cran-comments.md

In cbhagya/perfectphyloR: Reconstruct Perfect Phylogenies from DNA Sequence Data

Resubmission March 7, 2021:

• In this submission, a bug in calculating dCor statistics was fixed.

• Updated the version number to 0.2.1 to reflect the bug fix.

• Test Environments prior to resubmission

  • win-builder (oldrelease)

• R CMD check results

  0 errors | 0 warnings | 0 note

Resubmission December 8, 2019:

• In this resubmission, the following changes were made to the package.

  • included a function to create an object of class hapMat from VCF file.
  • changed the default value of the argument, minWindow, in the function reconstructPP(), to maximum of one and 2% of the total number of the SNVs.
  • changed the function name reconsPPregion() to reconstructPPregion().
  • added an option to the function reconstructPPregion() to reconstruct perfect phylogenies between a given range of SNV positions.
  • added some warning messages to the function, reconstructPPregion(), to warn about the timing, and to show the current focal SNV of the hapMat object.
  • made the packages HHG and dendextend optional to install with the package.
  • added the bioRxiv preprint of the package as the PDF vignette.
  • updated the DESCRIPTION file:
    • updated the version number to 0.2.0 to reflect the new function added, and the modifications of reconstructPP() and reconstructPPregion().
    • included R.rsp as VignetteBuilder.
    • made the packages HHG, dendextend, vcfR, and R.rsp as suggests.

• Test Environments prior to resubmission

  • local Windows OS install, R 3.4.2
  • local Linux, R 3.5.0
  • win-builder (oldrelease)

• R CMD check results

  0 errors | 0 warnings | 1 note

  checking CRAN incoming feasibility ... NOTE Maintainer: 'Charith Karunarathna [e-mail]'

  This submission comes actually from this maintainer, Charith Karunarathna, and not anybody else.

Resubmission June 2019:

Third resubmission in June 2019

• In this submission according to a reviewer's suggestion, I have:

  • fixed the 'Description' field in the DESCRIPTION start with "Reconstructs perfect ...".
  • fixed the reference in the 'Description' field of the DESCRIPTION file to be of the form: authors (year) .
  • added more small executable examples in the Rd-files to illustrate the use of the exported functions (internal functions) and enabled those examples for automatic testing.

• I also updated the version number in the DESCRIPTION file to 0.1.3 to reflect the above modification.

Second resubmission in June 2019

• In this submission, vignette files were modified to comply with CRAN requirements.

• Updated the version number in the DESCRIPTION file to 0.1.2 to reflect the modification in vignette folder.

First resubmission in June 2019

• Fixed a note related to SHLIB_OPENMP_*FLAGS in Makefiles following URL: https://stat.ethz.ch/pipermail/r-package-devel/2019q2/003764.html. I thank Iñaki Ucar and Dirk Eddelbuettel for proving me the guidances.

• Updated the version number in the DESCRIPTION file to Version: 0.1.1

Test environments

• local Windows install, R 3.4.2
• local Linux, R 3.5.0
• win-builder (oldrelease)

R CMD check results

0 errors | 0 warnings | 1 note

Possibly mis-spelled words in DESCRIPTION: Charith (8:167) Jinko (8:194) Karunarathna (8:177) Phylogenies (3:28)

• The words Charith, Jinko and Karunarathna are not misspelled. These are the names of authors.
• The word Phylogenies is not misspelled.

Downstream Dependencies

There are currently no downstream dependencies for this package.

cbhagya/perfectphyloR documentation built on Aug. 1, 2021, 1:17 p.m.