[Bioc-devel] sudden errors in the build reports for the development branch

Martin Morgan mtmorgan at fhcrc.org
Sun Jun 12 19:02:44 CEST 2011

On 06/12/2011 09:36 AM, Greg Finak wrote:
> Hi,
> A question for the bioconductor maintainers:
> I noticed today that some packages I maintain have build errors,
> even
though they were building fine last time I checked a couple of weeks ago
and I haven't made any significant changes. Looking more closely at some
of the errors, they are caused by missing C libraries on some machines,
and missing R packages on others. Specifically, flowClust 2.11.0 fails
to build on moscato1 because the gsl_math.h header cannot be found (as
if the gsl library is missing). flowWorkspace fails to build on
liverpool because the XML package is missing, and fails on pelham
because of some error in the C CallEntries array, which doesn't manifest
on any other machine. Other packages (which I don't maintain) also show
surprising missing dependencies (i.e. frma has errors due to missing
affy and oligo, and oligoClasses dependencies on liverpool, gewurtz, and
> Has something unexpected happened?

Not unexpected, but (a) moscato1 is a new build machine; these machines 
requiring set-up and configuration (2-fold, since this is building both 
32- and 64-bit versions of the package) and it is still a work in 
progress. (b) R-devel no longer supports a full zlib on Windows. This 
breaks any package using R's zlib, including affyio and all of its 
dependent packages, and the breakage became apparent when R was updated 
on the build machines over the last week or so. The solution we're 
working on is the zlibbioc package, which is designed to provide this 
functionality. The Rsamtools and ShortRead packages are test cases; you 
can see from the build report that there are still issues here. These 
are the big issues; XML on liverpool (and perhaps the pelham issue you 
mention) is likely a standard build system maintenance issue.

The situation will improve greatly over the next several days.


> Greg Finak, PhD
> Post-doctoral Research Associate
> PS Statistics, Vaccine and Infectious Disease Division.
> Fred Hutchinson Cancer Research Center
> Seattle, WA
> (206)667-3116
> gfinak at fhcrc.org
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

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