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harmony

Fast, Sensitive, and Accurate Integration of Single Cell Data

v2.0.5 · Jun 12, 2026 · GPL-3
CRAN GitHub Mirror

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.

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CRAN Check Status

1 ERROR
12 OK
Show all 13 flavors
Flavor Status
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 ERROR
r-devel-windows-x86_64 OK
r-oldrel-macos-arm64 OK
r-oldrel-macos-x86_64 OK
r-oldrel-windows-x86_64 OK
r-patched-linux-x86_64 OK
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 (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

Dependencies Reverse dependencies Rcpp dplyr cowplot ggplot2 Matrix tibble rlang RhpcBLASctl cli RaceID ProFAST Seurat harmony

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