[pkg-bioc] State of BioC compilations

[Steffen Moeller]

Ooops, the email below was supposed to go to the list. Many thanks, Dirk, for 
spotting this.

Steffen

> > On 9 February 2007 at 12:00, Steffen Moeller wrote:
> > | in principle it all works. Some issues I get with my 2.4 R installation
> > | that does not accept some apparent novel language construct 1L or 0L,
> > | which apparently  denote a vector of zeros or ones.
> >
> > Could you (briefly yet concisely) describe what happens, and where?  I am
> > not aware of unpatched faults in Debian's R 2.4.1, and R Core would not
> > change the language just for kicks. Or are you referring to C/C++
> > constructs?  Here long foo = 0L;
> > is legal AFAIK and no compiler should stumble.
> 
> If you check out the patches directory then you will see that this is all I 
> patched:
> 
> --- biobase-1.13.36/R/strings.R 2007-02-02 10:28:39.000000000 +0100
> +++ biobase-1.13.36/R/strings.R 2007-02-08 11:12:04.000000000 +0100
> @@ -37,7 +37,7 @@
>          ## The +1 and +2 are because substr is funny
>         ss = substr(x, nc - i + 1, nc)
>         if( any(ss != ss[1] )) {
> -           if (i == 1L)                 # trailing char mismatch
> +           if (i == 1)                 # trailing char mismatch
>               return("")
>             return(substr(x[1], nc - i + 2, nc))
>         }
> 
> It is supposed to be plain R code.
> 
> > | I have ongoing problems to install the graph package. Both the devel and
> > | the release versions build a nice packages but nothing pops up in the
> > | library() call. Any clues? This blocks some much seeked after packages
> > | like Rgraphviz.
> >
> > It probably means that dpkg/debhelper et al install in the wrong place, so
> > nothing gets tar'ed up. Doing the package manually with the generated
> > debian/rules and turning debhelper verbosity on may help.
> 
> That was my first thought, too. But is all looks so nicely:
> moeller at pc02:~/debian_moeller/debian/alioth/bioc/tools/patches$ dpkg -L 
> r-bioc-graph | head -12 | tail -5
> /usr/lib/R/site-library/graph/R/graph
> /usr/lib/R/site-library/graph/R/all.rda
> /usr/lib/R/site-library/graph/GXL
> /usr/lib/R/site-library/graph/GXL/attributesExample.gxl
> /usr/lib/R/site-library/graph/GXL/graphExample-16.gxl.gz
> 
> >
> > | Something that does not work are the dependencies. This is real bad. And
> > | I wished, a compilation would not be attempted when a known build-dep is
> > | not installed. I had a quick look at the AptPkg perl package but only a
> > | quick one. No proper dependencies and the continues broken build 
attempts
> > | are no fun.
> >
> > I do not understand. Dependencies are resolved by dpkg, we create them
> > based on control info we read. That already worked in Albrecht's scrip 
that
> > I hacked way when. So again: what fails, where, how?  Reproducible 
example?
> 
> Sorry, I meant the order at which the packages' .tar.gz files are unpackage 
> and dpkg-buildpackage is called. The detection of missing installs by 
> dpkg-buildpackage is perfectly fine ... but that is too late and ends the 
> build process.
> 
> > | The download script works but does not download any indirectly required
> > | packages. Hence the initial constraint on the lite package is
> > | unpractical. We should eventually come up with a concise list of 
packages
> > | that we want in Debian and directly specify just that.
> >
> > As I understand it, that is a BioC design choice. They make it hard to 
read
> > the directory, so we have to query via R code as BioCLite.R et al do.
> >
> > Both CRAN and BioC also get too big, so we should have 'Debian task views'
> > (better term suggestions welcomes) that cover subareas.
> 
> BioC procides groups already. We could adapt them for debtags.
> 
> > | Does anybody have the r-omega-rcurl package available, even for
> > | submission to Debian maybe? It is required from several non-nonsense 
BioC
> > | packages.
> >
> > Was never packaged AFAIK but IIRC does exist in CRAN. Try building
> > r-cran-curl, maybe?
> >
> > | Package count:  ls builds/r-bioc-* | wc -l
> > | 54
> >
> > Not bad!  54 down, 900 at CRAN to go :)
> 
> Some are already done. We'd now need a repository. We once had the OK to use 
> Alioth for that. Though I presume we should not go such public before having 
> improved on our automisation a bit.
> 
> Many greetings
> 
> Steffen
> 
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