[Bioc-devel] ChemmineOB build failing on windows

Hervé Pagès hp@ge@ @end|ng |rom |redhutch@org
Thu Apr 23 22:21:35 CEST 2020

On 4/23/20 12:52, Hervé Pagès wrote:
> On 4/23/20 12:45, Hervé Pagès wrote:
>> On 4/23/20 10:45, Kevin Horan wrote:
>>> Bioc,
>>> The build of ChemmineOB is failing on windows, which is also causing 
>>> 3 other packages to fail (ChemmineR, eiR, and fmcsR). I was able to 
>>> build the package on my own windows machine (Windows Server 2012 R2 
>>> Standard) without any error. I used R devel. The content of this 
>>> package has not been changed since October 2018.
>> Right but the toolchain used for R 4.0.0 on Windows now is Rtool40 
>> which is a huge upgrade from the previous one. Could this be related 
>> to the compilation failure?
> It also occurs to me that we might need to recompile Open Babel with the 
> new toolchain on tokay2. Could that be the problem?

FWIW the RProtoBufLib/cytolib maintainers had to do this for the 
protobuf and they made the updated binaries available here: 

It seems to be pretty typical with C++ code that the binaries tend to 
break with major updates of the compiler (generally because of changes 
to how the compiler mangles method names).


> H.
>> Best,
>> H.
>>> Can someone please look into it? Thanks. The build link is 
>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_checkResults_devel_bioc-2DLATEST_ChemmineOB_tokay2-2Dbuildsrc.html&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=wmRn4CjxRi7ewvrtWLIyKM2Tockd3ZOaWfhhytkrbCM&s=hoMGH754DpRKnA8RGcuSStVub2IwW2BGrG6lvBK4io4&e= 
>>> Kevin
>>> _______________________________________________
>>> Bioc-devel using r-project.org mailing list
>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=wmRn4CjxRi7ewvrtWLIyKM2Tockd3ZOaWfhhytkrbCM&s=RuXC_DouGnZ1Y3CsW5TtbzVY-lzbyy3KiFm28uqNOos&e= 

Hervé Pagès

Program in Computational Biology
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