Martin Morgan wrote: > Hi Torsten -- I believe that this is a shortcoming in Sweave as current > in the R appropriate for Bioc 2.3 (unable to wrap commented lines, or > lines without spaces) and so not readily 'fixed'. On the other hand, > this is the reference manual and all detail can be found from within R, > e.g., > > ?duplicateCorrelation > > The package maintainer might update the source code for the man pages, > but this wouldn't have an effect on Bioc 2.3, which is not the current > version. Hmm, to follow through a bit on this, I wrongly blamed Sweave for formatting, and underestimated the amount of work required to make pdf versions of the manual 'pretty'. Sweave does not play a role in creating the manual. Instead, the R tools for processing the vignette place the usage section in a 'verbatim' tex environment (similarly for the examples code, too, I think). Thus the 'fix' is for each package maintainer to write 'man' pages that are consistent with reasonable display of this formatting -- a fairly daunting task. For the record, the way man pages are generated as pdf is R CMD Rd2dvi --pdf <pkg_name-or-rd_file> Martin > > Martin > > Torsten Waldminghaus wrote: >> Dear all, >> >> >> >> the limma documentation stored here: >> http://www.bioconductor.org/packages/2.3/bioc/manuals/limma/man/lim ma.pd >> f >> >> has some lines being cut at the end of the page leading to loss of >> sometimes important information (see for example p. 55 or 70). >> >> >> >> >> >> Can somebody fix this or is there a full version somewhere? >> >> >> >> Cheers, >> >> Torsten >> >> >> >> Torsten Waldminghaus >> >> Department of Cell Biology >> >> Institute for Cancer Research >> >> Rikshospitalet-Radiumhospitalet-HF >> >> Ullernchaussen 70 >> >> 0310 Oslo >> >> tel: 47-22935973 >> >> fax: 47-22934580 >> >> e-mail: Torsten.Waldminghaus at rr-research.no >> >> http://openwetware.org/wiki/User:Torsten_Waldminghaus >> >> >> >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor