[Bioc-devel] Build/check report news

Seth Falcon sfalcon at fhcrc.org
Wed Apr 26 07:05:04 CEST 2006

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?

>    * 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

>    * 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.


+ seth

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