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harmony

Fast, Sensitive, and Accurate Integration of Single Cell Data

v1.2.4 · Oct 9, 2025 · GPL-3
CRAN GitHub Mirror

Description

Implementation of the Harmony algorithm for single cell integration, described in Korsunsky et al <doi:10.1038/s41592-019-0619-0>. Package includes a standalone Harmony function and interfaces to external frameworks.

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CRAN Check Status

7 NOTE
7 OK
Show all 14 flavors
Flavor Status
r-devel-linux-x86_64-debian-clang NOTE
r-devel-linux-x86_64-debian-gcc NOTE
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 NOTE
r-oldrel-macos-arm64 NOTE
r-oldrel-macos-x86_64 NOTE
r-oldrel-windows-x86_64 NOTE
r-patched-linux-x86_64 NOTE
r-release-linux-x86_64 OK
r-release-macos-arm64 OK
r-release-macos-x86_64 OK
r-release-windows-x86_64 OK
Check details (7 non-OK)
NOTE r-devel-linux-x86_64-debian-clang

compiled code

File ‘harmony/libs/harmony.so’:
  Found non-API call to R: ‘R_UnboundValue’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
NOTE r-devel-linux-x86_64-debian-gcc

compiled code

File ‘harmony/libs/harmony.so’:
  Found non-API call to R: ‘R_UnboundValue’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
NOTE r-devel-windows-x86_64

compiled code

File 'harmony/libs/x64/harmony.dll':
  Found non-API call to R: 'R_UnboundValue'

Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
NOTE r-oldrel-macos-arm64

installed package size

installed size is 11.8Mb
  sub-directories of 1Mb or more:
    data   2.9Mb
    doc    2.5Mb
    libs   6.3Mb
NOTE r-oldrel-macos-x86_64

installed package size

installed size is 11.8Mb
  sub-directories of 1Mb or more:
    data   2.9Mb
    doc    2.5Mb
    libs   6.3Mb
NOTE r-oldrel-windows-x86_64

installed package size

installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    2.5Mb
    libs   1.3Mb
NOTE r-patched-linux-x86_64

compiled code

File ‘harmony/libs/harmony.so’:
  Found non-API call to R: ‘R_UnboundValue’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.

Check History

NOTE 11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Mar 10, 2026
NOTE r-oldrel-macos-arm64

installed package size

installed size is 11.8Mb
  sub-directories of 1Mb or more:
    data   2.9Mb
    doc    2.5Mb
    libs   6.3Mb
NOTE r-oldrel-macos-x86_64

installed package size

installed size is 11.8Mb
  sub-directories of 1Mb or more:
    data   2.9Mb
    doc    2.5Mb
    libs   6.3Mb
NOTE r-oldrel-windows-x86_64

installed package size

installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    2.5Mb
    libs   1.3Mb

Reverse Dependencies (7)

imports

PRECAST ProFAST RaceID SCdeconR scAnnotate symphony

suggests

Seurat

Dependency Network

Dependencies Reverse dependencies Rcpp dplyr cowplot ggplot2 Matrix tibble rlang RhpcBLASctl PRECAST ProFAST RaceID SCdeconR scAnnotate symphony Seurat harmony

Version History

new 1.2.4 Mar 10, 2026
updated 1.2.4 ← 1.2.3 diff Oct 9, 2025
updated 1.2.3 ← 1.2.1 diff Nov 27, 2024
updated 1.2.1 ← 1.2.0 diff Aug 27, 2024
updated 1.2.0 ← 1.1.0 diff Nov 28, 2023
updated 1.1.0 ← 1.0.3 diff Oct 22, 2023
updated 1.0.3 ← 1.0.1 diff Sep 30, 2023
updated 1.0.1 ← 0.1.1 diff Sep 19, 2023
updated 0.1.1 ← 0.1.0 diff Nov 13, 2022
new 0.1.0 Jun 1, 2021