I was notified recently my package has build errors going in to bioc 3.11.
So begins the biannual saga of updating everything to see what's new.
My package has quite a few dependencies, so it's normal for someone to
change their API and break my scripted usage. This time a default parameter
changed
, 2019 at 7:47 PM Pages, Herve wrote:
> Hi Karl,
>
> On 4/2/19 15:03, Karl Stamm wrote:
> > I'm having a build error on only the OSX servers.
> >
> > * creating vignettes ... ERROR
> > --- re-building ‘rgsepd.Rnw’ using knitr
> > Error: processing v
I'm having a build error on only the OSX servers.
* creating vignettes ... ERROR
--- re-building ‘rgsepd.Rnw’ using knitr
Error: processing vignette 'rgsepd.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'rgsepd.tex' failed.
LaTeX errors:
! Use of \blx@bbl@verbadd@i doesn't match its definiti
ioc-devel@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 wrote:
>>
>> > My package rgsepd has failed build re
ote:
> 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 wrote:
>
>> My package rgsepd has failed build recently.
>>
>> I don't understand the er
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 au
oconductor.org/developers/gitlog/
> to see if you commit is available on that list.
>
> Best,
>
> Nitesh
>
>
>
> > On Jan 2, 2019, at 10:49 AM, Karl Stamm wrote:
> >
> > I think there's a disconnect between the github and the bioconductor
> build
>
I think there's a disconnect between the github and the bioconductor build
server. I cannot seem to get any updates to go into the Bioc devel
packages.
I have added a few things to v1.15.x and the Bioc website still lists me as
1.15.0.
I have the workstation set up as such
git remote -v
origin g.
https://urldefense.proofpoint.
>> com/v2/url?u=http-3A__bioconductor.org_developers_gitlog_&d=
>> DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0W
>> YiZvSXAJJKaaPhzWA&m=_UN1AYHwq08NwBbWAg1aVKxVhgfzC6Kw4xHSZwV_
>> -Ng&s=De6-RIOuVqDeKOJbsyThMPIz7ZNegINb7haUTl8X
an "master"? How can I tell what the build servers are using
?
On Mon, Apr 23, 2018 at 11:14 AM, Turaga, Nitesh <
nitesh.tur...@roswellpark.org> wrote:
> Please check out the documentation
>
> http://bioconductor.org/developers/how-to/git/push-to-github-bioc/
>
> &
Bioconductor server if the
> changes have to propagate.
>
> RELEASE_3_6 is now frozen forever. We announced this on April 11th. You
> cannot push to this anymore. You can still make your changes on your master
> branch.
>
> https://stat.ethz.ch/pipermail/bioc-devel/2018-April/0132
I got a message this morning that malbec2 has build errors on my package.
It's a bug I fixed a few days ago, but it looks like I didn't push changes
to the right branches or something. How do I get the bioc systems to take
from the github updates?
The help documents on the bioconductor website say
How can I debug an error that occurs on the build server and not on my PC ?
I am having build errors on two of the three build servers with a line
about vignette compilation and the latex error does not have enough detail
to find the source of the problem.
I've recompiled the package on my machine
I've had this problem for a long time, so it might be a configuration
setting, and I need your help.
When running CHECK --as-cran etc the vast majority passes, but it always
fails when running the examples before it gets to my code.
* checking examples ... ERROR
Running examples in 'rgsepd-Ex.R'
Happened to look if my package rgsepd was building correctly, and it
seems as if some kind of change to a dependency is causing an
installation error for me. I was explicitly importing and calling
GenomicRanges::assay() for a year, and this month it is not exported.
Error : object ‘assay’ is not e
ad. Next step, I have to learn how to use the package
onLoad().
On Sat, Nov 22, 2014 at 5:32 AM, Sean Davis wrote:
>
>
> On Sat, Nov 22, 2014 at 12:53 AM, Karl Stamm wrote:
>
>> Question regarding gene name conversions. Once upon a time, I was doing a
>> lot of gene n
Question regarding gene name conversions. Once upon a time, I was doing a
lot of gene name conversions, particularly from NM_ to HGNC symbol or
Entrez GeneID. I used bioMaRt successfully, and developed a cache matrix so
I could quickly merge() it instead of calling out to a webservice
repeatedl
ust put them in the old-fashioned way (i.e. by
> hand).
>
> Kind regards,
> Sander Bollen.
>
> 2014-09-30 7:04 GMT+02:00 Karl Stamm :
>
>> I'm trying to put together a new package submission, "rgsepd", and I've
>> ran
>> into an error I can
I'm trying to put together a new package submission, "rgsepd", and I've ran
into an error I can't figure out. Hoping to talk with someone with more
experience on the bioconductor build system.
The build report is here
http://bioconductor.org/spb_reports/rgsepd_0.99.2_buildreport_20140929213816.htm
19 matches
Mail list logo
