On Wed, Sep 23, 2020 at 07:34:50PM +0100, Shayan Doust wrote:
> This [commit] now rectifies the build issue for r-cran-prophet.
>
> I can build r-cran-prophet successfully after re-building r-cran-rstan with
> the
> new patch.
Strange, when I try to build r-cran-rstan with your patch I get:
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I"../inst/include"
-I"../inst/include/boost_not_in_BH" -I"." -DBOOST_DISABLE_ASSERTS
-DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -DBOOST_NO_AUTO_PTR -D_REENTRANT
-DSTAN_THREADS -I'/usr/lib/R/site-library/Rcpp/include'
-I'/usr/lib/R/site-library/RcppEigen/include'
-I'/usr/lib/R/site-library/BH/include'
-I'/usr/lib/R/site-library/StanHeaders/include'
-I'/usr/lib/R/site-library/RcppParallel/include' -fpic -g -O2
-fdebug-prefix-map=/build/r-base-OT058M/r-base-4.0.2=. -fstack-protector-strong
-Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c
stan/lang/grammars/whitespace_grammar_inst.cpp -o
stan/lang/grammars/whitespace_grammar_inst.o
g++ -std=gnu++14 -shared -L/usr/lib/R/lib -Wl,-z,relro -o rstan.so Module.o
chains.o init.o misc.o pointer-tools.o sparse_extractors.o stan_fit_base.o
stan_fit_rccp.o stanc.o stan/lang/ast_def.o
stan/lang/grammars/bare_type_grammar_inst.o
stan/lang/grammars/block_var_decls_grammar_inst.o
stan/lang/grammars/expression07_grammar_inst.o
stan/lang/grammars/expression_grammar_inst.o
stan/lang/grammars/functions_grammar_inst.o
stan/lang/grammars/indexes_grammar_inst.o
stan/lang/grammars/local_var_decls_grammar_inst.o
stan/lang/grammars/program_grammar_inst.o
stan/lang/grammars/semantic_actions_def.o
stan/lang/grammars/statement_2_grammar_inst.o
stan/lang/grammars/statement_grammar_inst.o
stan/lang/grammars/term_grammar_inst.o
stan/lang/grammars/whitespace_grammar_inst.o /usr/lib/x86_64-linux-gnu -ltbb
-ltbbmalloc -L/usr/lib/R/lib -lR
/usr/bin/ld: cannot find /usr/lib/x86_64-linux-gnu: file format not recognized
collect2: error: ld returned 1 exit status
make[1]: *** [/usr/share/R/share/make/shlib.mk:6: rstan.so] Error 1
It looks as if some variable is not resloved properly resolved in the chroot
I substituted
s/inst.o /usr/lib/x86_64-linux-gnu -ltbb/inst.o -L/usr/lib/x86_64-linux-gnu
-ltbb/
(in the very end) and it worked. I guess the patch in R/plugin.R is responsible
for this since this is where I can find the string -ltbb.
Any idea how to fix this?
Kind regards
Andreas.
> Within r-cran-prophet:
> $ autopkgtest . -- null
>
> [TRUNCATED]
>
> /usr/bin/ld: cannot find -lStanHeaders
> collect2: error: ld returned 1 exit status
> make: *** [/usr/share/R/share/make/shlib.mk:6: sourceCpp_2.so] Error 1
> -- 2. Error: (unknown) (@test_stan_functions.R#9)
> -----------------------------
> $ operator is invalid for atomic vectors
> Backtrace:
> 1. base::tryCatch(...)
> 2. base:::tryCatchList(expr, classes, parentenv, handlers)
> 3. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
> 4. value[[3L]](cond)
> 5. rstan::expose_stan_functions(...)
>
> == testthat results
> ===========================================================
> [ OK: 160 | SKIPPED: 0 | WARNINGS: 3 | FAILED: 2 ]
> 1. Error: (unknown) (@test_prophet.R#9)
> 2. Error: (unknown) (@test_stan_functions.R#9)
>
> There exists some failed tests, however 160 pass!
>
> Kind regards,
> Shayan Doust
>
>
> [commit]:
> https://salsa.debian.org/r-pkg-team/r-cran-rstan/-/commit/7351289242ba080c112b1c15784e57f154a79076
pub RSA 4096/19D02395 2019-09-04 Shayan Doust (Personal EMAIL)
<he...@shayandoust.me>
> sub RSA 4096/00484410 2020-06-26
>
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