TmCalculator
A Calculator for Melting Temperature of Nucleic Acid Sequences
Description
A comprehensive R package for calculating melting temperatures of nucleic acid sequences. Implements three calculation methods: 1. Wallace rule (Thein & Wallace, 1986) 2. Empirical formulas based on GC content (Marmur, 1962; Schildkraut, 2010; Wetmur, 1991; Untergasser, 2012; von Ahsen, 2001) 3. Nearest neighbor thermodynamics (Breslauer, 1986; Sugimoto, 1996; Allawi, 1998; SantaLucia, 2004; Freier, 1986; Xia, 1998; Chen, 2012; Bommarito, 2000; Turner, 2010; Sugimoto, 1995; Allawi, 1997; Santalucia, 2005) Includes corrections for: - Salt ions (SantaLucia, 1996, 1998; Owczarzy, 2004, 2008) - Chemical compounds (dimethyl sulfoxide, formamide) Supports both direct sequence input and FASTA file input.
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CRAN Check Status
Show all 14 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 | OK |
| r-devel-macos-arm64 | ERROR |
| r-devel-windows-x86_64 | OK |
| r-oldrel-macos-arm64 | ERROR |
| r-oldrel-macos-x86_64 | ERROR |
| r-oldrel-windows-x86_64 | OK |
| r-patched-linux-x86_64 | OK |
| r-release-linux-x86_64 | OK |
| r-release-macos-arm64 | ERROR |
| r-release-macos-x86_64 | ERROR |
| r-release-windows-x86_64 | OK |
Check details (6 non-OK)
package dependencies
Package required but not available: ‘karyoploteR’ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual.
package dependencies
Packages required but not available: 'Gviz', 'karyoploteR' Package suggested but not available for checking: ‘BSgenome.Hsapiens.UCSC.hg38’ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual.
package dependencies
Package suggested but not available for checking: ‘BSgenome.Hsapiens.UCSC.hg38’
re-building of vignette outputs
Error(s) in re-building vignettes:
--- re-building ‘TmCalculator.Rmd’ using rmarkdown
Quitting from TmCalculator.Rmd:12-25 [setup]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `library()`:
! there is no package called 'BSgenome.Hsapiens.UCSC.hg38'
---
Backtrace:
▆
1. └─base::library(BSgenome.Hsapiens.UCSC.hg38)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'TmCalculator.Rmd' failed with diagnostics:
there is no package called 'BSgenome.Hsapiens.UCSC.hg38'
--- failed re-building ‘TmCalculator.Rmd’
SUMMARY: processing the following file failed:
‘TmCalculator.Rmd’
Error: Vignette re-building failed.
Execution halted
package dependencies
Packages required but not available: 'ggbio', 'karyoploteR' Package suggested but not available for checking: ‘BSgenome.Hsapiens.UCSC.hg38’ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual.
package dependencies
Packages required but not available: 'ggbio', 'karyoploteR' Package suggested but not available for checking: ‘BSgenome.Hsapiens.UCSC.hg38’ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual.
Check History
ERROR 7 OK · 2 NOTE · 0 WARNING · 5 ERROR · 0 FAILURE Mar 20, 2026
CRAN incoming feasibility
Maintainer: ‘Junhui Li <junhuili@cau.edu.cn>’
No Authors@R field in DESCRIPTION.
Please add one, modifying
Authors@R: person(given = "Junhui",
family = "Li",
role = c("aut", "cre"),
email = "junhuili@cau.edu.cn")
as necessary.
CRAN incoming feasibility
Maintainer: ‘Junhui Li <junhuili@cau.edu.cn>’
No Authors@R field in DESCRIPTION.
Please add one, modifying
Authors@R: person(given = "Junhui",
family = "Li",
role = c("aut", "cre"),
email = "junhuili@cau.edu.cn")
as necessary.
package dependencies
Package required but not available: ‘karyoploteR’ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual.
whether package can be installed
Installation failed. See 'd:/Rcompile/CRANpkg/local/4.6/TmCalculator.Rcheck/00install.out' for details.
package dependencies
Packages required but not available: 'ggbio', 'karyoploteR' Package suggested but not available for checking: ‘BSgenome.Hsapiens.UCSC.hg38’ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual.
package dependencies
Packages required but not available: 'Gviz', 'karyoploteR' Package suggested but not available for checking: ‘BSgenome.Hsapiens.UCSC.hg38’ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual.
package dependencies
Package suggested but not available for checking: ‘BSgenome.Hsapiens.UCSC.hg38’
NOTE 12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Mar 10, 2026
CRAN incoming feasibility
Maintainer: ‘Junhui Li <junhuili@cau.edu.cn>’
No Authors@R field in DESCRIPTION.
Please add one, modifying
Authors@R: person(given = "Junhui",
family = "Li",
role = c("aut", "cre"),
email = "junhuili@cau.edu.cn")
as necessary.
CRAN incoming feasibility
Maintainer: ‘Junhui Li <junhuili@cau.edu.cn>’
No Authors@R field in DESCRIPTION.
Please add one, modifying
Authors@R: person(given = "Junhui",
family = "Li",
role = c("aut", "cre"),
email = "junhuili@cau.edu.cn")
as necessary.