I am actively working on Rgraphviz right now following some
reports by CRAN about
- issues with the package failing on the C23 standard
- issues with the package failing on Windows using the new R
toolset for the next R release
- a switch from sprintf to snprintf
Tomas and Brian have been super helpful, and I have several times
though I had nailed down the issue. Currently, Rgraphviz 2.51.4
is failing; it seems that I didn't manage to submit 2.51.5 in time.
So I am working on it, albeit (clearly) not very successfully
right now. Some of the stuff I see on the build servers do not
follow what I see on my local machines but the changes are all
related so I hope to get it fixed "soon".
Best,
Kasper
On Thu, Mar 13, 2025 at 1:52 PM Robert Castelo via Bioc-devel
<bioc-devel@r-project.org> wrote:
Hi,
I'm experiencing a similar issue with qpgraph, which is
failing on
'nebbiolo1' (ubuntu 24.02) only:
https://bioconductor.org/checkResults/3.21/bioc-LATEST/qpgraph/nebbiolo1-buildsrc.html
giving the following error when building one of the vignettes:
--- re-building ‘qpgraphSimulate.Rnw’ using Sweave
*** buffer overflow detected ***: terminated
Aborted (core dumped)
just as Ramon below, I cannot reproduce the error either in
my linux box
with R-devel (2025-03-07 r87894) , nor with the R-devel from the
Bioconductor docker image (2025-02-24 r87814). qpgraph is using
Rgraphviz too, which is also failing in the same way when
building the
Rgraphviz.Rnw vignette:
--- re-building ‘Rgraphviz.Rnw’ using Sweave
Loading required package: graph
Loading required package: BiocGenerics
Loading required package: generics
Attaching package: ‘generics’
The following objects are masked from ‘package:base’:
as.difftime, as.factor, as.ordered, intersect,
is.element, setdiff,
setequal, union
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
Filter, Find, Map, Position, Reduce, anyDuplicated,
aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, is.unsorted,
lapply,
mapply, match, mget, order, paste, pmax, pmax.int
<http://pmax.int>, pmin, pmin.int <http://pmin.int>,
rank, rbind, rownames, sapply, saveRDS, table, tapply,
unique,
unsplit, which.max, which.min
Loading required package: grid
*** buffer overflow detected ***: terminated
Aborted (core dumped)
and I cannot reproduce this error on my machine either,
Rgraphviz builds
just fine.
does anyone here has an idea what we could do to chase this
error that
seems to be triggered by some C code in the Rgraphviz package?
something that could help diagnosing the problem is if the build
machines could call the Sweave engine with
--options="debug=TRUE", e.g.,
R CMD Sweave --options="debug=TRUE" xx.Rnw
not sure how one could do that when building a package. This
would show
in the build output the line in the vignette that is actually
triggering
the core dump.
Thanks!
robert.
On 3/7/25 03:42, Ramon Diaz-Uriarte wrote:
> Dear All,
>
> A package I maintain, OncoSimulR, is failing in all
platforms with
>
> Error: processing vignette 'OncoSimulR.Rmd' failed with
diagnostics:
> no slot of name "name" for this object of class "pEdge"
>
>
(https://bioconductor.org/checkResults/3.21/bioc-LATEST/OncoSimulR/kunpeng2-buildsrc.html)
>
> However, using the latest Rgraphviz source package,
2.51.1, and R-devel from 2025-02-20 (r87772) on Linux, with
all dependencies up to date, I am unable to reproduce the
error, either running R CMD build or just executing the
supposedly problematic code.
>
>
> Interestingly, at least four other packages that depend on
Rgraphviz seem to be failing with the same error:
>
> -
CellNOptR:https://bioconductor.org/checkResults/3.21/bioc-LATEST/CellNOptR/nebbiolo1-buildsrc.html
>
> -
CytoML:https://bioconductor.org/checkResults/3.21/bioc-LATEST/CytoML/nebbiolo1-buildsrc.html
>
> -
fowWorkspace:https://bioconductor.org/checkResults/3.21/bioc-LATEST/flowWorkspace/nebbiolo1-buildsrc.html
>
> -
TRONCO:https://bioconductor.org/checkResults/3.21/bioc-LATEST/TRONCO/nebbiolo1-buildsrc.html
>
> How can I try to solve this issue?
>
> Best,
>
> --
> Ramon Diaz-Uriarte
> Department of Biochemistry, Lab B-31
> Facultad de Medicina
> Universidad Autónoma de Madrid
> Arzobispo Morcillo, 4
> 28029 Madrid
> Spain
>
> Phone: +34-91-497-2412
>
> Email:rdia...@gmail.com <mailto:email%3ardia...@gmail.com>
> r.d...@uam.es
> ramon.d...@iib.uam.es
>
> https://ligarto.org/rdiaz
>
> _______________________________________________
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Robert Castelo, PhD
Associate Professor
Dept. of Medicine and Life Sciences
Universitat Pompeu Fabra (UPF)
Barcelona Biomedical Research Park (PRBB)
Dr Aiguader 88
E-08003 Barcelona, Spain
telf: +34.933.160.514
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Best,
Kasper
