braces; missing escapes or markup?
    18 |   \item{H}{an N by N projection matrix X(X'X)^{-1}X' }
       |                                               ^

NOTE r-release-linux-x86_64

Rd files

checkRd: (-1) IPODFUN.Rd:18: Lost braces; missing escapes or markup?
    18 |   \item{H}{an N by N projection matrix X(X'X)^{-1}X' }
       |                                               ^

NOTE r-release-macos-arm64

Rd files

checkRd: (-1) IPODFUN.Rd:18: Lost braces; missing escapes or markup?
    18 |   \item{H}{an N by N projection matrix X(X'X)^{-1}X' }
       |                                               ^

NOTE r-release-macos-x86_64

Rd files

checkRd: (-1) IPODFUN.Rd:18: Lost braces; missing escapes or markup?
    18 |   \item{H}{an N by N projection matrix X(X'X)^{-1}X' }
       |                                               ^

NOTE r-release-windows-x86_64

Rd files

checkRd: (-1) IPODFUN.Rd:18: Lost braces; missing escapes or markup?
    18 |   \item{H}{an N by N projection matrix X(X'X)^{-1}X' }
       |                                               ^

Check History

NOTE 0 OK · 14 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Mar 24, 2026

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

CRAN incoming feasibility

Maintainer: ‘Yunting Sun <yunting.sun@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Yunting",
                      family = "Sun",
                      role = c("aut", "cre"),
             
...[truncated]...
   role = "aut",
                      email = "nzhang@stanford.edu"),
               person(given = "Art",
                      family = "B.Owen",
                      role = "aut",
                      email = "owen@stanford.edu"))
as necessary.

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

CRAN incoming feasibility

Maintainer: ‘Yunting Sun <yunting.sun@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Yunting",
                      family = "Sun",
                      role = c("aut", "cre"),
             
...[truncated]...
   role = "aut",
                      email = "nzhang@stanford.edu"),
               person(given = "Art",
                      family = "B.Owen",
                      role = "aut",
                      email = "owen@stanford.edu"))
as necessary.

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

Rd files

checkRd: (-1) IPODFUN.Rd:18: Lost braces; missing escapes or markup?
    18 |   \item{H}{an N by N projection matrix X(X'X)^{-1}X' }
       |                                               ^

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

Rd files

checkRd: (-1) IPODFUN.Rd:18: Lost braces; missing escapes or markup?
    18 |   \item{H}{an N by N projection matrix X(X'X)^{-1}X' }
       |                                               ^

NOTE r-devel-macos-arm64

Rd files

checkRd: (-1) IPODFUN.Rd:18: Lost braces; missing escapes or markup?
    18 |   \item{H}{an N by N projection matrix X(X'X)^{-1}X' }
       |                                               ^

NOTE r-devel-windows-x86_64

Rd files

checkRd: (-1) IPODFUN.Rd:18: Lost braces; missing escapes or markup?
    18 |   \item{H}{an N by N projection matrix X(X'X)^{-1}X' }
       |                                               ^

NOTE r-patched-linux-x86_64

Rd files

checkRd: (-1) IPODFUN.Rd:18: Lost braces; missing escapes or markup?
    18 |   \item{H}{an N by N projection matrix X(X'X)^{-1}X' }
       |                                               ^

NOTE r-release-linux-x86_64

Rd files

checkRd: (-1) IPODFUN.Rd:18: Lost braces; missing escapes or markup?
    18 |   \item{H}{an N by N projection matrix X(X'X)^{-1}X' }
       |                                               ^

NOTE r-release-macos-arm64

Rd files

checkRd: (-1) IPODFUN.Rd:18: Lost braces; missing escapes or markup?
    18 |   \item{H}{an N by N projection matrix X(X'X)^{-1}X' }
       |                                               ^

NOTE r-release-macos-x86_64

Rd files

checkRd: (-1) IPODFUN.Rd:18: Lost braces; missing escapes or markup?
    18 |   \item{H}{an N by N projection matrix X(X'X)^{-1}X' }
       |                                               ^

NOTE r-release-windows-x86_64

Rd files

checkRd: (-1) IPODFUN.Rd:18: Lost braces; missing escapes or markup?
    18 |   \item{H}{an N by N projection matrix X(X'X)^{-1}X' }
       |                                               ^

NOTE r-oldrel-macos-arm64

Rd files

checkRd: (-1) IPODFUN.Rd:18: Lost braces; missing escapes or markup?
    18 |   \item{H}{an N by N projection matrix X(X'X)^{-1}X' }
       |                                               ^

NOTE r-oldrel-macos-x86_64

Rd files

checkRd: (-1) IPODFUN.Rd:18: Lost braces; missing escapes or markup?
    18 |   \item{H}{an N by N projection matrix X(X'X)^{-1}X' }
       |                                               ^

NOTE r-oldrel-windows-x86_64

Rd files

checkRd: (-1) IPODFUN.Rd:18: Lost braces; missing escapes or markup?
    18 |   \item{H}{an N by N projection matrix X(X'X)^{-1}X' }
       |                                               ^

WARNING 0 OK · 13 NOTE · 1 WARNING · 0 ERROR · 0 FAILURE Mar 20, 2026

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

CRAN incoming feasibility

Maintainer: ‘Yunting Sun <yunting.sun@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Yunting",
                      family = "Sun",
                      role = c("aut", "cre"),
             
...[truncated]...
   role = "aut",
                      email = "nzhang@stanford.edu"),
               person(given = "Art",
                      family = "B.Owen",
                      role = "aut",
                      email = "owen@stanford.edu"))
as necessary.

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

CRAN incoming feasibility

Maintainer: ‘Yunting Sun <yunting.sun@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Yunting",
                      family = "Sun",
                      role = c("aut", "cre"),
             
...[truncated]...
   role = "aut",
                      email = "nzhang@stanford.edu"),
               person(given = "Art",
                      family = "B.Owen",
                      role = "aut",
                      email = "owen@stanford.edu"))
as necessary.

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

Rd files

checkRd: (-1) IPODFUN.Rd:18: Lost braces; missing escapes or markup?
    18 |   \item{H}{an N by N projection matrix X(X'X)^{-1}X' }
       |                                               ^

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

Rd files

checkRd: (-1) IPODFUN.Rd:18: Lost braces; missing escapes or markup?
    18 |   \item{H}{an N by N projection matrix X(X'X)^{-1}X' }
       |                                               ^

NOTE r-devel-macos-arm64

Rd files

checkRd: (-1) IPODFUN.Rd:18: Lost braces; missing escapes or markup?
    18 |   \item{H}{an N by N projection matrix X(X'X)^{-1}X' }
       |                                               ^

NOTE r-devel-windows-x86_64

Rd files

checkRd: (-1) IPODFUN.Rd:18: Lost braces; missing escapes or markup?
    18 |   \item{H}{an N by N projection matrix X(X'X)^{-1}X' }
       |                                               ^

NOTE r-patched-linux-x86_64

Rd files

checkRd: (-1) IPODFUN.Rd:18: Lost braces; missing escapes or markup?
    18 |   \item{H}{an N by N projection matrix X(X'X)^{-1}X' }
       |                                               ^

NOTE r-release-linux-x86_64

Rd files

checkRd: (-1) IPODFUN.Rd:18: Lost braces; missing escapes or markup?
    18 |   \item{H}{an N by N projection matrix X(X'X)^{-1}X' }
       |                                               ^

NOTE r-release-macos-arm64

Rd files

checkRd: (-1) IPODFUN.Rd:18: Lost braces; missing escapes or markup?
    18 |   \item{H}{an N by N projection matrix X(X'X)^{-1}X' }
       |                                               ^

NOTE r-release-macos-x86_64

Rd files

checkRd: (-1) IPODFUN.Rd:18: Lost braces; missing escapes or markup?
    18 |   \item{H}{an N by N projection matrix X(X'X)^{-1}X' }
       |                                               ^

WARNING r-release-windows-x86_64

whether package can be installed

Found the following significant warnings:
  Warning: package 'mgcv' was built under R version 4.6.0
  Warning: package 'nlme' was built under R version 4.6.0
See 'd:/Rcompile/CRANpkg/local/4.5/leapp.Rcheck/00install.out' for details.

NOTE r-oldrel-macos-arm64

Rd files

checkRd: (-1) IPODFUN.Rd:18: Lost braces; missing escapes or markup?
    18 |   \item{H}{an N by N projection matrix X(X'X)^{-1}X' }
       |                                               ^

NOTE r-oldrel-macos-x86_64

Rd files

checkRd: (-1) IPODFUN.Rd:18: Lost braces; missing escapes or markup?
    18 |   \item{H}{an N by N projection matrix X(X'X)^{-1}X' }
       |                                               ^

NOTE r-oldrel-windows-x86_64

Rd files

checkRd: (-1) IPODFUN.Rd:18: Lost braces; missing escapes or markup?
    18 |   \item{H}{an N by N projection matrix X(X'X)^{-1}X' }
       |                                               ^

NOTE 0 OK · 14 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Mar 10, 2026

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

CRAN incoming feasibility

Maintainer: ‘Yunting Sun <yunting.sun@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Yunting",
                      family = "Sun",
                      role = c("aut", "cre"),
             
...[truncated]...
   role = "aut",
                      email = "nzhang@stanford.edu"),
               person(given = "Art",
                      family = "B.Owen",
                      role = "aut",
                      email = "owen@stanford.edu"))
as necessary.

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

CRAN incoming feasibility

Maintainer: ‘Yunting Sun <yunting.sun@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Yunting",
                      family = "Sun",
                      role = c("aut", "cre"),
             
...[truncated]...
   role = "aut",
                      email = "nzhang@stanford.edu"),
               person(given = "Art",
                      family = "B.Owen",
                      role = "aut",
                      email = "owen@stanford.edu"))
as necessary.

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

Rd files

checkRd: (-1) IPODFUN.Rd:18: Lost braces; missing escapes or markup?
    18 |   \item{H}{an N by N projection matrix X(X'X)^{-1}X' }
       |                                               ^

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

Rd files

checkRd: (-1) IPODFUN.Rd:18: Lost braces; missing escapes or markup?
    18 |   \item{H}{an N by N projection matrix X(X'X)^{-1}X' }
       |                                               ^

NOTE r-devel-macos-arm64

Rd files

checkRd: (-1) IPODFUN.Rd:18: Lost braces; missing escapes or markup?
    18 |   \item{H}{an N by N projection matrix X(X'X)^{-1}X' }
       |                                               ^

NOTE r-devel-windows-x86_64

Rd files

checkRd: (-1) IPODFUN.Rd:18: Lost braces; missing escapes or markup?
    18 |   \item{H}{an N by N projection matrix X(X'X)^{-1}X' }
       |                                               ^

NOTE r-patched-linux-x86_64

Rd files

checkRd: (-1) IPODFUN.Rd:18: Lost braces; missing escapes or markup?
    18 |   \item{H}{an N by N projection matrix X(X'X)^{-1}X' }
       |                                               ^

NOTE r-release-linux-x86_64

Rd files

checkRd: (-1) IPODFUN.Rd:18: Lost braces; missing escapes or markup?
    18 |   \item{H}{an N by N projection matrix X(X'X)^{-1}X' }
       |                                               ^

NOTE r-release-macos-arm64

Rd files

checkRd: (-1) IPODFUN.Rd:18: Lost braces; missing escapes or markup?
    18 |   \item{H}{an N by N projection matrix X(X'X)^{-1}X' }
       |                                               ^

NOTE r-release-macos-x86_64

Rd files

checkRd: (-1) IPODFUN.Rd:18: Lost braces; missing escapes or markup?
    18 |   \item{H}{an N by N projection matrix X(X'X)^{-1}X' }
       |                                               ^

NOTE r-release-windows-x86_64

Rd files

checkRd: (-1) IPODFUN.Rd:18: Lost braces; missing escapes or markup?
    18 |   \item{H}{an N by N projection matrix X(X'X)^{-1}X' }
       |                                               ^

NOTE r-oldrel-macos-arm64

Rd files

checkRd: (-1) IPODFUN.Rd:18: Lost braces; missing escapes or markup?
    18 |   \item{H}{an N by N projection matrix X(X'X)^{-1}X' }
       |                                               ^

NOTE r-oldrel-macos-x86_64

Rd files

checkRd: (-1) IPODFUN.Rd:18: Lost braces; missing escapes or markup?
    18 |   \item{H}{an N by N projection matrix X(X'X)^{-1}X' }
       |                                               ^

NOTE r-oldrel-windows-x86_64

Rd files

checkRd: (-1) IPODFUN.Rd:18: Lost braces; missing escapes or markup?
    18 |   \item{H}{an N by N projection matrix X(X'X)^{-1}X' }
       |                                               ^

Dependency Network

Version History

new 1.3 Mar 10, 2026

updated 1.3 ← 1.2 diff Jun 18, 2022

updated 1.2 ← 1.1 diff Jul 21, 2014

updated 1.1 ← 1.0 diff Jan 5, 2014

new 1.0 Apr 6, 2012