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://github.com/Bioconductor/Contributions/issues/1187)
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.kitanov...@uni-due.de <mailto:simo.kitanov...@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://cran.r-project.org/doc/manuals/r-release/R-exts.html#Using-C_002b_002b14-code > > > > 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-boun...@r-project.org > <mailto:bioc-devel-boun...@r-project.org> on behalf of > kasperdanielhan...@gmail.com > <mailto:kasperdanielhan...@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.kitanov...@uni-due.de <mailto:simo.kitanov...@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@r-project.org > <mailto:Bioc-devel@r-project.org> mailing list > > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > > > > > > > -- > > Best, > > Kasper > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org> > mailing list > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > > > > -- > Best, > Kasper [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
