Dear All,

The reference manual for the development version of TRONCO (https://www.bioconductor.org/packages/3.3/bioc/manuals/TRONCO/man/TRONCO.pdf) disagrees with the actual functions available. In particular, at least some functions in the reference manual do not exist and some arguments for existing functions are different.  Thus, at least some examples from the PDF reference manual do not run.

A couple of examples:

   - p. 71 of the PDF shows that function "tronco.bootstrap" takes an argument "silent" and another argument "cores.ratio". However, the actual argument instead of "silent" seems to be "verbose" (silent is not a valid argument, and this can be checked also looking at the code) and neither "cores.ratio" nor anything like it is a valid argument.

  - p.8 of the PDF shows a function called "as.bootstrap.scores". However, that function does not exist (it is not in the namespace of TRONCO).

The help source files on the svn repo actually seem to be wrong in a weird way. There is a "as.bootstrap.scores.Rd" file in https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/TRONCO/man/  ) but that file is not present in the TRONCO_2.3.0.tar.gz file. Likewise, the file  https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/TRONCO/man/tronco.bootstrap.Rd has the (wrong) arguments "silent" and "cores.ratio" which are not in the file "tronco.bootstrap.Rd" of the tar.gz. I do not understand how this is possible.

Best,

R

This concerns the development version of the package.

The root of the problem is that the package was changed but the version not 'bumped', and at some point after the change the public repository (what you get with biocLite()) was reset (completely replaced), probably for an exceptional maintenance need. The public repository was then repopulated with the current version of all packages. I guess the repopulation involved tar balls, but not documentation products, so one has the new tarball and the old documentation.

The documentation in the installed package itself, and in SVN, is consistent, I think?

I bumped TRONCO's version number (to 2.3.1) so when this builds it'll be pushed to the public repository, and the documentation updated correctly. We'll look in to the underlying issue on our side. Developers should generally always remember to bump the version number with each commit (version numbers are cheap!).