The error reported by the build system is reproducible on my mac running R
CMD check on
banocc_1.8.0.tar.gz
The check error is pretty terse. I turned your vignette into
an R script using knitr::purl and ran into
> compiled_banocc_model <- rstan::stan_model(model_code =
banocc::banocc_model)
DIAGNOSTIC(S) FROM PARSER:
Info: integer division implicitly rounds to integer. Found int division: (P
* (P - 1)) / 2
Positive values rounded down, negative values rounded up or down in
platform-dependent way.
*Error in compileCode(f, code, language = language, verbose = verbose) : *
* Compilation ERROR, function(s)/method(s) not created! In file included
from file15ef4c04043e.cpp:8:*
*In file included from
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/model/model_header.hpp:4:*
*In file included from
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math.hpp:4:*
*In file included from
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:4:*
*In file included from
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:5:*
*In file included from
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/core/build_vari_array.hpp:4:*
*In file included from
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4:*
*In file included from
/Library/Frameworks/R.framework/Versions/3.6/Resources/l*
*In addition: Warning message:*
*In system(cmd, intern = !verbose) :*
* running command '/Library/Frameworks/R.framework/Resources/bin/R CMD
SHLIB file15ef4c04043e.cpp 2> file15ef4c04043e.cpp.err.txt' had status 1*
Selection:
I don't know how to interpret this as I don't make much use of rstan.
Even though you have not changed anything in this version of banocc,
other software that you rely on may be changing ... perhaps
https://github.com/stan-dev/rstan/issues/666 is relevant?
On Mon, Jun 24, 2019 at 10:27 PM George Weingart
wrote:
> Hello !
>
> I am receiving these messages.
>
> We haven't changed anything in the package and all of a sudden we are
> getting errors to the effect that the "vignette build failed" "because a
> connect error"
>
> I do not know what causes the error (Since we haven't changed anything in
> the package) and how to recreate it.
>
> Can you assist solving the issue ?
>
> Thanks!
>
> George Weingart PhD
> Huttenhower Lab
> Harvard School of Pubilc Health
>
>
>
> -- Forwarded message -
> From:
> Date: Mon, Jun 24, 2019 at 11:36 AM
> Subject: banocc problems reported in the Multiple platform build/check
> report for BioC 3.9
> To:
>
>
> [This is an automatically generated email. Please don't reply.]
>
> Hi banocc maintainer,
>
> According to the Multiple platform build/check report for BioC 3.9,
> the banocc package has the following problem(s):
>
> o ERROR for 'R CMD build' on malbec2. See the details here:
>
>
> https://master.bioconductor.org/checkResults/3.9/bioc-LATEST/banocc/malbec2-buildsrc.html
>
> Please take the time to address this by committing and pushing
> changes to your package at git.bioconductor.org
>
> Notes:
>
> * This was the status of your package at the time this email was sent to
> you.
> Given that the online report is updated daily (in normal conditions)
> you
> could see something different when you visit the URL(s) above,
> especially if
> you do so several days after you received this email.
>
> * It is possible that the problems reported in this report are false
> positives,
> either because another package (from CRAN or Bioconductor) breaks your
> package (if yours depends on it) or because of a Build System problem.
> If this is the case, then you can ignore this email.
>
> * Please check the report again 24h after you've committed your changes
> to the
> package and make sure that all the problems have gone.
>
> * If you have questions about this report or need help with the
> maintenance of your package, please use the Bioc-devel mailing list:
>
> https://bioconductor.org/help/mailing-list/
>
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>
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