Update steps

Make your desired changes to the development version of the package (see: /net/home/bgrant/tmpwork/Rpackage/ver_devel/ ).

Then follow these steps:

• Update the version number in the file "bio3d/DESCRIPTION".
• Remove the old tar.gz version of the package "rm bio3d_1.0-?.tar.gz"
• Build a new version with "R64 CMD build bio3d"
• Run "R64 CMD check bio3d"
• Remove your old bio3d installation "R64 CMD REMOVE bio3d"
• Install the new version "R64 CMD INSTALL bio3d_1.0-?.tar.gz"
• Assuming everything works "cp bio3d_1.0-?.tar.gz ~/public_html/bio3d/."
• Make a windows .zip version by changing to your package library dir:  "cd /net/home/bgrant/software/R-local/R-2.7.2/library"
  • Run zip -r bio3d_1.0-?.zip bio3d
• Copy the zip file to the web space or windows box for testing "cp bio3d_1.0-?.zip ~/public_html/bio3d/."
• Update the webpage links accordingly (see ~/public_html/bio3d/download/download.html ).
• Update the package manual and other documentation.
  • To make the manual run "R64 CMD Rd2dvi --pdf --title="The bio3d Package" bio3d"
  • Copy this pdf to the web site "cp bio3d.pdf ~/public_html/bio3d/."
• Comment on changes in the wiki

To Do Notes

• New functions to add
• Existing functions to improve
• Documentation to add or improve
• Web site issues and improvements
• package manual and vignettes to include

Priorities

1. write paper DONE
2. mail Leo DONE
3. mail Karim DONE
4. make bio3d web site DONE
5. make windows executable DONE (see Windows page)
6. tidy package vingnette (see dvi file in bio3d.Rcheck dir)
7. update package CITATION file in the 'inst' subdirectory, ... see citEntry()
8. write bio3d wiki tutorals (add more notes to the wiki about Leo's ccbp tutoral)
9. add more functions ( -dssp-, -stride-, -torsions-, -seqaln-, -aaindex-, hbond, ... see the New functions page)
10. improve existing functions (see Existing functions page)
11. upload to CRAN
12. upload to NBCR