Hi Jason,
On 10/05/2016 05:08 AM, jason.r...@csiro.au wrote:
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?
The error message is confusing: mzR.dll is actually here but it cannot
be loaded.
The man page for dyn.load (src/library/base/man/dynload.Rd) contains:
Users have been confused by messages like
\preformatted{
error: unable to load shared object
'.../library/rJava/libs/x64/rJava.dll':
LoadLibrary failure: The specified module could not be found.
}
The final line is a Windows (not \R) diagnostic: the \sQuote{module}
that could not be found is not \file{rJava.dll} but something else
Windows is looking for (here most likely Java DLLs): if you are lucky
there will be a dialog box with more details.
Note that you don't see this when you open the man page on a
non-Windows system because this part of the man page is in a
#ifdef windows ... #endif directive.
Cheers,
H.
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...
Cheers,
Jason
________________________________________
From: Steffen Neumann <sneum...@ipb-halle.de>
Sent: Wednesday, 5 October 2016 5:28 PM
To: Ross, Jason (H&B, North Ryde); bioc-devel@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.r...@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,
yours,
Steffen
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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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