[Bioc-devel] Fwd: banocc problems reported in the Multiple platform build/check report for BioC 3.9

[Vincent Carey]

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 <george.weingart using gmail.com>
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: <BBS-noreply using bioconductor.org>
> 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: <george.weingart using gmail.com>
>
>
> [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/
>
>     (all package maintainers are requested to subscribe to this list)
>
> For immediate notification of package build status, please
> subscribe to your package's RSS feed. Information is at:
>
> https://bioconductor.org/developers/rss-feeds/
>
> Thanks for contributing to the Bioconductor project!
>
>         [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioc-devel using r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

-- 
The information in this e-mail is intended only for the ...{{dropped:18}}