[Bioc-devel] Question about a package submission
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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