[Bioc-devel] tokay1 C++14 compiler
Simo Kitanovski
@|mo@k|t@nov@k| @end|ng |rom un|-due@de
Wed Jul 31 12:19:59 CEST 2019
Many thanks!
Best,
Simo
On 31.07.19 11:39 vorm., Pages, Herve wrote:
> Hi Simo,
>
> Glad you were able to switch from install-time to run-time compilation.
>
> The C++14 compiler box for tokay1 shows that this compiler is not
> available on this machine. What you see below the box under "Compiler
> version" is produced by some code that tries to detect the version
> of the compiler despite the compiler not being available. Of course
> this fails which is why the output we see doesn't make sense.
>
> I've modified the report generation code so that it doesn't try to
> detect or display the version of a compiler that is not available.
> The change will take a couple of days before it's reflected on the
> report.
>
> Cheers,
> H.
>
>
> On 7/29/19 12:54, Simo Kitanovski wrote:
>> Surprisingly, if I design the package such that the stan models are
>> compiled only at run-time I get no issues -> all servers build the
>> package correctly.
>> (https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_Bioconductor_Contributions_issues_1187&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=sHIMsdC1yymiiBP9Su71j-Nb__FVDm6lsLIyYkEEr5A&s=HrgUU-zHwrAXjSjgnDtDmCDYZPQRr7vxZuwz7wfhTtk&e= )
>>
>> On the other hand, if I follow the rstan instructions on how to design
>> an R package that depends on rstan, based on which the stan models are
>> compiled only once during the build, then I get the previously mentioned
>> failure only on the windows-based server.
>>
>> BTW: Recent updates from stan community suggest that the new rstan
>> version 2.20 will reduce the model compilation time from ~35sec to
>> ~7sec, which makes the decision of sticking with the run-time
>> compilation setup not so bad.
>>
>> On 29.07.19 8:37 nachm., Kasper Daniel Hansen wrote:
>>> My understanding - and I could be wrong - is that Stan compiles a
>>> model, so the compiler needs to be available at run time and not just
>>> at build time.
>>>
>>> On Thu, Jul 25, 2019 at 4:02 PM Simo Kitanovski
>>> <simo.kitanovski using uni-due.de <mailto:simo.kitanovski using uni-due.de>> wrote:
>>>
>>> Thanks!
>>>
>>> I will try to revise the code to avoid CXX14 if this is that case.
>>>
>>> Best
>>>
>>>
>>> On 25.07.19 11:52 nachm., Martin Morgan wrote:
>>> > Windows (and macOS) CRAN packages are installed as binaries (as
>>> experienced by the typical user), so don't need compilation--
>>> Rstan is built by CRAN through whatever magic / agreement.
>>> >
>>> > The paragraph at the very end of
>>> >
>>> >
>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__cran.r-2Dproject.org_doc_manuals_r-2Drelease_R-2Dexts.html-23Using-2DC-5F002b-5F002b14-2Dcode&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=sHIMsdC1yymiiBP9Su71j-Nb__FVDm6lsLIyYkEEr5A&s=nRNDMBFrGqIX4JT8Gbn27HYfN8iZv0av3-ISM3aBGyk&e=
>>> >
>>> > suggests
>>> >
>>> > Note that g++ 4.9.x (as used for R on Windows at the time of
>>> writing) has only partial C++14 support, and the flag to obtain
>>> that support is not included in the default Windows build of R
>>> >
>>> > so my understanding of this is that CXX14 is not supported on
>>> Windows. The options are either to revise your code to avoid CXX14
>>> or to anticipate that your package will be 'Unsupported on
>>> Windows' (thereby losing 1/2 your user base).
>>> >
>>> > The expert on this (Hervé) will not be back for several days.
>>> >
>>> > Martin
>>> >
>>> > On 7/25/19, 6:33 PM, "Bioc-devel on behalf of Kasper Daniel
>>> Hansen" <bioc-devel-bounces using r-project.org
>>> <mailto:bioc-devel-bounces using r-project.org> on behalf of
>>> kasperdanielhansen using gmail.com
>>> <mailto:kasperdanielhansen using gmail.com>> wrote:
>>> >
>>> > What's weird here is that you supposedly depend on rstan
>>> which also
>>> > requires a C++14. How can the build system have that
>>> package installed
>>> > without having a compliant compiler?
>>> >
>>> >
>>> > On Thu, Jul 25, 2019 at 12:05 PM Simo Kitanovski
>>> <simo.kitanovski using uni-due.de <mailto:simo.kitanovski using uni-due.de>>
>>> > wrote:
>>> >
>>> > > Hello Bioconductor community,
>>> > >
>>> > > I maintain the Bioconductor package genphen which depends
>>> on rstan for
>>> > > MCMC sampling. To build the package one needs a C++14
>>> compiler.
>>> > >
>>> > > I have no problem building the package on malbec1 and
>>> merida1, but not
>>> > > on tokay1. Any idea of what might have gone wrong on this
>>> server and how
>>> > > to use C++14? I have submitted a new package
>>> (IgGeneUsage) which also
>>> > > uses rstan and have the same problem (see build report
>>> below).
>>> > >
>>> > > BTW: why do we see this under the C++14 compiler box for
>>> tokay1:
>>> > > Compiler version (' --version' output):
>>> > > '--version' is not recognized as an internal or external
>>> command,
>>> > > operable program or batch file.
>>> > >
>>> > > Any ideas?
>>> > >
>>> > > Best
>>> > >
>>> > > ===============================
>>> > >
>>> > > R CMD BUILD
>>> > >
>>> > > ===============================
>>> > > * checking for file 'IgGeneUsage/DESCRIPTION' ... OK
>>> > > * preparing 'IgGeneUsage':
>>> > > * checking DESCRIPTION meta-information ... OK
>>> > > * cleaning src
>>> > > * installing the package to build vignettes
>>> > > -----------------------------------
>>> > > * installing *source* package 'IgGeneUsage' ...
>>> > > ** using staged installation
>>> > > ** libs
>>> > > Error in .shlib_internal(args) :
>>> > > C++14 standard requested but CXX14 is not defined
>>> > > * removing
>>> > >
>>> > >
>>> 'C:/Users/pkgbuild/AppData/Local/Temp/RtmpUDyHnY/Rinst315c22dc5ac/IgGeneUsage'
>>> > > -----------------------------------
>>> > > ERROR: package installation failed
>>> > >
>>> > > _______________________________________________
>>> > > Bioc-devel using r-project.org
>>> <mailto: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=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=sHIMsdC1yymiiBP9Su71j-Nb__FVDm6lsLIyYkEEr5A&s=DYZvwT8c2RnG6YyuI_x7VRCPjkW1k68doGh_6k0tJXg&e=
>>> > >
>>> >
>>> >
>>> > --
>>> > Best,
>>> > Kasper
>>> >
>>> > [[alternative HTML version deleted]]
>>> >
>>> > _______________________________________________
>>> > Bioc-devel using r-project.org <mailto:Bioc-devel using r-project.org>
>>> mailing list
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>>> >
>>>
>>>
>>>
>>> --
>>> Best,
>>> Kasper
>> [[alternative HTML version deleted]]
>>
>> _______________________________________________
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>>
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