[Bioc-devel] tokay1 C++14 compiler
Pages, Herve
hp@ge@ @end|ng |rom |redhutch@org
Wed Jul 31 11:39:11 CEST 2019
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
>> > 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]]
>
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--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
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