Re: [Bioc-devel] ExperimentHub ft resource with password
Hi,
I think this is an analogous question to the one brought up about year
and a half ago by Martin Morgan in this issue:
https://github.com/Bioconductor/AnnotationHub/issues/45
on how could we ask the user to accept a license before downloading the
corresponding AlphaMissense data from the AnnotationHub.
In GenomicScores, which also provides access to AlphaMissense data, I
implemented a temporary solution until we have a general solution for
all AH resources, by which if the resource metadata (that I created
myself) included a license, this is displayed to the user, who must
accept it to use the data:
> library(GenomicScores)
> am <- getGScores("AlphaMissense.v2023.hg38")
snapshotDate(): 2024-10-28
loading from cache
These data is shared under the license CC BY-NC-SA 4.0 (see
https://creativecommons.org/licenses/by-nc-sa/4.0), do you accept it?
[y/n]: y
> am
GScores object
# organism: Homo sapiens (UCSC, hg38)
# provider: Google DeepMind
# provider version: v2023
# download date: Oct 10, 2023
# loaded sequences: chr1
# maximum abs. error: 0.005
# license: CC BY-NC-SA 4.0, see
https://creativecommons.org/licenses/by-nc-sa/4.0
# use 'citation()' to cite these data in publications
so, I guess a similar strategy could be applied, but requiring a
password instead of accepting a license. this of course implies
implementing a hub package that handles this, as GenomicScores is doing.
cheers,
robert.
On 6/2/25 10:53, Laurent Gatto via Bioc-devel wrote:
> Dear hub developers, dear Lori,
>
> Section 7.1 'Hosting Data on a Publicly Accessible Site' from the 'Creating A
> Hub Package' vignette (HubPub package) [1] describes how to define resources
> stored on ftp servers. Is there a way to specify a password to download such
> a resource?
>
> The data I would like to share as a hub resource needs a password. The
> password is public (it's spelled out in the associated publication). I
> imagine that at some point, the data will become accessible without password,
> but that can be a bit of a hit and miss situation. I would prefer avoiding
> re-sharing the files elsewhere or to have to wait until the data becomes
> accessible without password.
>
> Thank you in advance.
>
> Laurent
>
> [1]https://bioconductor.org/packages/3.20/bioc/vignettes/HubPub/inst/doc/CreateAHubPackage.html#storage-of-data-files
> ___
> 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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Re: [Bioc-devel] failing with non-reproducible error "no slot of name "name" for this object of class "pEdge"" from Rgraphviz
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, pmin, 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 > 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 [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] failing with non-reproducible error "no slot of name "name" for this object of class "pEdge"" from Rgraphviz
Hi Kasper,
thanks for your efforts, it seems that you wrote this email just a few
hours too early because the build reports for Monday 17th do not display
the buffer overflow error anymore for Rgraphviz:
https://bioconductor.org/checkResults/3.21/bioc-LATEST/Rgraphviz
and neither for qpgraph (hooray!):
https://bioconductor.org/checkResults/3.21/bioc-LATEST/qpgraph
although the problems described by the OP of this thread persist in the
following packages that depend on Rgraphviz:
* OncoSimulR:
https://bioconductor.org/checkResults/3.21/bioc-LATEST/OncoSimulR/kunpeng2-buildsrc.html
* 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
with the error "no slot of name "name" for this object of class "pEdge",
which seems related to Rgraphviz, which defines a class 'pEdge' as follows:
##end type can be arrow or -| or none
##which can be from, to or both
setClass("pEdge", representation(from="character",
to="character",
attrs="list",
subG="integer"),
prototype=list(subG=as.integer(0))
)
and the backtrace shown in some of the reports points out to
'Rgraphviz::buildEdgeList()'. so, maybe this problem was unrelated with
the buffer overflow after all.
I've looked at the code or 'Rgraphviz::buildEdgeList()' but I can't see
anything suspicious there.
robert.
On 3/17/25 15:20, Kasper Daniel Hansen wrote:
> We're now to version 2.51.5 and that works on everything but
> nebbiolo1. On this platform it compiles but fails to build the
> vignettes with a buffer overflow. This may be related to moving to
> snprintf from sprintf because, well, the difference between those two
> functions has to do with preventing buffer overflows (this may be
> completely wrong though).
>
> I am unable to reproduce this error on
> - my mac
> - the HPC linux system I have access to
> - the bioconductor docker devel container (emulating amd64 on my M2
> mac). This test is kind of incomplete because latex is not in the
> docker container, but R CMD check seems to run the vignette and only
> fail when it is time to produce a PDF output
>
> So this is looking to be harder to diagnose. I am not sure I am done
> with trying with docker, but so far it didn't work (despite having the
> same gcc version ad nebbiolo1).
>
> Best,
> Kasper
>
> On Fri, Mar 14, 2025 at 9:22 AM Robert Castelo
> wrote:
>
> Thanks Kasper, let me know if there is anything I could help with.
>
> cheers,
>
> robert.
>
> On 13/3/25 22:54, Kasper Daniel Hansen wrote:
>> 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
>> 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 (2025-03-0
Re: [Bioc-devel] failing with non-reproducible error "no slot of name "name" for this object of class "pEdge"" from Rgraphviz
- 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 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 >>
Re: [Bioc-devel] mail notification support forum stopped
Hi, on Feb 12 I brought up this problem in the #support-site channel of the Bioconductor Slack workspace (it's currently the last message on that channel), and it was there where Lori said: "We made some adjustments to try and fix the exposed emails in digest and appears to have broken sending". robert. On 3/26/25 14:33, James W. MacDonald wrote: It's busted. I think Lori said something about it, but I can't find that now. You could put in an issue https://github.com/Bioconductor/support.bioconductor.org/issues -Original Message- From: Bioc-devel On Behalf Of Hooiveld, Guido via Bioc-devel Sent: Wednesday, March 26, 2025 3:54 AM To: bioc-devel@r-project.org Subject: [Bioc-devel] mail notification support forum stopped Hi, Apologies if this is not the appropriate place to ask. I noticed that since January 30 I don't receive any mail notifications from the support forum; for example when I reply to a question. To find out why this happens I wonder whether it is just me, or if there is an issue with this feature. The sender is 'nore...@bioconductor.org'. I have contacted the IT dept of my university, and they claim it is not 'them' (= address being on a blacklist or so). Thanks, Guido - Guido Hooiveld, PhD Nutrition, Metabolism & Genomics Group Division of Human Nutrition & Health Wageningen University the Netherlands Visiting address: Mail address: HELIX (Building 124), room 2048 Stippeneng 4 PO Box 17 6708 WE Wageningen 6700 AA Wageningen the Netherlands the Netherlands tel: (+) 31 317 485788 fax: (+) 31 317 483342 email: guido.hooiv...@wur.nl internet: https://urldefense.com/v3/__http://www.humannutrition.nl__;!!K-Hz7m0Vt54!lUG2Mp-5eSzspinagZOVqhTMnAhD2N-HwCQIcg7atnmSswkPUdnIv4VfhlvH4eVq0OzgLzItoB14xHZ6HqOOyA$ https://urldefense.com/v3/__http://scholar.google.com/citations?user=qFHaMnoJ__;!!K-Hz7m0Vt54!lUG2Mp-5eSzspinagZOVqhTMnAhD2N-HwCQIcg7atnmSswkPUdnIv4VfhlvH4eVq0OzgLzItoB14xHa33gn3kA$ https://urldefense.com/v3/__http://www.scopus.com/authid/detail.url?authorId=6603101814__;!!K-Hz7m0Vt54!lUG2Mp-5eSzspinagZOVqhTMnAhD2N-HwCQIcg7atnmSswkPUdnIv4VfhlvH4eVq0OzgLzItoB14xHZr5dby7g$ [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/bioc-devel__;!!K-Hz7m0Vt54!lUG2Mp-5eSzspinagZOVqhTMnAhD2N-HwCQIcg7atnmSswkPUdnIv4VfhlvH4eVq0OzgLzItoB14xHasQDx78A$ ___ 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 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] failing with non-reproducible error "no slot of name "name" for this object of class "pEdge"" from Rgraphviz
Thanks Kasper, let me know if there is anything I could help with. cheers, robert. On 13/3/25 22:54, Kasper Daniel Hansen wrote: > 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 > 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: > > > > - > >
