[Bioc-devel] Help needed: Rdisop on Windows "File format not recognized"

Mike Smith gr|mbough @end|ng |rom gm@||@com
Thu Apr 18 14:38:01 CEST 2019

I can reproduce the error using R-3.6.0beta and running the following two
steps to replicate the Bioc builder commands:

R CMD build --keep-empty-dirs --no-resave-data Rdisop
rm -rf Rdisop.buildbin-libdir && mkdir Rdisop.buildbin-libdir &&
C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch
--build --library=Rdisop.buildbin-libdir Rdisop_1.43.4.tar.gz

Bit of a guess, and I don't know why this would have changed, but
the Rdisop_1.43.4.tar.gz produced by step one contains the *.o files
referenced in the error.  If these were produced for 64-bit architecture
then they'll fail when the build process tries to use them for the 32-bit
binary.  Perhaps your Rcpp edits removed some cleanup code that was there
before?  I note there's no Makevars.win or cleanup.win but my memory is a
bit fuzzy on whether only versions with *.win will be run on Windows or if
that's just a way to provide alternative code if needed.

On Thu, 18 Apr 2019 at 11:35, Neumann, Steffen <sneumann using ipb-halle.de>

> Hi,
> with the next release coming up, I am out of wits regarding the failure at
> http://bioconductor.org/checkResults/devel/bioc-LATEST/Rdisop/tokay2-buildbin.html
> which exists since before April this year, when we committed
> some changes to get rid of the RcppClassic dependency.
> Max Helf succeeded to build locally on windows without problem.
> So it seems that Rdisop has issues with the BioC windows build
> environment, but I totally fail to see the reason.
> Could it be the new staged installation ?
> But I wouldn't know why that'd affect the compile/linking.
> The issue is tracked at
> https://github.com/sneumann/Rdisop/issues/13
> Any help/pointers appreciated.
> Yours,
> Steffen
> --
> IPB Halle                    AG Massenspektrometrie & Bioinformatik
> Dr. Steffen Neumann          http://www.IPB-Halle.DE
> Weinberg 3                   Tel. +49 (0) 345 5582 - 1470
> 06120 Halle                       +49 (0) 345 5582 - 0
> sneumann(at)IPB-Halle.DE     Fax. +49 (0) 345 5582 - 1409
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