[Bioc-devel] use bioc docker images to reproduce linux build error?

[Paul Shannon]

Hi Val,

Thanks for the pointer.  I now import RMariaDB in the NAMESPACE and the DESCRIPTION files.  That seemed to solve the problem.   When I updated from RMySQL, I failed to do that.  

I changed .BBSoptions to simply “win” as you suggest, but just as a temporary measure.  I don’t remember why we excluded the windows build - perhaps that is not necessary any more.  After the package builds clean on macOS and linux, I will experiment with removing the win exclusions.

Thank you!

 - Paul


> On Nov 16, 2018, at 3:04 PM, Obenchain, Valerie <Valerie.Obenchain using RoswellPark.org> wrote:
> 
> Hi Paul,
> 
> I can reproduce the error on my Linux system but not on the Mac and am 
> not sure why this is. Haven't tried Windows yet but from the looks of 
> the build report that one is fine too.
> 
> R CMD check on Linux is failing on this line in 
> getRegulatoryRegions,HumanDHSFilter-method:
> 
>   db <- dbConnect(driver, user = user, host = host, dbname = dbname)
> 
> Does this need a password (and probably DBI::dbConnect for completeness)?
> 
> 
> There is a similar line in 
> getEncodeRegulatoryTableNames,HumanDHSFilter-method which isn't failing 
> R CMD check because the man page example is wrapped in /dontrun but it 
> does fail for me when run manually. I think this one may also need a 
> password - if you want to give me one off-line I can test this theory.
> 
>   db <- DBI::dbConnect(driver, user = user, host = host, dbname = dbname)
> 
> I see a .BBSoptions in trena for exclusion on Windows. The reason it's 
> not being respected is because it's malformed and needs a space after 
> the comma between the platforms. Just curious, what was the reason for 
> excluding this on Windows?
> 
> Val
> 
> 
> 
> 
> On 11/15/18 9:23 AM, Paul Shannon wrote:
>> Our package “trena” has had build errors these last two weeks.  I have not yet been able to reproduce them on a macOS laptop.
>> 
>> Would it be sensible to get the latest release and devel docker images for Bioconductor?  Are they similar enough to the build system to give me good odds on reproducing the errors seen there?
>> 
>>  - Paul
>> 
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>> 
> 
> 
> 
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