Warnings on Windows

[lgatto]

Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpoDKv8N/R.INSTALL1ddc6a06ea8/MSnbase/man/MSnExp-class.Rd:243: file link 'isolationWindow' in package 'mzR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpoDKv8N/R.INSTALL1ddc6a06ea8/MSnbase/man/MSnSet-class.Rd:510: file link 'write.exprs' in package 'MSnbase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpoDKv8N/R.INSTALL1ddc6a06ea8/MSnbase/man/OnDiskMSnExp-class.Rd:489: file link 'normalize' in package 'MSnbase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpoDKv8N/R.INSTALL1ddc6a06ea8/MSnbase/man/chromatogram-MSnExp-method.Rd:70: file link 'Chromatogram' in package 'MSnbase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpoDKv8N/R.INSTALL1ddc6a06ea8/MSnbase/man/combineFeatures.Rd:49: file link 'NTR' in package 'MSnbase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpoDKv8N/R.INSTALL1ddc6a06ea8/MSnbase/man/combineFeatures.Rd:156: file link 'NTR' in package 'MSnbase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpoDKv8N/R.INSTALL1ddc6a06ea8/MSnbase/man/estimateNoise-method.Rd:45: file link 'estimateNoise' in package 'MALDIquant' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.8-bioc/meat/MSnbase.Rcheck/00install.out' for details.

@sgibb @jotsetung - I'll look into #367 now, but also saw the warnings above on Windows. In case you know how to fix these, please let me know.

[jorainer]

I'll have a look at these.

[sgibb]

I had the same issue on topdownr. It is caused by wrong links generated by roxygen2 if you use the markdown syntax. We have to link against the name of the manual page (and not against an alias).
E.g. I had a warning for:

[MSnbase::calculateFragments()]

which could be fixed by:

[`MSnbase::calculateFragments()`][MSnbase::calculateFragments-methods]

The format [link text][link target]. Please note that link text is not typeset as code. That's why we need to add ` here.

For the MALDIquant warning it should be:

[`MALDIquant::estimateNoise()`][MALDIquant::estimateNoise-methods]

[sgibb]

Oh, I see the same is true if you don't use roxygen2 at all (e.g. the MALDIquant part seems to be in estimateNoise.Rd). In that case the correct format is:

\code{\link[MALDIquant:estimateNoise-methods]{MALDIquant::estimateNoise()}}

I can't fix it right now. Maybe tonight.

[jorainer]

I have a hard time reproducing the warnings above. On my Windows build system (R-3.5.1) I don't get any warnings. Will check if they/I have a special setup.

[sgibb]

I (hopefully) did all the changes but can't run roxygenise because pkgload throws the following error:

Error in add_classes_to_exports(ns = nsenv, package = package, exports = exports, :
in ‘MSnbase’ methods for export not found: reduce

Simply adding @export to reduce,data.frame-methods in utils.R doesn't solve the problem.
(It is the same error that prevents pkgdown::build_site() to run successfully on travis.)

Please see the https://github.com/lgatto/MSnbase/tree/man branch.

[jorainer]

@sgibb are you fixing also the remaining man problems? Tonight or tomorrow morning I would have time and could also help.

[sgibb]

@jotsetung Which remaining problems? The https://github.com/lgatto/MSnbase/tree/man branch contains the fixes for all of the above warnings. But I have no idea how to run roxygenize to complete it (ok I could manually edit the Rd files but then we will have the problem the next time we need roxygen2).

[jorainer]

Aren't the affected links all in static man pages? For these it should be OK to edit the Rd files as they will not be replaced running devtools::document() on the package. Or am I missing something?

Re remaining problems: I checked the man branch on Windows but still got some warnings.

[sgibb]

Aren't the affected links all in static man pages?

At least man/chromatogram-MSnExp-method.Rd is generated by roxygen2::roxygenise/devtools::document.

I found some unicode characters in R/utils.R that cause the error in roxygenise: 6be3d77

Now it is working again (pkgdown::build_site() is also working now! and travis runs successful, too 🎉)

@jotsetung I don't have a windows build machine currently. I just addressed the WARNINGs @lgatto posted above. Hopefully the fix is working (at least it doesn't generates ERROR/WARNINGs on linux). Do you refer to the g++ compiler warnings (unused variables/functions?). I didn't want to touch these warnings because I am not familiar with the code. So if you would review these warnings it would be great.

[jorainer]

Nice @sgibb! I'll check on my Windows build machine.

[jorainer]

All warnings are gone now on my Windows build machine! 🎉

[lgatto]

Thanks - pushed to Bioc.