harmony

Fast, Sensitive, and Accurate Integration of Single Cell Data

v2.0.5 · Jun 12, 2026 · GPL-3

Description

Implementation of the Harmony algorithm for single cell integration, described in Patikas, Yao, et al. <doi:10.64898/2026.03.16.711825>. Package includes a standalone Harmony function and interfaces to external frameworks.

Downloads

21K

Last 30 days

816th

67.8K

Last 90 days

221.8K

Last year

Trend: -19.7% (30d vs prior 30d)

CRAN Check Status

1 ERROR

12 OK

Show all 13 flavors

Flavor	Status	Time
r-devel-linux-x86_64-debian-clang	OK	277.6s
r-devel-linux-x86_64-debian-gcc	OK	203s
r-devel-linux-x86_64-fedora-clang	OK	461.3s
r-devel-linux-x86_64-fedora-gcc	ERROR	534.4s
r-devel-windows-x86_64	OK	317s
r-oldrel-macos-arm64	OK	76s
r-oldrel-macos-x86_64	OK	263s
r-oldrel-windows-x86_64	OK	413s
r-patched-linux-x86_64	OK	263s
r-release-linux-x86_64	OK
r-release-macos-arm64	OK	80s
r-release-macos-x86_64	OK	281s
r-release-windows-x86_64	OK	316s

Check details (1 non-OK)

ERROR r-devel-linux-x86_64-fedora-gcc

tests

Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(harmony)
  Loading required package: Rcpp
  • This is Harmony2 version 2.0.5
  • Read the guide: run vignette("quickstart", package="harmony")
  • Get help: Visit the website at <https://korsunskylab.github.io/harmony2/> and
  report issues on <https://github.com/immunogenomics/harmony/issues>
  > 
  > test_check("harmony")
  253exists, retrying for cluster 26 3.45943
  118exists, retrying for cluster 28 0.624635
  7exists, retrying for cluster 33 0.87125
  118exists, retrying for cluster 41 3.36873
  147exists, retrying for cluster 42 3.01096
  119exists, retrying for cluster 47 3.38714
  Saving _problems/test_integration-40.R
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 12 ]
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • empty test (1):
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_integration.R:37:5'): increasing theta decreases chi2 between Cluster and Batch assign ──
  Expected `sum(((obj0$O - obj0$E)^2)/obj0$E)` > `sum(((obj1$O - obj1$E)^2)/obj1$E)`.
  Actual comparison: 376.2 <= 382.6
  Difference: -6.4 <= 0
  
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 12 ]
  Error:
  ! Test failures.
  Execution halted

Check History

ERROR 12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Jun 27, 2026

ERROR r-devel-linux-x86_64-fedora-gcc

tests

Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(harmony)
  Loading required package: Rcpp
  • This is Harmony2 version 2.0.5
  • Read the guide: run vignette("quickstart", packag
...[truncated]...
tch assign ──
  Expected `sum(((obj0$O - obj0$E)^2)/obj0$E)` > `sum(((obj1$O - obj1$E)^2)/obj1$E)`.
  Actual comparison: 376.2 <= 382.6
  Difference: -6.4 <= 0
  
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 12 ]
  Error:
  ! Test failures.
  Execution halted

OK 9 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Jun 13, 2026

Archived

Jun 11, 2026

ERROR 12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE May 14, 2026

ERROR r-devel-linux-x86_64-fedora-clang

tests

Running ‘testthat.R’ [8s/18s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(harmony)
  Loading required package: Rcpp
  • This is Harmony2 version 2.0.3
  • Read the guide: run vignette()
  • Get h
...[truncated]...
tchList(expr, classes, parentenv, handlers)
   5.   └─harmony:::harmonize(harmonyObj, max.iter.harmony, verbose)
   6.     └─harmonyObj$moe_correct_ridge_cpp()
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 13 ]
  Error:
  ! Test failures.
  Execution halted

OK 13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE May 2, 2026

NOTE 11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Apr 22, 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

ERROR 10 OK · 3 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Apr 18, 2026

ERROR r-devel-windows-x86_64

whether package can be installed

Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.6/harmony.Rcheck/00install.out' for details.

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 8 OK · 6 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Apr 10, 2026

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-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-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.

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

ERROR 7 OK · 6 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Apr 9, 2026

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.

ERROR r-devel-linux-x86_64-debian-gcc

whether package can be installed

Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/harmony.Rcheck/00install.out’ for details.

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-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.

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 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 (3)

imports

RaceID

suggests

ProFAST Seurat

Dependency Network

Version History

15 tracked

new 2.0.5 Jun 12, 2026

removed 2.0.4 Jun 11, 2026

updated 2.0.4 ← 2.0.3 diff Jun 4, 2026

updated 2.0.3 ← 2.0.2 diff May 13, 2026

updated 2.0.2 ← 1.2.4 diff Apr 25, 2026

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