[Bioc-devel] Question about a package submission

c(GRanges(), GRanges())

(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> 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

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> 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>
Date: Friday 28 October 2016 at 12:38
To: Martin Morgan <martin.morgan at roswellpark.org>
Cc: Vincent Carey <stvjc at channing.harvard.edu>, Ioannis Vardaxis <
ioannis.vardaxis at math.ntnu.no>, "bioc-devel at r-project.org" <
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
).
I have tried quite about 20 different combinations of settings in my
YAML file (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> 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

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>
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> 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

        [[alternative HTML version deleted]]

        [[alternative HTML version deleted]]

        [[alternative HTML version deleted]]

This email message may contain legally privileged and/or confidential
information.  If you are not the intended recipient(s), or the employee or
agent responsible for the delivery of this message to the intended
recipient(s), you are hereby notified that any disclosure, copying,
distribution, or use of this email message is prohibited.  If you have
received this message in error, please notify the sender immediately by
e-mail and delete this email message from your computer. Thank you.