CRAN Check

[Xinqiu Yao]

We got 1 WARNING and 2 NOTES (v 2.0-1):

• checking installed package size ... NOTE installed size is 6.1Mb sub-directories of 1Mb or more: doc 3.8Mb

• checking data for ASCII and uncompressed saves ... OK WARNING ‘qpdf’ is needed for checks on size reduction of PDFs

• checking re-building of vignette PDFs ... NOTE Error in re-building vignettes: ... Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, : Running 'texi2dvi' on 'Bio3D_install.tex' failed. Messages: /usr/bin/texi2dvi: no such file or directory: Bio3D_install.pdf Calls: buildVignettes -> texi2pdf -> texi2dvi Execution halted

Not sure what happed with vignette (maybe because of the dummy Rnw?) Also not so clear about "qpdf" (Software installed on local machine?)

The question is: Do we plan to upload v2.0 or v2.0-1 to CRAN?

[Xinqiu Yao]

3rd point is solved by adding non-empty content in dummy .Rnw vignettes 2nd point, I need to install qpdf on local machine. But it raise a new warning saying we should compact vignette PDFs with "tools::compactPDF". Will consider later

[Xinqiu Yao]

The complain about PDF size can be removed by repeatedly running command:

tools::compactPDF("bio3d/vignettes", gs_quality="ebook")

until no size changes. However, the new PDF files have very low quality and sometimes images are lost. We should think another way to compress images embeded in PDF, an issue in the next release (to be submitted to CRAN).

[Xinqiu Yao]

Have been resolved with release v2.1-1 on CRAN!