[Bioc-devel] Build/check report news

Kasper Daniel Hansen khansen at stat.Berkeley.EDU
Wed Apr 26 07:21:43 CEST 2006

On Apr 25, 2006, at 10:05 PM, Seth Falcon wrote:

> Hi Kasper,
> Kasper Daniel Hansen <khansen at stat.berkeley.edu> writes:
>> In my opinion one of the greatest assets of the BioC build/check
>> routine is the ability to get your code tested on various platforms,
>> and that is most important for non-R code (typically C but it may
>> include other languages).
>> I would like to see
>>    * Other automatic build platforms like Solaris, Windows and MacOS
>> X. Perhaps a 32bit Linux as well? (I am sure that this will be the
>> case in due time, just wanted to mention it :)
> I'm glad to hear you find the automated builds useful.  Note that
> Herve's announcement for the 1.9 build page is just what we have
> available _today_.  As we did for 1.8, we will have:
> - Windows
> - 32 and 64 bit Linux
> - Solaris
> And we hope to add at least one OS X build as well. :-)
>>    * More details on the build platform especially compiler versions.
>> Eg. I have no idea about the difference between SuSE 9.2 and 10.0
> That's a nice suggestion.  I think we will be able to add that easily.
>>    * A build timestamp.
> I'm not really sure what you want when you say timestamp (I know it
> sounds obvious, but humor me).  The build report says at the top of
> the page:
>     This is the Multiple platform build/check report for BioC 1.8:
>     - SVN URL: https://hedgehog.fhcrc.org/bioconductor/branches/ 
> RELEASE_1_8/madman
>     - SVN Revision: 17679
>     - SVN Last Changed Date: 2006-04-24 22:18:08 -0700 (Mon, 24 Apr  
> 2006)
> This tells you that the report is for a build based on rev 17679 which
> last changed on 24 April at 22:18.  What else can we tell you?

I have cleaned my glasses and found the above mentioned information.  
That was indeed was I was looking for :)

>>    * The ability to see the contents of the 00INSTALL file which
>> contains compiler warnings/errors. I would like to see this _even if
>> the package build successfully_ as there can be some differences in
>> the warnings the different compilers/platforms yields. This is
>> something that the old pages lacked as well. At first I looked at the
>> aCGH package and did indeed see appropriate g++ output, but then I
>> check the affxparser package and saw none. A bit strange... - indeed
>> I do not even see the building of help pages? (hmm this difference
>> also exists on the BioC 1.8 page - why?)
> We had this same conversation 6 months ago.  We'll see what we can do
> about making the install log available.
> But all you have to do is add a vignette to your package; it is
> supposed to have one anyway.  Any vignette will do.  Then your package
> will be compiled during R CMD build and you will be able to view the
> output. :-P


>>    * perhaps it should be considered to use the -Wall flag for gcc
>> and/or -pendantic?
> I believe -Wall is already being set for the build, don't know about
> -pedantic.

If I look at the build output for aCGH (using g++) and affy (using  
gcc) I do not see the -Wall flag. Also -std=g99 is only set for gcc,  
not g++. I have no idea if that matters.

>>    * If the building process takes too much time, perhaps one only
>> needs to check code in /src on the various platforms - eg. skip the
>> generation of help pages?
> Hmm, that's another interesting idea.
> Thanks for the comments, hope we can get around to some of the
> improvements over the next few weeks.

Thanks, Kasper

> Best,
> + seth
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