Hi Matthias,
I have a (non-BioC) package depending on ShinyBS,
could you give a hint what to watch out for that's working different as
expected ? Any suggestion what to use as replacement ?
Thanks in advance,
Danke,
Steffen
On Sat, 2024-01-13 at 22:48 +0100, Matthias Döring via Bioc-devel
wrote:
Hi,
so far I am doing this manually, I have my github as remote origin,
and the bioc git as upstream, and indeed after the releases I pull from
upstream the changed version number and push it to my origin on github.
Yours,
Steffen
On Sat, 2023-11-11 at 09:35 +0100, migdal migdal wrote:
> Hi guys
... And as a reviewer I'd never have an issue if a paper describes
something and mentions in which Version (x.y.z) it is released,
regardless in what BioC release/devel that is.
Yours,
Steffen
On Mon, 2023-06-19 at 11:46 -0400, Vincent Carey wrote:
> Hi Adam, thanks for your note.
>
> Changes
Hi,
On Wed, 2023-05-03 at 12:23 -0400, Vincent Carey wrote:
> Hi Franck, thanks for writing. I think it would be great to hear
> from users about performance concerns.
Super-crazy idea, would it make sense to enable some R profiling
on the build system, and report what takes the most time ?
We
Hi,
On Wed, 2023-03-15 at 16:18 +, TYLER H WINTERMUTE via Bioc-devel
wrote:
> I�m encountering the following issue when loading mzR,
As Laurent mentioned, the warning below can safely be ignored,
this was an issue when Rcpp changed more rapidly.
> and my session immediately crashes.
If her
Hi,
On Tue, 2023-01-10 at 14:45 +, Kern, Lori wrote:
> It looks like the download got corrupted. I reset the cache for that
> EH number and it should clear up on the next build.
not knowing the EH infrastructure in detail,
are there file checksums which, on failure, should
trigger cache inv
Hi Sergio,
thanks for putting this together. I am not maintaining MSW, but we're
using it as dependency in xcms. I am optimistic it will be taken up at
some stage.
Yours,
Steffen
On Mon, 2022-03-21 at 12:11 +0100, Sergio Oller wrote:
> Dear Bioc-devel,
>
> I would like to submit two fixes
Hi,
mzR will soon get the long-awaited update of the embedded proteowizard
[1] as a nice christmas present. Part of that update is the removal of
the older Ramp Backend, which results in dropping the ability to read
the mass spectrometry file format mzDdata.
If there is anyone out there who need
Dear metaRbolomics enthusiasts,
We would like to invite you to the three-day face2face “3rd
de.NBI/ELIXIR-DE metaRbolomics Hackathon” taking place on 22.-
24.11.2021 at the venerable Leucorea in Lutherstadt Wittenberg.
The official program will start Monday 22.11. @ 10:00 (but it is
possible to
Hi,
On Fri, 2021-09-24 at 07:28 -0400, Martin Morgan wrote:
> Errors that are intermittent and platform-specific are often due to
> memory corruption, and can be investigated on Linux platforms with
> valgrind or similar tools. Have you taken this approach?
I am afraid that is beyond my skillset
Hi,
for several years xcms is suffering from absolutely spurious
issues on macOS.
There is no pattern regarding release/devel, R versions, different
macOS machines like merida1 in 2019, to machv2 today and a few
occurances inbetween. The tssue usually resolves itself after a few
days without any
ter: @rmflight
> > Web: rmflight.github.io <http://rmflight.github.io>
> > ORCID: http://orcid.org/-0001-8141-7788
> > EM rfligh...@gmail.com <mailto:rfligh...@gmail.com>
> > PH 502-509-1827
> >
> > To call in the statistician af
Hi,
Just wondering, is the 12854 the sum of unique IPs across 12 months ?
Could the 10905 be the number of unique IPs in that year ?
In the latter case, if I download a package every month, that would
count as one, while in the former as twelve. That might explain the
difference ?
Yours, Steffe
Dear all,
two ELIXIR All Hands keynotes turned into webinars:
Keynote I: Archaic genomics, Janet Kelso
26 May 2020, 11:00 CEST
Keynote II: Electric Butterflies - from field to bytes and back, Dimitris
Koureas,
5 June 2020, 11:00 CEST
participantion is open to
Hi,
this sounds very much like the bioconda approach,
they have self-archived / mirrored the packages,
which is not ideal.
The Bio.tools people also ran into that issue earlier,
and as mentioned in [1] is now fixed on the bioconductor side
with stable download links.
Yours,
Steffen
[1]
ht
Hi,
can you get me the URL that wants to be downloaded ?
The "tlsv1 alert protocol version" indicates that the proper
solution might be to notify the server to reconfigure
the web server supported TLS versions.
Yours,
Steffen
On Wed, 2020-03-18 at 19:55 +0100, Egon Willighagen wrote:
> Hi
//bioconductor.org/packages/3.11/bioc/html/atSNP.html. I updated
> both DESCRIPTION and graphic.R, but neither were updated.
>
>
> Best,
> Sunyoung
>
> > On Feb 17, 2020, at 1:38 AM, Neumann, Steffen <
> > sneum...@ipb-halle.de> wrote:
> >
> > Hi,
Hi,
please have a look at the build report first:
http://bioconductor.org/checkResults/devel/bioc-LATEST/atSNP/
where your commit 2020-02-12 has been picked up.
The check has an ERROR, most likely in the examples
to plotMotifMatch().
Also, I guess the version 1.3.0 was the version number
bum
Sounds like an incompatibility with your mailer,
maybe it tries to send the message as (signed / encrypted ?)
attachement, which are always automatically stripped by the listserver.
Try text only, or maybe use your webmailer ?
Yours,
Steffen
On Thu, 2020-02-06 at 23:54 +1100, Stefano Mangio
Hi,
I think there is quite some backlog from September
https://github.com/Bioconductor/Contributions/labels/1.%20awaiting%20moderation
Maybe the BioC team can use the momentum to assign more reviewers ?
Yours,
Steffen
On Tue, 2019-11-19 at 19:07 +, Turaga, Nitesh wrote:
> No problem at all
Hi,
that's not the git way to do it. Your previous commit is already
out in the open, if you git reset, that would be dangling in the air.
I really love this decision tree:
https://sethrobertson.github.io/GitFixUm/fixup.html
which in your case will get you probably to
https://sethrobertson.gi
Hi,
The package pages seem to have lost memory
when a package was introduced:
http://bioconductor.org/packages/3.7/bioc/html/xcms.html
http://bioconductor.org/packages/3.8/bioc/html/xcms.html
In Bioconductor since BioC 1.6 (R-2.1) or earlier (> 13.5 years)
but now it has reset to:
http://bi
Yours,
Steffen
>
> Maritn
>
> On 7/2/19, 10:52 AM, "Bioc-devel on behalf of Neumann, Steffen" <
> bioc-devel-boun...@r-project.org on behalf of sneum...@ipb-halle.de>
> wrote:
>
> Hi,
>
> last week over a beer some of us realized that (
Hi,
last week over a beer some of us realized that (technically)
it is possible to run most[1] Rmd vignettes as Jupiter Notebook.
So I created https://github.com/sneumann/bioc_notebooks
which takes some example packages and creates a Docker container
with converted vignettes. The resulting con
Hi,
On Sun, 2019-05-19 at 21:37 +, Patrick Casimir wrote:
> Where can I locate the best resources about Extending Bioconductor
> packages?
Can you be a bit more specific ? Do you want to extend your own package
with new functionality ? Or do you have some cool stuff,
that would fit well into
Hi,
thanks everyone for the input, I now have a few more leads to follow.
It would be great to have a general single package builder
even for existing packages to check if one has no direct access
to the failing architecture.
https://win-builder.r-project.org/ is discouraging BioC package upl
Hi,
with the next release coming up, I am out of wits regarding the failure at
http://bioconductor.org/checkResults/devel/bioc-LATEST/Rdisop/tokay2-buildbin.html
which exists since before April this year, when we committed
some changes to get rid of the RcppClassic dependency.
Max Helf succeede
the build and
> upload
> log files to an AWS bucket.
>
>
> You can see the details here:
>
> https://docs.travis-ci.com/user/uploading-artifacts/
>
>
> Best regards,
>
> Marcel
>
>
> On 3/4/19 2:34 PM, Neumann, Steffen wrote:
> > Hi,
Hi,
TL;DR: How can I get to see the *.log files for more information ?!
I am working on an upgrade of the C++ code in mzR,
which is challenging to build cross-platform,
so we use travis to check before pushing/breaking BioC.
The Travis config [1] is fairly simple, with main modification
that we
[Apologies for cross-posting]
Dear all,
We would like to invite to a CompMS metaRbolomics Hackathon
from Monday, April 1st to Wednesday April 3rd.
The official program will start Monday 01.04. @ 14:00 (but it is possible
to arrive already on Sunday). The closing is scheduled
for Wednesday 03
Hi,
we're seeing a problem with a S4Vectors::DataFrame
consisting of numbers and lists where write.table()
introduces "\n" linebreaks that render the written CSV
to be broken and unreadable.
The minimum example is:
library(S4Vectors)
l <- list(list(1), list(as.character(2:99)), list(3))
Hi,
On Fri, 2018-05-18 at 10:00 -0400, Martin Morgan wrote:
>
> > ...
> > i.e. a package from a given BioC release, or a specific version
> > of a package, regardless from which release it comes.
>
> I guess there are so many ways to shoot oneself in the foot that it
> is a wonder that we still
Hi,
On Wed, 2018-05-09 at 18:11 -0400, Martin Morgan wrote:
>
> ...
>- version() version of Bioconductor in use
>- valid() are all Bioconductor packages from the same
> Bioconductor
> version?
I'd like to challenge the concept of the release
and the pretty strong term valid(). I think
Hi,
we currently can easily check for broken packages using:
http://bioconductor.org/checkResults/devel/bioc-LATEST/index.html#show=timeout,error
It would be great to also subset the packages:
http://bioconductor.org/checkResults/devel/bioc-LATEST/index.html#package=mzR,MSnbase,xcms,CAMERA
to ea
Hi,
this is a Call for Help (CfH) to fix mzR. There has been a report
of a build failure on macOS. We're tracking this in
https://github.com/sneumann/mzR/issues/152 but were unable to reproduce
so far, it works on build machines and the macs we have access to.
The underlying issue is that for mz
Hi BioC team,
I have R W for several packages I am involved in,
but not for mtbls2 that I maintain. Please add W
for "s.neumann" for mtbls2 as well, or is there
any mistake on my side ?
Thanks in advance,
yours,
Steffen
R Wpackages/msdata
R packages/mtbls2
R Wpackages/mzR
'll test on mac and windows
>
> cheers, jo
>
> > On 7 Jan 2018, at 22:57, Neumann, Steffen
> > wrote:
> >
> > Hi,
> >
> > Following the bug report in
> > https://github.com/sneumann/mzR/issues/143
> >
> > there is a branch wi
dencies in Bioc.
>
> Martin
>
> On 01/03/2018 04:18 AM, Mike Smith wrote:
> > Rhdf5lib is in the release branch too. I'm happy to help try and
> > get mzR
> > working with it.
> >
> > On 2 January 2018 at 21:31, Martin Morgan > k.org>
Dear BioC team,
a happy new year to you as well ;-)
for a while we have a build error for mzR on windows
due to missing HDF5 libs:
https://github.com/sneumann/mzR/issues/143
I am looking for some hints how to fix this.
The https://bioconductor.org/packages/release/bioc/html/rhdf5.html
package ha
/orcid.org/-0001-8141-7788
> > EM rfligh...@gmail.com
> > PH 502-509-1827
> >
> > To call in the statistician after the experiment is done may be no
> > more than asking him to perform a post-mortem examination: he may
> > be able to say what the experiment died
://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/msdata/inst/cdf/ko15.CDF
(which still works, but is probably outdated)
So is there anything equivalent in the new git setup ?
Yours,
Steffen
On Fri, 2017-11-17 at 04:31 -0500, Martin Morgan wrote:
> On 11/17/2017 04:08 AM, Neumann, Steffen wr
Hi,
I would like to have a URL to individual files
we have in BioC packages. This is useful
e.g. if I need test data from, say, the msdata package,
in another context.
In the SVN days, I was able to point directly
into the SVN repo with readonly:readonly access.
We also had the (now deprecat
ich is 1000 secs before the timeout would kick in.
Not sure if upon the first compile after the fresh R installation
there is a cache built up by mingw somewhere, which would explain
why it is faster afterwards.
Yours,
Steffen
>
> Best,
> Kasper
>
> On Fri, Oct 13, 2017 at 4:2
Hi,
we've had binary compiles a while ago, but we were glad
when we could revert that to "normal" compilation a long time ago.
Another observation from years ago was that the linker step
was what took the longest, and even with a precompiled libpwiz.a
this took very long.
Thanks Herve for t
Indeed, is magically fixed today.
Thanks for the clarification.
Yours,
Steffen
On Fri, 2017-08-11 at 11:38 -0400, Martin Morgan wrote:
> On 08/10/2017 04:14 PM, Neumann, Steffen wrote:
> > Hi BioC,
> >
> > since that build error we have updated xcms to 2.99.6,
> >
converting the vignettes will fix the symptoms,
but we should really fix the cause of the error, for that
we need some more diagnostics, we weren't yet able to reproduce.
Any ideas ?
Yours,
Steffen
On Sun, 2017-07-30 at 19:42 +0000, Neumann, Steffen wrote:
> Hi,
>
> Hi,
>
>
Hi,
Hi,
any suggestions or better diagnostics that could help us
fixing this, in case it really is something in xcms ?
There were a few earlier reports with similar messages,
back in 2013, slightly hinting at virus scanners:
http://r.789695.n4.nabble.com/quot-Failed-to-locate-the-texi2pdf-
[1] http://developer.r-project.org/R_svnlog_2013
On Mi, 2017-04-12 at 22:07 -0400, Martin Morgan wrote:
> On 04/12/2017 11:31 AM, Neumann, Steffen wrote:
> >
> > Hi,
> >
> > certainly these are good suggestions, but I would tend
> > to simply add some whitelisti
ly, these issues should be dealt
> > with.
> > So perhaps there is nothing to do and I always have to click on
> > each build
> > report to verify that there is only 1 warning from this issues and
> > not
> > others.
> >
> > Best,
> > Kasper
&g
On So, 2017-04-02 at 10:01 -0400, Martin Morgan wrote:
>
> On 04/02/2017 06:52 AM, Neumann, Steffen wrote:
> >
> > [...]
> > in preparation for the release, we are hunting down WARNINGS
> > "Found ‘abort’, possibly from ‘abort’ (C)" in xcms/mzR.
> > The ab
Hi,
in preparation for the release, we are hunting down WARNINGS
"Found ‘abort’, possibly from ‘abort’ (C)" in xcms/mzR.
The abort() call is not coming from XCMS, but rather
from the C++ code in the STL, and we have no idea
how to get rid of it.
We are tracking this in: https://github.com/sneum
Hi,
sometimes I am forced to R CMD check packages on windows,
and my problem is that both the system-wide library and
the personal library with BiocStyle contain spaces, so that
BiocStyle::latex() results in:
\RequirePackage{C:/Program Files/R/R-3.1.0/library/BiocStyle/sty/Bioconductor}
which c
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