[Bioc-devel] ChemmineOB build failing on windows

Hervé Pagès hp@ge@ @end|ng |rom |redhutch@org
Thu Apr 23 22:25:28 CEST 2020

On 4/23/20 13:18, Kevin Horan wrote:
> Hervé,
>      It could be. The test I did today was on a clean windows machine, 
> so I did build open babel from scratch with Rtools40. I don't have an 
> openbabel built with the old version to check. The INSTALL file of 
> ChemmineOB provides detail instructions for building OpenBabel on windows.

We'll try this. That is unfortunate as it requires more time than we can 
realistically spend on the builders to satisfy the needs of 1800+ 
software packages. It would be really appreciated if in the future you 
could provide Open Babel binaries that we can just unzip on the Windows 


> Kevin
> On 4/23/20 12:52 PM, 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?
>> 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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