[Bioc-devel] Build/check questions
James MacDonald wrote:
Hi! I have two questions about results on the build/check page for release 1.9. First, for my affycoretools package, the build on Solaris says OK, but in the output I see this line: creating vignettes ...Segmentation Fault - core dumped OK I suppose the build page *should* say OK, since this step returned an OK. However, I am pretty sure a segfault is A Bad Thing. Maybe I should ask on R-devel why this returns an OK? Should I expect that the build page would be able to return something other than OK in this situation?
Hi Jim, Since this is a bug in 'R CMD build', IMHO yes, it would be worth reporting the problem on R-devel. I've already reported it back in May and never got an answer but may be you'll be more lucky than I was. A workaround for now could be to add some code to our build system to parse the output returned by 'R CMD build' but I never really took the time to implement this :-/
Second, on all three Linux boxes (and on mine as well, but not on
windows), there is a cryptic warning that I don't understand:
* checking whether the name space can be loaded with stated
dependencies ... WARNING
Loading required package: methods
Error in if (mustFind) stop(gettextf("no generic function found for
\"%s\"", :
argument is not interpretable as logical
In addition: Warning message:
the condition has length > 1 and only the first element will be used
in: if (mustFind) stop(gettextf("no generic function found for \"%s\"",
Execution halted
A namespace must be able to be loaded with just the base namespace
loaded:
otherwise if the namespace gets loaded by a saved object, the session
will
be unable to start.
Probably some imports need to be declared in the NAMESPACE file.
Is there a reasonable way to track down what imports are missing?
I agree that this kind of message could be more usefull. The problem seems to occur when the GOstats NAMESPACE is imported into your NAMESPACE (I've tried to remove GOstats from import(annaffy, GOstats, biomaRt) in your NAMESPACE and didn't get the warning anymore). The check result for the GOstats package itself shows the same error. I've done been further and don't know what's wrong with the GOstats NAMESPACE. Are there some imports that need to be declared here? BTW, something that could be reported on R-devel too is that the "checking whether the name space can be loaded with stated dependencies" at least says for which NAMESPACE loading the warning is currently issued. Imagine a situation where we have to track down 20 levels of nested NAMESPACE importation :-/ Best, H.
------------------------ Herv? Pag?s E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319