[Bioc-devel] Question about a package submission
Martin Morgan
martin.morgan at roswellpark.org
Fri Oct 28 16:12:46 CEST 2016
On 10/28/2016 10:08 AM, Kevin RUE wrote:
> Seems to be a MS Windows thing indeed.
>
> I have installed R-devel from scratch on a Window machine, then a fresh
> installation of BioC (biocLite()), then installed my package, and I get
> the error:
>> c(GRanges(), GRanges())
> Error in c(GRanges(), GRanges()) :
> could not find symbol "recursive" in environment of the generic function
>
> I have also run the following, but then I got the above error message again:
> biocLite(c("rtracklayer", "S4Vectors", "XVector", "IRanges",
> "Biostrings", "GenomicRanges", "GenomicAlignments"))
it could be that our zip files are themselves a victim of this problem,
and that installing from source (type="source", but needing Rtools
https://cran.r-project.org/bin/windows/Rtools/) addresses this.
Martin
>
>
> I'll keep digging... :)
>
> Kevin
>
>
>
>
> On Fri, Oct 28, 2016 at 1:48 PM, Kevin RUE <kevinrue67 at gmail.com
> <mailto:kevinrue67 at gmail.com>> wrote:
>
> (What puzzles me most is that it builds fine on Travis CI
> <https://travis-ci.org/kevinrue/TVTB>, just not on AppVeyor
> <https://ci.appveyor.com/project/kevinrue/tvtb>).
>
> MS Windows issue?
>
> Best,
> Kevin
>
>
> On Fri, Oct 28, 2016 at 12:30 PM, Kevin RUE <kevinrue67 at gmail.com
> <mailto:kevinrue67 at gmail.com>> wrote:
>
> Thanks for sharing your solution Ioannis.
> Unfortunately, it did not solve my situation on AppVeyor:
> https://ci.appveyor.com/project/kevinrue/tvtb/build/1.0.29
> <https://ci.appveyor.com/project/kevinrue/tvtb/build/1.0.29>
>
> I'll keep trying a few more things.
>
> Best
> Kevin
>
> On Fri, Oct 28, 2016 at 12:13 PM, Ioannis Vardaxis
> <ioannis.vardaxis at math.ntnu.no
> <mailto:ioannis.vardaxis at math.ntnu.no>> wrote:
>
> For me, running biocLite(c("rtracklayer", "S4Vectors",
> "XVector", "IRanges",
> "Biostrings", "GenomicRanges", "GenomicAlignments"))
> Worked and solved the error.
>
> Ioannis
> --
> Ioannis Vardaxis
> Stipendiat IMF
> NTNU
>
> From: Kevin RUE <kevinrue67 at gmail.com
> <mailto:kevinrue67 at gmail.com>>
> Date: Friday 28 October 2016 at 12:38
> To: Martin Morgan <martin.morgan at roswellpark.org
> <mailto:martin.morgan at roswellpark.org>>
> Cc: Vincent Carey <stvjc at channing.harvard.edu
> <mailto:stvjc at channing.harvard.edu>>, Ioannis Vardaxis
> <ioannis.vardaxis at math.ntnu.no
> <mailto:ioannis.vardaxis at math.ntnu.no>>,
> "bioc-devel at r-project.org <mailto:bioc-devel at r-project.org>"
> <bioc-devel at r-project.org <mailto:bioc-devel at r-project.org>>
> Subject: Re: [Bioc-devel] Question about a package submission
>
> Dear Martin,
>
> Sorry for slightly diverting the thread solely based on the
> error message:
>
> Error in .Primitive("c")(<S4 object of class "Rle">, <S4
> object of class "Rle">) :
> could not find symbol "recursive" in environment of
> the generic function
>
>
> I can somewhat picture the issue from your explanation.
>
> I think that the generic was redefined in base R, but
> you have packages that were installed before the generic
> was redefined. The methods in the installed packages
> think that they are associated with the generic at the
> time of installation, rather than at runtime.
>
> Unfortunately I think this means manually re-installing
> even up-to-date packages that define S4 "c" methods;
> likely this is a complicated stack of dependencies
> including rtracklayer, S4Vectors, XVector, IRanges,
> Biostrings, GenomicRanges, GenomicAlignments, ...
>
>
> However, I cannot figure out how to avoid this issue on
> AppVeyor
> (https://ci.appveyor.com/project/kevinrue/tvtb/build/job/srkobac85uksgcht
> <https://ci.appveyor.com/project/kevinrue/tvtb/build/job/srkobac85uksgcht>).
> I have tried quite about 20 different combinations of
> settings in my YAML file
> (https://github.com/kevinrue/TVTB/commits/master
> <https://github.com/kevinrue/TVTB/commits/master>) without
> success.
> I am not not sure how I may "manually reinstall" said
> packages, or somehow make sure the generic is define before
> all the relevant packages are installed.
>
> I'll admit that setting up a second Continuous Integration
> system is not the most pressing issue in my life, but I'm so
> close to succeeding that it is fairly frustrating to leave
> it at that :)
>
> Kind regards,
> Kevin
>
>
> On Thu, Oct 27, 2016 at 1:28 PM, Martin Morgan
> <martin.morgan at roswellpark.org
> <mailto:martin.morgan at roswellpark.org>> wrote:
>
> On 10/27/2016 08:22 AM, Kevin RUE wrote:
>
> Hi Ioannis, Vincent,
>
> I'm in the middle of debugging a similar situation
> myself, which may
> provide a reproducible example at a package level.
>
> I am in the process of setting up AppVeyor CI for my
> package, and my R CMD
> check fails because of the same error.
> https://ci.appveyor.com/project/kevinrue/tvtb/build/1.0.11
> <https://ci.appveyor.com/project/kevinrue/tvtb/build/1.0.11>
>
> To debug the issue, I am also currently updating my
> local installation to
> the latest devel packages (until biocValid() returns
> TRUE).
> Once that is done, I may be able to provide a more
> practical minimal
> working example for the issue (i.e. the code in one
> of my man pages).
>
>
> I think that the generic was redefined in base R, but
> you have packages that were installed before the generic
> was redefined. The methods in the installed packages
> think that they are associated with the generic at the
> time of installation, rather than at runtime.
>
> Unfortunately I think this means manually re-installing
> even up-to-date packages that define S4 "c" methods;
> likely this is a complicated stack of dependencies
> including rtracklayer, S4Vectors, XVector, IRanges,
> Biostrings, GenomicRanges, GenomicAlignments, ...
>
> Marin
>
>
>
> Best,
> Kevin
>
>
>
> On Thu, Oct 27, 2016 at 12:23 PM, Vincent Carey
> <stvjc at channing.harvard.edu
> <mailto:stvjc at channing.harvard.edu>>
> wrote:
>
> Please send a reproducible example with value of
> sessionInfo() at time of
> error.
>
> On Thu, Oct 27, 2016 at 7:06 AM, Ioannis Vardaxis <
> ioannis.vardaxis at math.ntnu.no
> <mailto:ioannis.vardaxis at math.ntnu.no>> wrote:
>
> Hi,
>
> I am using the R-devel version for writing
> an R package. I tried to use
> the c(Granges,Granges) command to merge two
> Granges objects and I get the
> following error:
>
> Error in .Primitive("c")(<S4 object of class
> "Rle">, <S4 object of class
> "Rle">) :
> could not find symbol "recursive" in
> environment of the generic
>
> function
>
>
> I also get the same error when I use
> InteractionSet::GInteractions(
>
> Granges,
>
> Granges).
>
> I downloaded IRanges, GenomicRanges and
> InteractionSet packages from the
> source.
>
> How can I solve this error?
>
> Best,
> Ioannis
> --
> Ioannis Vardaxis
> Stipendiat IMF
> NTNU
>
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>
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