[Bioc-devel] Harman not building on Windows due to mzR

Jason.Ross at csiro.au Jason.Ross at csiro.au
Wed Oct 5 14:08:39 CEST 2016

Hi Steffen,

I also develop on Linux, so I'm at a loss with compiling Bioconductor libs on Windows.

As a guess, if there are no compiler errors but 'mzR.dll' cannot be found, I suppose the final linking of the compiled objects failed? 

I did a quick search and there seems to be a precedence for incompatibility between mzR and certain Rcpp versions: http://stackoverflow.com/questions/11181691/r-bioconductor-mzr-library-load-error

Also on another tack, the line that seems to be doing the linking (prior to "installing to C:/Users/biocbuild/bbs-3.4-bioc/meat/mzR.buildbin-libdir/mzR/libs/i386") is fairly long. Has it has been clipped? Is it overflowing a shell variable? Windows has a very low command line limit of 8192 characters. By comparison, a typical Linux box has an arg limit of 2,097,152 chars (which can be found with `echo $(getconf ARG_MAX)`). https://mcuoneclipse.com/2015/03/29/solving-the-8192-character-command-line-limit-on-windows/

Maybe overflowing is not the case? I expect it would throw an error and that line is only 3,845 chars in length.

Anyway a couple of shots in the dark...


From: Steffen Neumann <sneumann at ipb-halle.de>
Sent: Wednesday, 5 October 2016 5:28 PM
To: Ross, Jason (H&B, North Ryde); bioc-devel at r-project.org
Subject: Re: [Bioc-devel] Harman not building on Windows due to mzR

Hi, Jason,

On Mi, 2016-10-05 at 03:40 +0000, Jason.Ross at csiro.au wrote:
> [...]
> This is arising from the vignette and is due to the package msmsEDA
> not being present. If I keep peeling the dependencies back, I get to
> mzR, which has trouble loading the Windows dynamic link library. See:
> http://bioconductor.org/checkResults/3.4/bioc-LATEST/mzR/tokay1-
> install.html

Together with the BioC team we're currently trying to find out
what's going on there, we have the problem at least since the move
to the new Tokay1 build host. Any help on the issue of "LoadLibrary
failure:  The specified module could not be found." is highly welcome.

On Linux I'd have ideas how to dig into the problem,
and I'd be happy to try suggestions what to try next to fix
the windows build.

Sorry for the hassle,

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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