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

Vincent Carey @tvjc @end|ng |rom ch@nn|ng@h@rv@rd@edu
Tue Jun 25 13:03:08 CEST 2019

The error reported by the build system is reproducible on my mac running R
CMD check on


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 =


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

*In file included from

*In file included from

*In file included from

*In file included from

*In file included from

*In file included from

*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*


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>

> 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:
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