[Bioc-devel] Unclear build failure ‘appending gaps’

[Shepherd, Lori]

The following will give you some info on the windows server:


http://bioconductor.org/checkResults/devel/bioc-LATEST/tokay2-NodeInfo.html


There have been some updates in other packages that should propagate on tomorrows build report.  I might suggest you wait to see if the package continues to have these ERRORs after then.


Cheers,



Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Karl Stamm <karl.stamm using gmail.com>
Sent: Tuesday, March 26, 2019 4:08:15 PM
To: Yue Zhao (Jason)
Cc: bioc-devel using r-project.org
Subject: Re: [Bioc-devel] Unclear build failure �appending gaps�

Is there a standard system loadout I should be matching? Something must be
different between my Windows build server and the bioconductor one.
I need to reproduce the error in order to debug it, but everything is
building fine locally.

On Tue, Mar 26, 2019 at 12:21 PM Yue Zhao (Jason) <yuezh using bu.edu> wrote:

> A new error showed up: logical subscript contains NAs
>
>
> *--*
>
> *Yue (Jason) Zhao*
>
> PhD Candidate, Bioinformatics Program
>
> Boston University
>
> yuezh using bu.edu
>
>
> On Sat, Mar 23, 2019 at 11:22 AM Michael Lawrence via Bioc-devel <
> bioc-devel using r-project.org> wrote:
>
>> This is due to some buggy changes to the internals of the S4Vectors
>> package. I should be able to fix these today.
>>
>> On Sat, Mar 23, 2019 at 7:41 AM Karl Stamm <karl.stamm using gmail.com> wrote:
>>
>> > My package rgsepd has failed build recently.
>> >
>> > I don't understand the error message, and need some guidance. It says
>> Error
>> > building vignette, "appending gaps is not supported"
>> >
>> > I can't find that statement anywhere in Google, so I don't know what
>> it's
>> > referring to.  Unfortunately, my package is an automation pipeline, so
>> > there's one line of code that runs many others, and the line triggering
>> the
>> > error could represent any part of my pipeline.
>> >
>> > I've checked the build on my end before uploading code changes, so I
>> cant
>> > reproduce the error. My build was okay until very recently, I have
>> added a
>> > CITATION file which is rather lengthy, and may be impacting the vignette
>> > build?
>> >
>> >         [[alternative HTML version deleted]]
>> >
>> > _______________________________________________
>> > Bioc-devel using r-project.org mailing list
>> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> >
>>
>>         [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> Bioc-devel using r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>

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