misha

Toolkit for Analysis of Genomic Data

v5.6.6 · Mar 19, 2026 · MIT + file LICENSE

Description

A toolkit for analysis of genomic data. The 'misha' package implements an efficient data structure for storing genomic data, and provides a set of functions for data extraction, manipulation and analysis. Some of the 2D genome algorithms were described in Yaffe and Tanay (2011) <doi:10.1038/ng.947>.

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CRAN Check Status

10 OK

Show all 10 flavors

Flavor	Status	Time
r-devel-linux-x86_64-debian-clang	OK	656.9s
r-devel-linux-x86_64-debian-gcc	OK	483.4s
r-devel-linux-x86_64-fedora-clang	OK	1033.7s
r-devel-linux-x86_64-fedora-gcc	OK	1333.7s
r-oldrel-macos-arm64	OK	57s
r-oldrel-macos-x86_64	OK	458s
r-patched-linux-x86_64	OK	626.9s
r-release-linux-x86_64	OK
r-release-macos-arm64	OK	54s
r-release-macos-x86_64	OK	277s

Additional Issues

rchk Details →

Check History

OK 10 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Jun 9, 2026

WARNING 9 OK · 0 NOTE · 1 WARNING · 0 ERROR · 0 FAILURE Jun 8, 2026

WARNING r-devel-linux-x86_64-debian-gcc

for missing documentation entries

/usr/bin/tar: trackdb/test/tracks/dense_track.track: Cannot mkdir: No space left on device
/usr/bin/tar: trackdb/test/tracks/dense_track.track: Cannot mkdir: No space left on device
/usr/bin/tar: trackdb/test/tracks/dense_track.track/.attributes: Can
...[truncated]...
 open the connection
Calls: <Anonymous> -> .load_package_quietly -> .try_quietly
Execution halted
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.

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

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

R code for possible problems

/usr/bin/tar: trackdb/test/tracks/array_track.track/chrX: Cannot open: No space left on device
/usr/bin/tar: trackdb/test/tracks/annotations.interv: Cannot open: No space left on device
/usr/bin/tar: trackdb/test/tracks/subdir: Cannot mkdir: No space
...[truncated]...
 error: %s", 
       hookname, "loadNamespace", pkgname, deparse(conditionCall(res))[1L], 
       conditionMessage(res)), call. = FALSE, domain = NA)
2: runHook(".onLoad", env, package.lib, package)
1: loadNamespace(package, lib.loc)
Execution halted

OK 10 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE May 11, 2026

WARNING 9 OK · 0 NOTE · 1 WARNING · 0 ERROR · 0 FAILURE May 10, 2026

WARNING r-devel-linux-x86_64-debian-gcc

PDF version of manual

LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:

OK 10 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE May 2, 2026

NOTE 5 OK · 6 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Apr 10, 2026

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

compiled code

File ‘misha/libs/misha.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-fedora-clang

compiled code

File ‘misha/libs/misha.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-fedora-gcc

compiled code

File ‘misha/libs/misha.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-patched-linux-x86_64

compiled code

File ‘misha/libs/misha.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 36.8Mb
  sub-directories of 1Mb or more:
    libs  34.8Mb

NOTE r-oldrel-macos-x86_64

installed package size

installed size is 38.0Mb
  sub-directories of 1Mb or more:
    libs  36.1Mb

ERROR 4 OK · 6 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Apr 9, 2026

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

compiled code

File ‘misha/libs/misha.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/misha.Rcheck/00install.out’ for details.

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

compiled code

File ‘misha/libs/misha.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-fedora-gcc

compiled code

File ‘misha/libs/misha.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-patched-linux-x86_64

compiled code

File ‘misha/libs/misha.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 36.8Mb
  sub-directories of 1Mb or more:
    libs  34.8Mb

NOTE r-oldrel-macos-x86_64

installed package size

installed size is 38.0Mb
  sub-directories of 1Mb or more:
    libs  36.1Mb

NOTE 9 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Mar 10, 2026

NOTE r-oldrel-macos-arm64

installed package size

installed size is 36.3Mb
  sub-directories of 1Mb or more:
    libs  34.4Mb

NOTE r-oldrel-macos-x86_64

installed package size

installed size is 37.5Mb
  sub-directories of 1Mb or more:
    libs  35.6Mb

Dependency Network

Version History

13 tracked

updated 5.6.6 ← 5.4.5 diff Mar 19, 2026

new 5.4.5 Mar 10, 2026

updated 5.4.5 ← 5.4.0 diff Feb 19, 2026

updated 5.4.0 ← 5.3.2 diff Jan 26, 2026

updated 5.3.2 ← 5.3.1 diff Dec 13, 2025

updated 5.3.1 ← 4.3.12 diff Dec 9, 2025

updated 4.3.12 ← 4.3.11 diff Aug 30, 2025

updated 4.3.11 ← 4.3.6 diff Aug 24, 2025

updated 4.3.6 ← 4.2.9 diff Mar 5, 2025

updated 4.2.9 ← 4.2.8 diff Jan 14, 2024

updated 4.2.8 ← 4.2.6 diff Dec 4, 2023

updated 4.2.6 ← 4.2.3 diff Sep 13, 2023

new 4.2.3 Sep 4, 2023