Re: [Bioc-devel] Deprecation Request for openPrimeRui

[Neumann, Steffen]

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:
> Dear BioC Team,
>
> I'd like to request deprecation of the openPrimeRui package. The
> Shiny
> App no longer works properly since one of its dependencies, ShinyBS,
> is
> no longer working as expected.
>
> Best wishes,
>
> Matthias
>
> P.S. Of course, if another maintainer could be found to adjust the
> Shiny
> App, this would be even better.
>
> ___
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Re: [Bioc-devel] Diverging version numbering on Bioconductor RELEASE

[Neumann, Steffen]

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,
>
> recently I have realized that the version number in one of my
> packages does
> not match with the version in the bioconductor repository (
> https://github.com/Genentech/midasHLA/issues/27
> ). The reason is that, while
> I have been doing no changes past the last few releases a version
> bump was
> happening on each Bioconductor RELEASE.
>
> Does anyone use some automated way to synchronise between the
> repositories?
> GitHub Actions would be an ideal solution.
>
> Cheers Maciek
>
> [[alternative HTML version deleted]]
>
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Re: [Bioc-devel] Urgent minor deployment of a release?

[Neumann, Steffen]

... 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 to release branch sources must be limited to bug fixes or doc
> improvement.  Any new features
> must be introduced only in the devel branch.  Any features to be
> removed
> must be indicated as
> deprecated for one release and then labeled as defunct.  See
>
> http://contributions.bioconductor.org/deprecation.html
>
> for guidance on feature removal.
>
>
> On Mon, Jun 19, 2023 at 10:11 AM Park, Adam Keebum
> 
> wrote:
>
> > Hi all,
> >
> > I wonder if there is any room for deploying a modification to a
> > released
> > library(retrofit, 3.17), which was released last month.
> >
> > We are in a progress of a paper review, so the release schedule
> > (twice
> > each year) does not perfectly fit our need.
> >
> > Or do you think we should have used "devel" for such purposes?
> >
> > Sincerely,
> > Adam.
> >
> > [[alternative HTML version deleted]]
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>

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Re: [Bioc-devel] Participating in the development of Bioconductor

[Neumann, Steffen]

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 already do so for the tests (total time per test iirc),
and it probably won't make sense in the daily builds,
but maybe similar to (or including) the longtests builds
around the weekends ?

I never did propoer profiling, so I am way out of my comfort zone
here...

Yours,
Steffen


> We would like to do more profiling and instrumentation of key
> worksteps to help
> increase throughput and ensure available compute resources are used.
> In
> the cuda/gpu
> space we don't have anything touching
>
> https://github.com/NVIDIA-Genomics-Research/rapids-single-cell-examples
>
> as far as I know and it would be interesting if you would have a look
> at
> this and see whether
> the is a clear path to some development integrating these approaches.
>
> You might want to join our community slack for more interaction.
> slack.bioconductor.org
>
> Best regards
> Vince Carey
>
> On Wed, May 3, 2023 at 12:12 PM Franck RICHARD
> 
> wrote:
>
> > Hello community!
> >
> > I am the author of several software programs including this
> > astronomy
> > program:
> > https://winstars.net/en
> >  I recently had the opportunity to
> > participate in the activities of a neuroscience laboratory in
> > Madrid. I
> > learned how to use Bioconductor and I would like to participate in
> > the
> > development of new features (if possible). The researchers in the
> > lab
> > complain about the slowness of these tools when used on simple PCs.
> > So I
> > wonder if it would not be interesting to integrate Cuda in some
> > indexing
> > packages, I think of Bowtie2 or Salmon for example... (there is a
> > version of bowtie2 that works with cuda, but it seems old). But the
> > task
> > would be very complex I guess. There are simpler things to do, like
> > creating a wrapper for Salmon or something like that. What do you
> > think
> > would be useful to do at this moment for Bioconductor users?
> >
> > With my thanks,
> >
> > Franck
> >
> > [[alternative HTML version deleted]]
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>

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Re: [Bioc-devel] mzR crashing R session

[Neumann, Steffen]

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 here you mean Segfault or other nasty surprises terminating the
session, we need more information. Also, we've seen cases of different
behaviour between rstudio sessions and bare commandline R sessions. 

Yours,
Steffen


>  I�ve followed the instructions at the GitHub wiki link, but am
> continuing to have issues. The final instruction was to send an email
> to the mailing list, which I�m doing now. Do you have any suggestions
> on fixing this issue?
> 
> Loading required package: Rcpp
> Warning: mzR has been built against a different Rcpp version (1.0.9)
> than is installed on your system (1.0.10). This might lead to errors
> when loading mzR. If you encounter such issues, please send a report,
> including the output of sessionInfo() to the Bioc support forum at
> https://eur04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsupport.bioconductor.org%2F=05%7C01%7C%7C4d0b033f73e74f5f48e508db25713752%7C0934ee6c2a574efd80a9fc003defef4e%7C0%7C0%7C638144940408962856%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=Lemgo5U%2FjGB4n53AqPvvNWr%2FOKscaLJX7lC8SknpBWU%3D=0
> . For details see also
> https://eur04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fsneumann%2FmzR%2Fwiki%2FmzR-Rcpp-compiler-linker-issue=05%7C01%7C%7C4d0b033f73e74f5f48e508db25713752%7C0934ee6c2a574efd80a9fc003defef4e%7C0%7C0%7C638144940408962856%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=8U4UvB9QrG%2FyU0uMqjCTmpGjNsZnQ%2B962a4yrgRVD5Y%3D=0
> .
> 
> 
> Best,
> 
> Tyler
> 
> 
> [[alternative HTML version deleted]]
> 
> ___
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Re: [Bioc-devel] ExperimentHub: bad restore file magic number (file may be corrupted)

[Neumann, Steffen]

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 invalidation and (one) re-download attempt ? 

Yours,
Steffen



> 
> 
> 
> 
> Lori Shepherd - Kern
> 
> Bioconductor Core Team
> 
> Roswell Park Comprehensive Cancer Center
> 
> Department of Biostatistics & Bioinformatics
> 
> Elm & Carlton Streets
> 
> Buffalo, New York 14263
> 
> 
> From: Bioc-devel  on behalf of
> Michael Love 
> Sent: Tuesday, January 10, 2023 9:40 AM
> To: bioc-devel 
> Subject: [Bioc-devel] ExperimentHub: bad restore file magic number
> (file may be corrupted)
> 
> In the latest release, one of my files in ExperimentHub is giving the
> following error on Bioc machines. I haven't touched these files since
> they were submitted many years ago to EHub.
> 
> https://eur04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fsecure-web.cisco.com%2F12y5s79xt-pmTPP6fzsYkMo0aALvDKgR-cUjxZcIL7QocYem0ml4eV-pkh4oqQlVq8ZteIbXcu42Ee2A76ClYhjiLHejdzRpRUWm2tCUEwNc6KBS1AiYDSfsOBC3dQ5mK3b3HgrhfvfXRVwW9TNr64PoANtPMDKwcwCG6aYF-RqHQHmvHDx5W2NluvaWlSV8u3wLL4iE0yfBocZDajrHg02fNfdqKkIbJF_iMnVNrLL950twq0FdVn9plKReI2-Eb1eI4a4OxMYO82sikXLqQmnE3w6f5KD--82FtxHaPjkXqyQSvQbRXLuH3ZBS2ussl%2Fhttp%253A%252F%252Fbioconductor.org%252FcheckResults%252Frelease%252Fdata-experiment-LATEST%252FalpineData%252Fnebbiolo2-buildsrc.html=05%7C01%7C%7C7126a52586d641eff7c808daf31a6b71%7C0934ee6c2a574efd80a9fc003defef4e%7C0%7C0%7C638089592201758765%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000%7C%7C%7C=zf7IQJCqSGuWRhkvqO7FebkQZz%2FhLkFkZl96HTxjanA%3D=0
> 
> ...
> --- re-building �alpineData.Rmd� using knitr
> Quitting from lines 18-22 (alpineData.Rmd)
> Error: processing vignette 'alpineData.Rmd' failed with diagnostics:
> failed to load resource
>   name: EH167
>   title: ERR188088
>   reason: error in evaluating the argument 'x' in selecting a method
> for function 'get': bad restore file magic number (file may be
> corrupted) -- no data loaded
> --- failed re-building �alpineData.Rmd�
> 
> On my machine I can load this resource:
> 
>  > library(alpineData)
> !> ERR188088()
>  snapshotDate(): 2022-10-31
>  see ?alpineData and browseVignettes('alpineData') for documentation
>  loading from cache
>  GAlignmentPairs object with 28576 pairs, strandMode=1, and 0
> metadata columns:
>    seqnames strand   :  ranges  -- 
> ranges
>        :     --  
> 
>    [1]    1  -   : 108565979-108566053  -- 108565846-
> 108565920
>    [2]    1  -   : 108573341-108573415  -- 108573234-
> 108573308
>    [3]    1  +   : 108581087-108581161  -- 108581239-
> 108581313
>    [4]    1  +   : 108601105-108601179  -- 108601196-
> 108601270
>    [5]    1  -   : 108603628-108603701  -- 108603540-
> 108603614
>    ...  ...    ... ... ...
> ... ...
>    [28572]    X  -   : 119791266-119791340  -- 119791130-
> 119791204
>    [28573]    X  -   : 119791431-119791505  -- 119791358-
> 119791432
>    [28574]    X  -   : 119791593-119791667  -- 119786691-
> 119789940
>    [28575]    X  -   : 119791629-119791703  -- 119789951-
> 119791587
>    [28576]    X  -   : 119791637-119791711  -- 119789976-
> 119791612
>    ---
>    seqinfo: 194 sequences from an unspecified genome
> 
> > eh <- ExperimentHub()
> 
> !> eh[["EH167"]]
>  see ?alpineData and browseVignettes('alpineData') for documentation
>  loading from cache
>  GAlignmentPairs object with 28576 pairs, strandMode=1, and 0
> metadata columns:
>    seqnames strand   :  ranges  -- 
> ranges
>        :     --  
> 
>    [1]    1  -   : 108565979-108566053  -- 108565846-
> 108565920
>    [2]    1  -   : 108573341-108573415  -- 108573234-
> 108573308
>    [3]    1  +   : 108581087-108581161  -- 108581239-
> 108581313
>    [4]    1  +   : 108601105-108601179  -- 108601196-
> 108601270
>    [5]    1  -   : 108603628-108603701  -- 108603540-
> 108603614
>    ...  ...    ... ... ...
> ... ...
>    [28572]    X  -   : 119791266-119791340  -- 119791130-
> 119791204
>    [28573]    X  -   : 119791431-119791505  -- 119791358-
> 119791432
>    [28574]    X  -   : 119791593-119791667  -- 119786691-
> 119789940
>    [28575]    X  -   : 119791629-119791703  -- 119789951-
> 119791587
>    [28576]    X  -   : 119791637-119791711  -- 119789976-
> 119791612
>    ---
>    seqinfo: 194 sequences from an unspecified genome
> 
> !> sessionInfo()
>  R version 4.2.2 

Re: [Bioc-devel] Bugfix to MassSpecWavelet

[Neumann, Steffen]

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 to the MassSpecWavelet package. I
> tried contacting the maintainer but he/she was not replying after
> some
> weeks. I am not sure if I may have fallen into a spam folder.
> 
> I hope that either some Bioconductor maintainer may pull the fixes
> and
> apply them or the original package maintainer may see this and commit
> them.
> 
> The fixes consist of (1) fixing a warning triggered when the argument
> "wavelet" of cwt() is given as a matrix (and it is compared to a
> scalar string inside an if() ) and (2) using length.out=  in the
> seq()
> call instead of length= to avoid partial matching.
> 
> They could both be applied to the current release and the development
> one.
> 
> The diff of the changes is available here for your convenience:
> https://eur04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fzeehio%2FMassSpecWavelet%2Fpull%2F1%2Ffilesdata=04%7C01%7C%7Ce21b95a347cc4d8f962908da0ca9580a%7C0934ee6c2a574efd80a9fc003defef4e%7C0%7C0%7C637836219271127401%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000sdata=XoAyQ2n8GEIFsZFXBHSQeMAhLHerGjfoBO%2FYS357sds%3Dreserved=0
> 
> And it is available for you to pull in the fix-cwt-seq branch from
> the
> git repository: 
> https://eur04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fzeehio%2FMassSpecWavelet.gitdata=04%7C01%7C%7Ce21b95a347cc4d8f962908da0ca9580a%7C0934ee6c2a574efd80a9fc003defef4e%7C0%7C0%7C637836219271127401%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000sdata=p8jeWDfWybqsk80v69TuFy4g%2Bwmh8J%2Ba4otSVy8dAQ4%3Dreserved=0
> 
> If there is any other (better) procedure for me to follow to get this
> merged, my apologies. I will be happy to adapt and proceed as
> indicated. The documentation regarding git in bioconductor I read
> assumed I was committing to my own repository, and not trying to
> contribute to someone else's.
> 
> Thanks in advance,
> Sergio
> 
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[Bioc-devel] mzR will drop mzData file format support

[Neumann, Steffen]

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 needs mzData for some production
pipeline, please speak up now. It would be possible to port the old
mzData support on top the new proteowizard, but we will not be able 
to do that (I tried, and grew a fair amount of new grey hair). I can do
a bit of hand-holding on the steps that would be required. 

Conversion of mzData to mzML is possible with the OpenMS FileConverter
tool [2].

mzR will continue to support mzML, netCDF and mzXML.

We will accirdingly change mzData files in the msdata package to mzML. 

Yours,
Steffen

[1] https://github.com/sneumann/mzR/tree/feature/updatePwiz_3_0_21263
[2] 
https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_FileConverter.html

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[Bioc-devel] 3rd de.NBI/ELIXIR-DE metaRbolomics Hackathon 22.-24.11.2021 @ Wittenberg, Germany

[Neumann, Steffen]

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 arrive already on Sunday). The closing is scheduled for
Wednesday 24.11. @ 14:00, but we can stay in the seminar rooms longer
(in case some heavy hacking does not allow an interruption).

Aim of the workshop is to improve the interoperability of packages used
in metabolomics (e.g. using common data structures and interfaces),
combine efforts (use single implementation of common functions), create
and demonstrate complex workflows by integrating existing tools,
identify gaps in the metaRbolomics ecosystem that need to be covered.
We will also have enough discussion time to ponder challenges of the
future, taking metaRbolomics into the next decade.

Please apply until 11.10.2021 (next monday) at 
https://events.ipb-halle.de/event/95/ for attendance and accommodation.
In case the workshop is oversubscribed, we’ll make a very subjective
decision in October based on your application and which overall
participant composition could advance metaRbolomics best. You can
forward this mail to someone you consider very important for this
hackathon.

Looking forward to see you, 
yours, 
The 3rd de.NBI/ELIXIR-DE metaRbolomics Hackathon team

-- 

Upcoming events:
* Registration open: 22.-24.11.2021 3rd metaRbolomics Hackathon,
Wittenberg (Germany)
  
https://www.denbi.de/training/1177-3rd-de-nbi-elixir-de-metarbolomics-hackathon

---
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Weinberg 3   Tel. +49 (0) 345 5582 - 1470
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Re: [Bioc-devel] Spurious "dims [product 864] do not match the length of object [432]" on macOS

[Neumann, Steffen]

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 :-(

Yours,
Steffen


-- 

Upcoming events:
* Save-the-date: 22.-24.11.2021 3rd metaRbolomics Hackathon, Wittenberg
(Germany)
  
https://www.denbi.de/training/1177-3rd-de-nbi-elixir-de-metarbolomics-hackathon

---
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Dr. Steffen Neumann  http://www.IPB-Halle.DE
Weinberg 3   Tel. +49 (0) 345 5582 - 1470
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[Bioc-devel] Spurious "dims [product 864] do not match the length of object [432]" on macOS

[Neumann, Steffen]

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 code change. 

Interestingly, 864=432*2, so something is duplicated somewhere. Also,
today was the first time I saw BiocParallel mentioned near the error,
see below. 

=> Has anyone observed such a domension mismatch, maybe in other
packages, and has any idea what could be the (spurious) cause ?

Yours,
Steffen
 

Quitting from lines 149-152 (xcms-lcms-ms.Rmd) 
Error: processing vignette 'xcms-lcms-ms.Rmd' failed with diagnostics:
BiocParallel errors
  element index: 1
  first error: BiocParallel errors
  element index: 1
  first error: dims [product 864] do not match the length of object
[432]






https://github.com/sneumann/xcms/issues/422


-- 

Upcoming events:
* Save-the-date: 22.-24.11.2021 3rd metaRbolomics Hackathon, Wittenberg
(Germany)
  
https://www.denbi.de/training/1177-3rd-de-nbi-elixir-de-metarbolomics-hackathon

---
IPB HalleBioinformatics and Scientific Data
Dr. Steffen Neumann  http://www.IPB-Halle.DE
Weinberg 3   Tel. +49 (0) 345 5582 - 1470
06120 Halle   +49 (0) 345 5582 - 0
sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409
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Re: [Bioc-devel] Do we have an unpacked archive for BioC, so that we can URL link to individual files ?

[Neumann, Steffen]

Hi,

this is a follow-up to a rather old thread, but with 
Mike Smith's (twitter: @grimbough) 

https://code.bioconductor.org/

We now have exactly what I had been looking for. 
Thanks Mike and BioC team !

Yours,
Steffen

On Mon, 2017-11-20 at 17:07 -0500, Martin Morgan wrote:
> On 11/20/2017 04:58 PM, Robert M. Flight wrote:
> > So, what if there was a MetaBioconductor site and repo similar to
> > the 
> > MetaCRAN project? https://www.r-pkg.org/about
> > 
> > Not sure exactly who maintains it (probably someone at RStudio),
> > but it 
> > is largely automatic I believe, and it provides a full GitHub
> > archive of 
> > *all* the packages on CRAN, which if this were done for
> > Bioconductor 
> > would satisfy what I think Steffen is looking for, as well as lots
> > of 
> > other advantages.
> > 
> > It also has the advantage that it looks like 90% of the work would
> > be 
> > done for Bioconductor with likely very little work required for
> > the 
> > Bioconductor Admins (ideally 100% of work would be done for them).
> 
> there has been some discussion of that, e.g.,
> 
>
> https://stat.ethz.ch/pipermail/bioc-devel/2017-September/011455.html
> 
> but we will not do it (maintain a github mirror), for instance
> because 
> some experiment data packages have commits that would require lfs, 
> because of issues with reliably  syncing data, and because of
> confusion 
> it introduces on the 'official' repository.
> 
> We do intend to provide a browsable interface to the official 
> git.bioconductor.org that would allow Steffen's use case during the 
> present release cycle; it is not currently available.
> 
> A different solution would be to update the relevant ExperimentData 
> package to use ExperimentHub (see, e.g., 
> https://github.com/LTLA/TENxBrainData for a relatively simple
> example, 
> though not yet in Bioconductor) and the resource would then be
> available 
> at a URL https://annotationhub.bioconductor.org/fetch/...
> 
> Martin
> 
> > Just a thought.
> > 
> > -Robert
> > 
> > Robert M Flight, PhD
> > Bioinformatics Research Associate
> > Puller of Rabbits from Hats
> > Research Parasite
> > Resource Center for Stable Isotope Resolved Metabolomics
> > Manager, Systems Biology and Omics Integration Journal Club
> > Markey Cancer Center
> > CC434 Roach Building
> > University of Kentucky
> > Lexington, KY
> > 
> > Twitter: @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 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 of. - Ronald Fisher
> > 
> > On Mon, Nov 20, 2017 at 8:51 AM Martin Morgan 
> >  > martin.mor...@roswellpark.org>> 
> > wrote:
> > 
> > On 11/19/2017 06:11 PM, Neumann, Steffen wrote:
> >  > Hi,
> >  >
> >  > thanks for the answer, unfortunately
> >  > not exactly what I meant. To be more precise:
> >  >
> >  > I want to point Galaxy to download (test) MS data files
> >  > from either the faahKO package, or msdata or mtbls2 in BioC.
> >  >
> >  > For that I need an ftp/http/https link to the files,
> >  > and I was able to use
> >  >
> >  >
> > 
> > https://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 ?
> > 
> > no, not from git.bioconductor.org <http://git.bioconductor.org>
> > ;.
> > 
> > Martin
> > 
> >  >
> >  > Yours,
> >  > Steffen
> >  >
> >  >
> >  > On Fri, 2017-11-17 at 04:31 -0500, Martin Morgan wrote:
> >  >> On 11/17/2017 04:08 AM, Neumann, Steffen wrote:
> >  >>> 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 a

Re: [Bioc-devel] Sum up function in the stats pages

[Neumann, Steffen]

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, Steffen


On Wed, 2021-01-13 at 13:30 +, Bonatesta, Enrico via Bioc-devel
wrote:
> Dear bioconductor team,
> 
> I am writing to you, because I want to inform you, that the sum up
> function in the stats pages of Bioconductor didn't work the way it
> should.
> I recognized it after looking at my former package "msa" and I was
> wondering, why the sum isn't higher or nearly 12000, when you reach
> 1000 different IPs nearly all months.
> That's why I double checked it and if you look at the attached .Jpg,
> the overall number of distinct IP addresses should be 12854, not
> 10905 (if I am doing my math right).
> It's not a big issue, but if you can fix it easily, you should do it
> :)
> Btw: You're doing a nice job with Bioconductor, thumbs up!
> 
> Greetings,
> Enrico Bonatesta
> -
> Enrico Bonatesta
> 
> BWI GmbH
> Innovation & Technology (I)
> Architecture. & Portfolio (AP)
> IT Architecture Management Team Blue
> Karl-Legienstr. 188/192
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[Bioc-devel] ELIXIR All Hands Keynotes by Janet Kelso & Dimitris Koureas as webinars

[Neumann, Steffen]

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 all, see below. 

Yours, 
Steffen


 Forwarded Message 
From: John Hancock (ELIXIR) 
Subject: [Metabolomics] Fwd: [HDCs] ELIXIR All Hands Keynote talks
 
registration
Date: Fri, 22 May 2020 17:59:41 +0100

> Dear all, 
> 
> Please note that two of our planned All Hands keynote talks have been
> turned into webinars, the first of which is taking place already next
> week! To join the webinars you need to register separately - you will
> receive an email with information on how to join the webinar
> immediately after you register.
>  
> 26 May 2020, 11:00 CEST,Keynote I: Archaic genomics, Janet Kelso, Max
> Planck Institute for Evolutionary Anthropology, Germany
> Register at: 
> https://attendee.gotowebinar.com/register/8392966286897847823
> 
> 5 June 2020, 11:00 CEST, Keynote II: Electric Butterflies - from
> field to bytes and back, Dimitris Koureas, Naturalis Biodiversity
> Center, the Netherlands
> Register at: 
> https://attendee.gotowebinar.com/register/3862528680204923663 
> 
> These webinars are open to anyone (not just to ELIXIR members),
> please share the registration links to anyone who might be
> interested.
> 
> All the best,
> 
> John
> 
> 
>   
> Dr. John Hancock
> ELIXIR Communities and Services Coordinator
> www.elixir-europe.org
> 
> ELIXIR Hub, South Building
> Wellcome Genome Campus
> Hinxton, Cambridge, CB10 1SD, UK
> Tel: +44 (0) 1223 492594
> E-Mail: john.hanc...@elixir-europe.org
> 
> Please note that I am now working part-time (50%). 
> You’re more likely to get a quick response from me Monday-Wednesday.
> 
> 
>  
> 
> 
-- 

Current bits of interest:

* ISMB 2020 is going virtual! July 13-16 
  https://www.iscb.org/ismb2020 including a metaRbolomics talk!

* Annual symposium of German Society for Metabolomics e.V. (DGMet)
  in Berlin 4.-5th November. https://www.mdc-berlin.de/dgmet-2020


---
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You are on this mailing list because you registered to join an ELIXIR group, 
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'child' group then you automatically become a member of the 'parent' group, and 
its mailing list. For example, if you joined the Bioschemas group, then you 
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TO UNSUBSCRIBE: please email webmas...@elixir-europe.org. Put "metabolomics" as 
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To view the groups you belong to, log in to the ELIXIR intranet: 
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Re: [Bioc-devel] How can I maintain a stable list of source urls

[Neumann, Steffen]

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] 
https://github.com/bio-tools/biotoolsRegistry/issues/425#issuecomment-557270484 


On Tue, 2020-03-31 at 12:27 -0700, Tim Sears wrote:
> Hi
> I am working to make bioconductor packages available through the nix
> package manager (https://nixos.org/). Currently nixpkgs points to a
> source
> url on one of the bioconductor mirrors. nixpkgs tracks the url and a
> sha256
> hash of the unpacked source link. Unfortunately the links themselves
> often
> disappear as the packages get updated either due to a version number
> change
> or changes inside the repo that affect the hash output. This breaks
> corresponding nix package. This happens even for stable bioconductor
> versions like 3.10. nixpkgs aims for reproducible builds, which means
> when
> things change, the url should reflect the change too and the contents
> behich old urls should be preserved long enough to manage
> the  change. Do
> you have any suggestions short of rebuilding a bioconductor mirror
> with
> immutable urls?
> 
> Thanks,
> TIm
> 
>   [[alternative HTML version deleted]]
> 
> ___
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Current bits of interest:


* PSI Spring Meeting Online, 23.-25.03.2020, 
  http://www.psidev.info/hupo-psi-meeting-2020

* Annual symposium of German Society for Metabolomics e.V. (DGMet)
  in Berlin 4.-5th November. https://www.mdc-berlin.de/dgmet-2020


---
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Re: [Bioc-devel] help with Win10 TLS problem?

[Neumann, Steffen]

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 all,
> 
> in the BridgeDbR package I have a TSL issue, just on Windows10 [0]:
> 
> > location <- getDatabase("Bacillus subtilis")
> 
> Error in function (type, msg, asError = TRUE)  :
>   error:1407742E:SSL routines:SSL23_GET_SERVER_HELLO:tlsv1 alert
> protocol version
> Calls: getDatabase ... getBridgeNames -> curlPerform -> 
> -> fun
> Execution halted
> 
> This method is using the download.file() method (see [1]). I am not
> sure
> what this method uses by default. I have been googling and found a
> number
> of suggestions on how to get RCurl to use other SSL version, such as:
> 
> CURL_SSLVERSION_TLSv1_2 <- 1Lopts <- RCurl::curlOptions(  verbose =
> TRUE, sslversion = CURL_SSLVERSION_TLSv1_2)download.file(url, file,
> mode = "wb", .opts=opts)
> 
> 
> But I haven't found something that works. Error messages are very
> cryptic,
> and I'm running out of ideas.
> 
> Does someone have a suggestion how to debug this? Maybe even have a
> solution?
> 
> All feedback is very much appreciated!
> 
> Egon
> 
> 
> 
> 0.
> 
https://bioconductor.org/checkResults/release/bioc-LATEST/BridgeDbR/tokay1-checksrc.html
> 1.
> https://github.com/bridgedb/BridgeDbR/blob/master/R/getDatabase.R#L23
> 
> 
> 
-- 

Current bits of interest:

* Computational Metabolomics PhD Position @ IPB
  
https://www.ipb-halle.de/en/career/job-vacancies/joboffer-detail/wissenschaftlichen-mitarbeiterin-doktorandin-bioinformatikmetabolomics-mwd/
 

* PSI Spring Meeting Online, 23.-25.03.2020, 
  http://www.psidev.info/hupo-psi-meeting-2020

* Annual symposium of German Society for Metabolomics e.V. (DGMet)
  in Berlin 4.-5th November. https://www.mdc-berlin.de/dgmet-2020


---
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Weinberg 3   Tel. +49 (0) 345 5582 - 1470
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Re: [Bioc-devel] "git push upstream master" does not work

[Neumann, Steffen]

Hi,

the source package on 3.11/bioc/html/atSNP.html 
will only be updated with a new one if all checks succeed. 
This prevents that you download a broken package. 

Nowadays one would call that a continuous integration pipeline,
but the BioC team already does that since, um, more than a decade ;-)

Yours,
Steffen


On Mon, 2020-02-17 at 07:44 +, Shin, Sunyoung wrote:
> Hello Steffen,
> 
> Thank you for the response. You are right, and I also recognized it.
> However, I don’t see the updates from the source package I downloaded
> from the package webpage at 
> http://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,
> > 
> > please have a look at the build report first:
> > 
https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fbioconductor.org%2FcheckResults%2Fdevel%2Fbioc-LATEST%2FatSNP%2Fdata=02%7C01%7CSunyoung.Shin%40utdallas.edu%7C5f2f92f942374791fab308d7b37c5b94%7C8d281d1d9c4d4bf7b16e032d15de9f6c%7C0%7C1%7C637175219027370173sdata=ygVFK7QyLbTTmaq3%2B54W5%2Fg7CL2w0YBMdJf4ZgHImCw%3Dreserved=0
> > 
> > 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 
> > bumped after the last BioC release, so consider 
> > to bump atSNP to 1.3.1 with you next commit. 
> > 
> > Hope that helped, 
> > 
> > Yours,
> > Steffen
> > 
> > 
> > On Mon, 2020-02-17 at 05:10 +, Shin, Sunyoung wrote:
> > > Dear all,
> > > 
> > > I used "git push upstream master” to commit changes for atSNP
> > > package
> > > to Bioconductor 4 days ago. But, Bioconductor does not take the
> > > updated version, but sticks with the old version of the package,
> > > which I committed in October. Does someone have an idea about how
> > > to
> > > fix it? Thanks.
> > > 
> > > 
> > > Best,
> > > Sunyoung
> > > ___
> > > Bioc-devel@r-project.org mailing list
> > > 
https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-develdata=02%7C01%7CSunyoung.Shin%40utdallas.edu%7C5f2f92f942374791fab308d7b37c5b94%7C8d281d1d9c4d4bf7b16e032d15de9f6c%7C0%7C1%7C637175219027370173sdata=nB10%2BrZJCkXf5CWqHXyQxqaQgIUvP4%2FnkRhLzAwiLnE%3Dreserved=0
> >  -- 
> > 
> > Current bits of interest:
> > 
> > * Computational Metabolomics PhD Position @ IPB
> > 
> > 
https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.ipb-halle.de%2Fen%2Fcareer%2Fjob-vacancies%2Fjoboffer-detail%2Fwissenschaftlichen-mitarbeiterin-doktorandin-bioinformatikmetabolomics-mwd%2Fdata=02%7C01%7CSunyoung.Shin%40utdallas.edu%7C5f2f92f942374791fab308d7b37c5b94%7C8d281d1d9c4d4bf7b16e032d15de9f6c%7C0%7C1%7C637175219027370173sdata=5ukkqm7owpb0KVwgtS8loZvZ7WmuLKmgfwzgrkihVb0%3Dreserved=0
> > 
> > 
> > * Leibniz Plant Biochemistry Symposium, 14./15.05.2020, Halle
> >  
> > https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fevents.ipb-halle.de%2Fevent%2F60%2Fdata=02%7C01%7CSunyoung.Shin%40utdallas.edu%7C5f2f92f942374791fab308d7b37c5b94%7C8d281d1d9c4d4bf7b16e032d15de9f6c%7C0%7C1%7C637175219027370173sdata=%2Bjxec3fj9e%2F%2Fd7CvOueC%2FAWZ%2BGYiRC7Xpx9%2FSanT5P4%3Dreserved=0
> > 
> > * HUPO PSI spring meeting, 23.-25.03.2020, San Diego, CA
> >  
> > https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.psidev.info%2Fhupo-psi-meeting-2020data=02%7C01%7CSunyoung.Shin%40utdallas.edu%7C5f2f92f942374791fab308d7b37c5b94%7C8d281d1d9c4d4bf7b16e032d15de9f6c%7C0%7C1%7C637175219027370173sdata=cAjXisCXzOCA9z%2FUXbSi%2F2Oz83vC6fEMlRL6WBH1uTQ%3Dreserved=0
> > 
> > ---
> > IPB HalleAG Massenspektrometrie & Bioinformatik
> > Dr. Steffen Neumann  
> > https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.IPB-Halle.DEdata=02%7C01%7CSunyoung.Shin%40utdallas.edu%7C5f2f92f942374791fab308d7b37c5b94%7C8d281d1d9c4d4bf7b16e032d15de9f6c%7C0%7C1%7C637175219027370173sdata=3jUg1A%2B3n8KpUR%2FBJEwQVQ%2FRcjf6KU4Ilm2kQUl3XP0%3Dreserved=0
> > Weinberg 3   Tel. +49 (0) 345 5582 - 1470
> > 06120 Halle   +49 (0) 345 5582 - 0
> > sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409
> 
> 
-- 

Current bits of interest:

* Computational Metabolomics PhD Position @ IPB
  
https://www.ipb-halle.de/e

Re: [Bioc-devel] "git push upstream master" does not work

[Neumann, Steffen]

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 
bumped after the last BioC release, so consider 
to bump atSNP to 1.3.1 with you next commit. 

Hope that helped, 

Yours,
Steffen


On Mon, 2020-02-17 at 05:10 +, Shin, Sunyoung wrote:
> Dear all,
> 
> I used "git push upstream master” to commit changes for atSNP package
> to Bioconductor 4 days ago. But, Bioconductor does not take the
> updated version, but sticks with the old version of the package,
> which I committed in October. Does someone have an idea about how to
> fix it? Thanks.
> 
> 
> Best,
> Sunyoung
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
-- 

Current bits of interest:

* Computational Metabolomics PhD Position @ IPB
  
https://www.ipb-halle.de/en/career/job-vacancies/joboffer-detail/wissenschaftlichen-mitarbeiterin-doktorandin-bioinformatikmetabolomics-mwd/
 

* Leibniz Plant Biochemistry Symposium, 14./15.05.2020, Halle
  https://events.ipb-halle.de/event/60/

* HUPO PSI spring meeting, 23.-25.03.2020, San Diego, CA
  http://www.psidev.info/hupo-psi-meeting-2020

---
IPB HalleAG Massenspektrometrie & Bioinformatik
Dr. Steffen Neumann  http://www.IPB-Halle.DE
Weinberg 3   Tel. +49 (0) 345 5582 - 1470
06120 Halle   +49 (0) 345 5582 - 0
sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409
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Re: [Bioc-devel] Compatibility of S4 and tidyverse

[Neumann, Steffen]

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 Mangiola wrote:
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
-- 

Current bits of interest:

* Computational Metabolomics PhD Position @ IPB
  
https://www.ipb-halle.de/en/career/job-vacancies/joboffer-detail/wissenschaftlichen-mitarbeiterin-doktorandin-bioinformatikmetabolomics-mwd/
 

* Leibniz Plant Biochemistry Symposium, 14./15.05.2020, Halle
  https://events.ipb-halle.de/event/60/

* HUPO PSI spring meeting, 23.-25.03.2020, San Diego, CA
  http://www.psidev.info/hupo-psi-meeting-2020

---
IPB HalleAG Massenspektrometrie & Bioinformatik
Dr. Steffen Neumann  http://www.IPB-Halle.DE
Weinberg 3   Tel. +49 (0) 345 5582 - 1470
06120 Halle   +49 (0) 345 5582 - 0
sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409

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Re: [Bioc-devel] New package submission : No reviewer communication.

[Neumann, Steffen]

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! 
> 
> We are happy to help. If you have further questions feel free to ask.
> 
> Best,
> 
> Nitesh 
> 
> On 11/19/19, 1:58 PM, "Kumar, Ashwath"  wrote:
> 
> Hi Nitesh,
> 
> Thanks a lot for the quick reply and clearing up the process.  I
> completely understand that the process is tedious and takes a lot of
> time. I just wanted to clarify with people with previous experience
> submitting packages as this is my first time. 
> 
> Thanks,
> Ashwath 
> 
> -Original Message-
> From: Turaga, Nitesh  
> Sent: Tuesday, November 19, 2019 1:56 PM
> To: Kumar, Ashwath ; 
> bioc-devel@r-project.org
> Subject: Re: [Bioc-devel] New package submission : No reviewer
> communication.
> 
> Hi,
> 
> Please be patient in this regard. The reviewer will get to your
> package as soon as they can. Each package takes time to review, and
> each reviewer is reviewing multiple packages. 
> 
> As far as asking for support regarding your package, it is best
> to ask your questions on the "Issue" which was created for the
> package contribution.  If you have general Bioconductor questions,
> the support site can help you as well, support.bioconductor.org. If
> you are unsure, bioc-devel mailing list is the right place. 
> 
> Best,
> 
> Nitesh 
> 
> On 11/19/19, 1:47 PM, "Bioc-devel on behalf of Kumar, Ashwath" <
> bioc-devel-boun...@r-project.org on behalf of ashku...@gatech.edu>
> wrote:
> 
> Hello all,
> 
> I recently submitted a package to Bioconductor and I have not
> heard back from the reviewer about any feedback or acceptance or
> otherwise. The package has indeed passed all the automated tests and
> is awaiting the revision on the next stage of review process. Is
> there a recommended period of time I wait before requesting help in
> this regard and if so, how do I go about requesting support. Thanks a
> lot !
> 
> Thanks,
> Ashwath
> 
> 
>   [[alternative HTML version deleted]]
> 
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> 
> 
> 
> 
> 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.
> 
> 
> 
> 
> 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.
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
-- 

Current bits of interest:

* Advances in Plant and Food Metabolomics 
  10./11. and 12.12.2019 Workshop & Symposium
  
https://www.wur.nl/en/activity/Advances-in-Plant-and-Food-Metabolomics-workshop.htm

* European RFMF-Metabomeeting 2020
  Toulouse, France, January 22-24 2020
  https://rfmf-mpf-2020.sciencesconf.org

* HUPO PSI spring meeting, 23.-25.03.2020, San Diego, CA
  Watch out: http://www.psidev.info/events

---
IPB HalleAG Massenspektrometrie & Bioinformatik
Dr. Steffen Neumann  http://www.IPB-Halle.DE
Weinberg 3   Tel. +49 (0) 345 5582 - 1470
06120 Halle   +49 (0) 345 5582 - 0
sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409
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Re: [Bioc-devel] Reset to a previous commit

[Neumann, Steffen]

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.github.io/GitFixUm/fixup.html#pushed_new_simple

and "create an positive commit to remove the effects 
of a simple (non-merge) commit".

Hope that helped, 
yours,
Steffen


On Tue, 2019-09-10 at 09:42 +0200, Simon Dirmeier wrote:
> Hi all,
> following our previous TensorFlow discussion, I am trying to reset to
> a
> previous commit and get rid of the TF changes in the
> meantime.Resetting
> back to the last working commit [1] that doesn't use TF gives me this
> error though:
> 
> $ git reset --hard 4e267949562a0b38b16495892c4ef4c0dcf7b6f3
> 
> 
> $ git push -f upstream master
> 
> $ remote: Error: Illegal version bump from '1.9.2' to '1.9.0'. Check
> $ remote: 
> http://bioconductor.org/developers/how-to/version-numbering/
> $ remote: for details
> $ To git.bioconductor.org:packages/netReg.git
> $  ! [remote rejected] master -> master (pre-receive hook declined)
> $ error: failed to push some refs to
> 'g...@git.bioconductor.org:packages/netReg.git'
> 
> Trying to circumvent this by incrementing to '1.9.3' doesn't do the
> trick either. Does anyone have any ideas how I could fix this issue?
> 
> Many thanks in advance again.
> 
> Best,
> Simon
> 
> [1]
> 
http://bioconductor.org/developers/how-to/git/abandon-changes/#reset-to-a-previous-commit
> 
> 
> 
> On 05.09.19 15:35, Martin Morgan wrote:
> > I'm with Simon on the value of using TensorFlow here, and it's too
> > bad the build system is unable to support more flexible use of
> > python (there are additional challenges, for instance inter-
> > operability between packages each depending on & starting their own
> > python interpreter...)
> > 
> > It seems like the keras model
> > 
> > https://github.com/rstudio/keras
> > https://keras.rstudio.com/
> > 
> > is reasonable -- providing an `install_keras()` and related
> > convenience functions, but writing the package so that it does not
> > depend on an available python for build & check. Obviously not
> > checking the TensorFlow interface on a daily basis compromises the
> > robustness of the software, and hopefully the build system will be
> > able to provide a more robust testing environment in the future.
> > 
> > Martin
> > 
> > On 9/5/19, 9:10 AM, "Bioc-devel on behalf of Kasper Daniel Hansen"
> >  > kasperdanielhan...@gmail.com> wrote:
> > 
> >  It might be true that the code is much easier on your end, but
> > it comes
> >  with the complexity of using TensorFlow, which is a huge
> > dependency. And
> >  that library can be easy or impossible to install depending on
> > your box.  I
> >  am not saying people shouldn't use TensorFlow, but I am saying
> > it brings a
> >  lot of complexities with it.
> > 
> >  And (trying to) installing TensorFlow as part of .onLoad seems
> > ... not the
> >  right way to deal with this.
> > 
> >  On Thu, Sep 5, 2019 at 6:27 AM Simon Dirmeier <
> > simon.dirme...@web.de> wrote:
> > 
> >  >
> >  > Hi Herve,
> >  >
> >  > > All this means that if you replace some old C++ code with
> > TensorFlow
> >  > > then we will need to mark your package as unavailable on
> > Windows and
> >  > > Mac, at least for now. Sorry. I wonder if there was
> > something wrong
> >  > > with this old C++ code. I would recommend that you stick
> > to it if you
> >  > can.
> >  > >
> >  > The code is fine, but still an impractical complexity that
> > doesn't need
> >  > to exist:
> >  >
> >  > 1) It's hard to extend and read for others.
> >  >
> >  > 2) It needs a custom configure.ac.
> >  >
> >  > 3) Extending the package to other models/families is a huge
> > pain, as one
> >  > needs to derive custom coordinate descents (or other
> > optimizers for that
> >  > matter) for each.
> >  >
> >  > On the other side:
> >  >
> >  > 1) TF allowed me to replace like 5000 lines of source code
> > with 100
> >  > lines of R.
> >  >
> >  > 2) TF allows to easily extend with other models with just a
> > few lines.
> >  >
> >  > 3) I don't need a huge test suite.
> >  >
> >  > 4) On GPUs it's a huge speedup.
> >  >
> >  > So, I'll revert the changes back on Bioc devel for now and
> > continue
> >  > development on another branch.
> >  >
> >  > Cheers,
> >  >
> >  > Simon
> >  >
> >  >
> >  > Am 04.09.19 um 16:53 schrieb Pages, Herve:
> >  > >
> >  > > Hi Simon,
> >  > >
> >  > > On 9/3/19 09:11, Simon Dirmeier wrote:
> >  > >> ...
> >  > >> Do you think it would be possible to install TensorFlow
> > and
> >  > >> TensorFlow-Probability on the builders? I'd assume that
> > many would
> >  > >> 

[Bioc-devel] "In Bioconductor since" date wrong

[Neumann, Steffen]

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://bioconductor.org/packages/3.9/bioc/html/xcms.html
http://bioconductor.org/packages/3.10/bioc/html/xcms.html
http://bioconductor.org/packages/devel/bioc/html/xcms.html
In Bioconductor since   BioC 3.9 (R-3.6) (< 6 months)

Not that it really matters, but in case you revisit 
how these pages are generated at some stage ...

Yours,
Steffen

-- 

Current bits of interest:

* NFDI4Chem needs your insights! 
  See https://doi.org/10.1002/anie.201907260 in Angewandte Chemie (Intl. Ed.)
  and the survey https://www.soscisurvey.de/NFDI4Chem/

* European RFMF-Metabomeeting 2020
  Toulouse, France, January 22-24 2020
  https://rfmf-mpf-2020.sciencesconf.org

---
IPB HalleAG Massenspektrometrie & Bioinformatik
Dr. Steffen Neumann  http://www.IPB-Halle.DE
Weinberg 3   Tel. +49 (0) 345 5582 - 1470
06120 Halle   +49 (0) 345 5582 - 0
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Re: [Bioc-devel] Using BioC vignettes as Jupyter Notebooks

[Neumann, Steffen]

Hi,

On Tue, 2019-07-02 at 09:50 +, Martin Morgan wrote:
> Do you think this approach could be re-cast in the same way that 
> https://github.com/Bioconductor/bioconductor_full has done, so that
> the container has all the software to _support_ the packages needed
> for the jupyter notebook, but that the user must do some kind of
> initialization to install the R libraries? In this way there would be
> one container instead of 1750, and it would not be heavy?

Hm, the Jupyter can not "talk" to the container that is hosting it, 
so this would have to be done upon startup. 

> One idea that we've been exploring is making _binary_ versions of
> Bioc packages available that are compatible with bioconductor_full,
> so that package installation would sometimes be much faster (a simple
> download, rather than compilation).

I like that idea to some extend. In particular, 
it'll help not having to carry the BUILD dependencies 
in the container as we currently have in e.g. release_metabolomics2.

A less known feature of Docker is to have two FROM in one Dockerfile, 
e
.g. https://github.com/ProteoWizard/container/blob/master/Dockerfile
where the second FROM can COPY from the above-built container, 
thus dropping any cruft. 

But how would the binary packages then be imported into 
the container ? The volumes work fine on the command line. 
What about a kubernetes cluster ? 

I'd like to suggest to avoid any dependency on the 
filesystem of the host, i.e. no 
-v host-site-library:/usr/local/lib/R/host-site-library

An established way to mount stuff into a container (like bioc-full)
is to use sidecar containers. Basically they share some of their 
filesystem with the "main" container (typical example: 
tomcat main container, sidecar with only the *.war file).

A challenge is duplication. If each binary with required /site-lib/content 
carries Biobase, we'd have 1750 copies of that. This would be solved if we can 
mount 
the required subset (=dependencies) of the 1750 binaries into site/lib/PACKAGE

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 (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 container 
> can be hosted locally, or on the binder system (see README).
> 
> We found this to be fun, and it could be used 
> as a great training resource. Only downside is 
> that the resulting containers are not exactly light-weight.
> 
> Yours,
> Steffen
> 
> [1] See the issue in the repo where it fails. 
> 
> -- 
> 
> IPB HalleAG Massenspektrometrie &
> Bioinformatik
> Dr. Steffen Neumann  http://www.IPB-Halle.DE
> Weinberg 3   Tel. +49 (0) 345 5582 - 1470
> 06120 Halle   +49 (0) 345 5582 - 0
> sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> 
-- 

IPB HalleAG Massenspektrometrie & Bioinformatik
Dr. Steffen Neumann  http://www.IPB-Halle.DE
Weinberg 3   Tel. +49 (0) 345 5582 - 1470
06120 Halle   +49 (0) 345 5582 - 0
sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409
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[Bioc-devel] Using BioC vignettes as Jupyter Notebooks

[Neumann, Steffen]

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 container 
can be hosted locally, or on the binder system (see README).

We found this to be fun, and it could be used 
as a great training resource. Only downside is 
that the resulting containers are not exactly light-weight.

Yours,
Steffen

[1] See the issue in the repo where it fails. 

-- 

IPB HalleAG Massenspektrometrie & Bioinformatik
Dr. Steffen Neumann  http://www.IPB-Halle.DE
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Re: [Bioc-devel] Documentation on Extending BioC Packages

[Neumann, Steffen]

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 somebody else's package ? 

Or do you want to do something useful, and think that this 
would be done best by extending someone's package, 
essentially looking for documentation and mentoring ? 

Yours,
Steffen

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Re: [Bioc-devel] Help needed: Rdisop on Windows "File format not recognized"

[Neumann, Steffen]

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 upload,
and might have a different build environment. 

Let's see if we get a working Rdisop for easter. 
A nice weekend everyone, 
yours,
Steffen
 

On Thu, 2019-04-18 at 13:25 +, Martin Morgan wrote:
> I second the idea of reproducing with the Windows build commands,
> which have to do more than 'just' build for a particular
> architecture. One might test the hypothesis that it is staged install
> that is causing the problem with 
> 
>   StagedInstalll: no
> 
> in the DESCRIPTION file.
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[Bioc-devel] Help needed: Rdisop on Windows "File format not recognized"

[Neumann, Steffen]

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 succeeded to build locally on windows without problem. 

So it seems that Rdisop has issues with the BioC windows build
environment, but I totally fail to see the reason. 

Could it be the new staged installation ? 
But I wouldn't know why that'd affect the compile/linking. 

The issue is tracked at 
https://github.com/sneumann/Rdisop/issues/13

Any help/pointers appreciated. 

Yours,
Steffen

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Re: [Bioc-devel] mzR update in the making: any Travis experts ?

[Neumann, Steffen]

Thanks, 

that got me on track. 

Yours, 
Steffen

On Mon, 2019-03-04 at 19:55 +, Ramos Perez, Marcel wrote:
> Hi Steffen,
> 
> I haven't played with it yet but Travis CI has an Artifacts addon
> that
> will trigger
> in the `after_script` or `after_failure` stages of 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,
> > 
> > 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 increase the timeouts. 
> > 
> > Issue is, the builds in [2] e.g. don't give me enough information
> > why the build fails. Build is OK:
> > 
> >   Still running (9 of 40): R CMD build .
> >   The command R CMD build . exited with 0.
> > 
> > but check fails:
> > 
> >   Still running (1 of 40): R CMD check --no-build-vignettes --no-
> > vignettes mzR_2.17.1.tar.gz
> >   The command R CMD check --no-build-vignettes --no-vignettes
> > mzR_2.17.1.tar.gz exited with 1.
> > 
> > and logs are not informative enough:
> > 
> >   * checking whether package ‘mzR’ can be installed ... ERROR
> > Installation failed.
> > See ‘/home/travis/build/sneumann/mzR/mzR.Rcheck/00install.out’
> > for
> > details.
> >   * DONE
> > Status: 1 ERROR, 2 NOTEs
> > See ‘/home/travis/build/sneumann/mzR/mzR.Rcheck/00check.log’
> > for
> > details.
> > 
> > => How can I get to see the *.log files for more information ?!
> > 
> > Thanks in advance, 
> > Yours,
> > Steffen
> > 
> > 
> > [1] 
> > 
https://github.com/sneumann/mzR/blob/feature/updatePwiz20190301/.travis.yml#L22
> > [2] https://travis-ci.org/sneumann/mzR/branches
> > [3] https://travis-ci.org/sneumann/mzR/builds/501622960
> > 
> > 
> 
> 
> 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
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[Bioc-devel] mzR update in the making: any Travis experts ?

[Neumann, Steffen]

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 increase the timeouts. 

Issue is, the builds in [2] e.g. don't give me enough information
why the build fails. Build is OK:

  Still running (9 of 40): R CMD build .
  The command R CMD build . exited with 0.

but check fails:

  Still running (1 of 40): R CMD check --no-build-vignettes --no-
vignettes mzR_2.17.1.tar.gz
  The command R CMD check --no-build-vignettes --no-vignettes
mzR_2.17.1.tar.gz exited with 1.

and logs are not informative enough:

  * checking whether package ‘mzR’ can be installed ... ERROR
Installation failed.
See ‘/home/travis/build/sneumann/mzR/mzR.Rcheck/00install.out’ for
details.
  * DONE
Status: 1 ERROR, 2 NOTEs
See ‘/home/travis/build/sneumann/mzR/mzR.Rcheck/00check.log’ for
details.

=> How can I get to see the *.log files for more information ?!

Thanks in advance, 
Yours,
Steffen


[1] 
https://github.com/sneumann/mzR/blob/feature/updatePwiz20190301/.travis.yml#L22
[2] https://travis-ci.org/sneumann/mzR/branches
[3] https://travis-ci.org/sneumann/mzR/builds/501622960


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[Bioc-devel] Invitation: 01.-03.04.2019 de.NBI CompMS metaRbolomics Hackathon

[Neumann, Steffen]

[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 03.04. @ 14:00, but we can stay in the seminar rooms longer 
(in case some heavy hacking does not allow an interruption).

Aim of the workshop is to improve the interoperability of packages 
for metabolomics (e.g. using common data structures and interfaces), 
combine efforts (use single implementation of common functions), 
create and demonstrate complex workflows by integrating existing tools, 
identify gaps in the metaRbolomics ecosystem that need to be covered. 
We will also have enough discussion time to ponder challenges of the future, 
taking metaRbolomics into the next decade. 

Please register at https://goo.gl/forms/tNmVonsMVR6cEMZn2 for attendance 
and accommodation. In case the workshop is oversubscribed, we’ll make 
a very subjective decision in December based on which overall participant 
composition 
could advance metaRbolomics best. You can forward this mail to someone 
you consider very important for this hackathon. There is also the announcement 
at https://www.denbi.de/training/466-de-nbi-compms-metarbolomics-hackathon.

For information on travel and accommodation, please see https://goo.gl/Xn7CG3.
Looking forward to see you next year, 

yours, 
The CompMS metaRbolomics Hackathon team

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[Bioc-devel] write.table() of DataFrame introduces \n linebreaks in CSV output

[Neumann, Steffen]

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))
  m <- matrix(1:9, nrow=3, ncol=3)
  df <- cbind(DataFrame(m), DataFrame(do.call(rbind, l)))
  write.table(df)

This results in

  V1" "V2" "V3" "V1.1"
  "1" 1 4 7 1
  "2" 2 5 8 c("2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", 
"14", "15", "16", "17", "18", "19", "20", "21", "22", "23", "24", "25", "26", 
"27", "28", "29", "30", "31", "32", "33", "34", "35", "36", "37", "38", "39", 
"40", "41", "42", "43", "44", "45", "46", "47", "48", "49", "50", "51", "52", 
"53", "54", "55", "56", "57", "58", "59", "60", "61", "62", "63", "64", "65", 
"66", "67", "68", "69", "70", "71", "72", "73", "74", "75", "76", "77", "78", 
"79", "80", "81", "82", "83", "84", "85", "86", 
=>"87", "88", "89", "90", "91", "92", "93", "94", "95", "96", "97", "98", "99")
  "3" 3 6 9 3

where the second row is line-wrapped after the "86",
and the next line starts with "87" and the rest of the second row. 
What we also observe is that as.character() of the offending cell 
indeed contains a "\n" at an unexpected place:

  > as.character(df[2,4])
  [1] "c(\"2\", [...], \"85\", \"86\", \n\"87\", \"88\", [...], \"99\")"

This happens for both R-devel 2018-10-17 and S4Vectors_0.19.22
as well as R-3.4.4 with S4Vectors_0.16.0
It affects us in 
https://github.com/workflow4metabolomics/xcms/issues/116#issuecomment-432684024

Any ideas ?

Yours, 
Steffen


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06120 Halle  Tel. +49 (0) 345 5582 - 1470
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Re: [Bioc-devel] BiocInstaller: next generation

[Neumann, Steffen]

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 have feet! I'm with Jim on this one...

Alright then, looking forward 
to the new BiocManager package.

Yours,
Steffen



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06120 Halle  Tel. +49 (0) 345 5582 - 1470
  +49 (0) 345 5582 - 0
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Re: [Bioc-devel] BiocInstaller: next generation

[Neumann, Steffen]

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 BioC 
is the only R package repository that has the release concept,
and this is good to have a consistent well tested environment 
of packages for a given R version. It is also great to pick 
the most recent package version within a release for installation,
but that also prevents installing a package newer than 
the one tied to the R version at hand. 

But R already has the concept of versioned dependencies,
so in theory we wouldn't /need/ the release concept. 

I'd like to suggest to make it easier to shoot yourself 
into the foot by installing less tested combinations 
of R and BioC packages, and to support installing

BiocManager::install(X, version=0.8.15)
BiocManager::install(X, release=3.8)
BiocManager::install(X, release=devel) 

i.e. a package from a given BioC release, or a specific version 
of a package, regardless from which release it comes.
The valid() is a bit unspecific name, what is probably meant here 
is BiocManager::tainted(), which indicates that packages come 
from different BioC versions, and all hell might break loose 
and it'll eat your kittens.

This also means that Package developers would ask for the tainted() 
status in bug reports, and (c|sh)ould refuse help for unsupported 
combination. It also means that packagers would have to be more careful
with the versioned dependencies, and supply minimal versions. 
If they give a versioned dependency on the Biobase, 
they essentially forbid installing on old BioC releases, 
which would be fine. 

Just my 2c, 

Yours,
Steffen

-- 

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[Bioc-devel] Subsetting Multiple platform build/check report

[Neumann, Steffen]

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 easily show the status of packages I am interested in.

Yours,
Steffen

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[Bioc-devel] CfH: mzR 2.13.5 on macOS duplicated symbols from HDF5

[Neumann, Steffen]

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 mz5 support in mzR 
we need to link to Rhdf5lib, but we also need to link 
to system netCDF libs.

Any help appreciated. 

Yours,
Steffen

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  +49 (0) 345 5582 - 0
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[Bioc-devel] need git push permission for mtbls2

[Neumann, Steffen]

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

sneumann@msbi-corei:/.../mtbls2$ git remote -v
origin  g...@github.com:sneumann/mtbls2.git (fetch)
origin  g...@github.com:sneumann/mtbls2.git (push)
upstreamg...@git.bioconductor.org:packages/mtbls2.git (fetch)
upstreamg...@git.bioconductor.org:packages/mtbls2.git (push)

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Re: [Bioc-devel] mzR build failure on Windows: missing HDF5 libraries

[Neumann, Steffen]

Hi, 

compiling and linking is fixed now on all architectures,
thanks to the Rhdf5lib team for fixing/changing Rhdf5lib 
to allow unmodified code to link against it, and to Juhannes 
for testing. 

Have a nice day,
yours,
Steffen



On Mon, 2018-01-08 at 05:21 +, Rainer Johannes wrote:
> I'll test on mac and windows
> 
> cheers, jo
> 
> > On 7 Jan 2018, at 22:57, Neumann, Steffen <sneum...@ipb-halle.de>
> > wrote:
> > 
> > Hi,
> > 
> > Following the bug report in 
> > https://github.com/sneumann/mzR/issues/143
> > 
> > there is a branch with a fix in 
> > https://github.com/sneumann/mzR/pull/144
> > 
> > that passes Travis in 
> > https://travis-ci.org/sneumann/mzR/builds/324960762
> > 
> > which we can merge once there is a bit more testing
> > on other platforms. Any takers ?
> > 
> > Yours,
> > Steffen
> > 
> > 
> > 
> > On Fri, 2018-01-05 at 10:55 -0500, Martin Morgan wrote:
> > > Would be great, Steffen, to update mzR to use Rhdf5lib. I believe
> > > CRAN 
> > > packages with mzR dependencies are also failing to build under
> > > devel,
> > > as 
> > > well as xcms and other mzR dependencies 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 <martin.morgan@roswel
> > > > lpar
> > > > k.org>
> > > > wrote:
> > > > 
> > > > > On 01/02/2018 03:16 PM, Neumann, Steffen wrote:
> > > > > 
> > > > > > 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/rhd
> > > > > > f5.h
> > > > > > tml
> > > > > > package has embedded rhdf5/src/libwin/x64/libhdf5ForBioC-
> > > > > > 7.dll
> > > > > > which we could try to use (It does not yet contain H5Cpp.h,
> > > > > > and we'd have to ask Bernd Fischer et al to include it.
> > > > > > 
> > > > > 
> > > > > Not a comprehensive answer or solution to release, but in
> > > > > devel
> > > > > there is
> > > > > Rhdf5lib which contains both the C and C++ headers. (I
> > > > > believe
> > > > > that rhdf5
> > > > > will move to using this library in the near future) Martin
> > > > > 
> > > > > 
> > > > > > ALternatively, it might already be present on the build
> > > > > > machines,
> > > > > > but we didn't have the include path set up:
> > > > > > https://github.com/r-hub/rhub/issues/91
> > > > > > "... the location of the hdf5 libraries is defined as
> > > > > > ${LIB_HDF5}/lib${R_ARCH}. "
> > > > > > 
> > > > > > So, any hints which way to go for a fix ?
> > > > > > 
> > > > > > Yours,
> > > > > > Steffen
> > > > > > 
> > > > > > 
> > > > > 
> > > > > This email message may contain legally privileged
> > > > > and/or...{{dropped:2}}
> > > > > 
> > > > > 
> > > > > ___
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> > > > > 
> > > > 
> > > > [[alternative HTML version deleted]]
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> > IPB HalleAG Massenspektrometrie & Bioinformatik
> > Dr. Steffen Neumann  http://www.IPB-Halle.DE
> > Weinberg 3   http://msbi.bic-gh.de
> > 06120 Halle  Tel. +49 (0) 345 5582 - 1470
> >  +49 (0) 345 5582 - 0
> > sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> 
> 
-- 

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Dr. Steffen Neumann  http://www.IPB-Halle.DE
Weinberg 3   http://msbi.bic-gh.de
06120 Halle  Tel. +49 (0) 345 5582 - 1470
  +49 (0) 345 5582 - 0
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Re: [Bioc-devel] mzR build failure on Windows: missing HDF5 libraries

[Neumann, Steffen]

Hi,

Following the bug report in 
https://github.com/sneumann/mzR/issues/143

there is a branch with a fix in 
https://github.com/sneumann/mzR/pull/144

that passes Travis in 
https://travis-ci.org/sneumann/mzR/builds/324960762

which we can merge once there is a bit more testing
on other platforms. Any takers ?

Yours,
Steffen



On Fri, 2018-01-05 at 10:55 -0500, Martin Morgan wrote:
> Would be great, Steffen, to update mzR to use Rhdf5lib. I believe
> CRAN 
> packages with mzR dependencies are also failing to build under devel,
> as 
> well as xcms and other mzR dependencies 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 <martin.morgan@roswellpar
> > k.org>
> > wrote:
> > 
> > > On 01/02/2018 03:16 PM, Neumann, Steffen wrote:
> > > 
> > > > 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.h
> > > > tml
> > > > package has embedded rhdf5/src/libwin/x64/libhdf5ForBioC-7.dll
> > > > which we could try to use (It does not yet contain H5Cpp.h,
> > > > and we'd have to ask Bernd Fischer et al to include it.
> > > > 
> > > 
> > > Not a comprehensive answer or solution to release, but in devel
> > > there is
> > > Rhdf5lib which contains both the C and C++ headers. (I believe
> > > that rhdf5
> > > will move to using this library in the near future) Martin
> > > 
> > > 
> > > > ALternatively, it might already be present on the build
> > > > machines,
> > > > but we didn't have the include path set up:
> > > > https://github.com/r-hub/rhub/issues/91
> > > > "... the location of the hdf5 libraries is defined as
> > > > ${LIB_HDF5}/lib${R_ARCH}. "
> > > > 
> > > > So, any hints which way to go for a fix ?
> > > > 
> > > > Yours,
> > > > Steffen
> > > > 
> > > > 
> > > 
> > > This email message may contain legally privileged
> > > and/or...{{dropped:2}}
> > > 
> > > 
> > > ___
> > > Bioc-devel@r-project.org mailing list
> > > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > > 
> > 
> > [[alternative HTML version deleted]]
> > 
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > 
> 
> 
> This email message may contain legally privileged
> and/or...{{dropped:2}}
> 
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Weinberg 3   http://msbi.bic-gh.de
06120 Halle  Tel. +49 (0) 345 5582 - 1470
  +49 (0) 345 5582 - 0
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[Bioc-devel] mzR build failure on Windows: missing HDF5 libraries

[Neumann, Steffen]

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 has embedded rhdf5/src/libwin/x64/libhdf5ForBioC-7.dll
which we could try to use (It does not yet contain H5Cpp.h,
and we'd have to ask Bernd Fischer et al to include it.

ALternatively, it might already be present on the build machines, 
but we didn't have the include path set up:
https://github.com/r-hub/rhub/issues/91
"... the location of the hdf5 libraries is defined as
${LIB_HDF5}/lib${R_ARCH}. "

So, any hints which way to go for a fix ?

Yours,
Steffen

-- 

IPB HalleAG Massenspektrometrie & Bioinformatik
Dr. Steffen Neumann  http://www.IPB-Halle.DE
Weinberg 3   http://msbi.bic-gh.de
06120 Halle  Tel. +49 (0) 345 5582 - 1470
  +49 (0) 345 5582 - 0
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Re: [Bioc-devel] Do we have an unpacked archive for BioC, so that we can URL link to individual files ?

[Neumann, Steffen]

Hi,

thanks for the answer, unfortunately 
not exactly what I meant. To be more precise:

I want to point Galaxy to download (test) MS data files 
from either the faahKO package, or msdata or mtbls2 in BioC.

For that I need an ftp/http/https link to the files,
and I was able to use 

https://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 wrote:
> > 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 deprecated) way to link to:
> > https://raw.githubusercontent.com/Bioconductor-mirror/xcms/master/D
> > ESCRIPTION
> > 
> > -> Is there anything comparable today ?
> 
> I think the git archive command might do the trick, but it requires
> ssh 
> (i.e., write) access to the repository
> 
> git archive --remote=g...@git.bioconductor.org:packages/xcms \
>   master DESCRIPTION | tar -xf -
> 
> 
> > 
> > It could be as simple as a directory tree
> > of a working copies of all https://git.bioconductor.org/
> > served by the apache (or whatever) web server,
> > or (a bit cooler) a gitweb or similar http interface.
> > 
> > Wouldn't that be a fantastic christmas present
> > for us users and developers :-) ?
> > 
> > Yours,
> > Steffen
> > 
> 
> 
> 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
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Weinberg 3   http://msbi.bic-gh.de
06120 Halle  Tel. +49 (0) 345 5582 - 1470
  +49 (0) 345 5582 - 0
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[Bioc-devel] Do we have an unpacked archive for BioC, so that we can URL link to individual files ?

[Neumann, Steffen]

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 deprecated) way to link to:
https://raw.githubusercontent.com/Bioconductor-mirror/xcms/master/DESCRIPTION

-> Is there anything comparable today ?

It could be as simple as a directory tree 
of a working copies of all https://git.bioconductor.org/
served by the apache (or whatever) web server,
or (a bit cooler) a gitweb or similar http interface. 

Wouldn't that be a fantastic christmas present 
for us users and developers :-) ?

Yours,
Steffen

-- 

IPB HalleAG Massenspektrometrie & Bioinformatik
Dr. Steffen Neumann  http://www.IPB-Halle.DE
Weinberg 3   http://msbi.bic-gh.de
06120 Halle  Tel. +49 (0) 345 5582 - 1470
  +49 (0) 345 5582 - 0
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Re: [Bioc-devel] EXTERNAL: Increase timeout for mzR on Windows?

[Neumann, Steffen]

Hi,

On Sat, 2017-10-14 at 14:04 -0400, Kasper Daniel Hansen wrote:
> I recognize that the code base is pretty complex (and that mass spec
> libraries are a mess at times), but could there be advantages to
> modularizing the code into more than 1 package, with a mzR master
> package. Could that help with linking etc?

Currently I can't think of a way here. Basically, mzR uses 
one top-level object from "msdata" proteowizard, and we only include
and compile the minimum of dependencies for msdata. 

And indeed, today mzR finished in 1475 seconds on Windows, 
which 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 4:24 PM, Neumann, Steffen <sneumann@ipb-halle
> .de> wrote:
> > 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 the observation about normal build times
> > vs. the "fresh R" case. This might show that, in general,
> > mzR does build in <40 minutes.
> > 
> > yours,
> > Steffen
> > 
> > On Wed, 2017-10-11 at 09:39 -0400, Martin Morgan wrote:
> > > On 10/11/2017 08:29 AM, Laurent Gatto wrote:
> > > >
> > > > On 11 October 2017 11:14, Rainer Johannes wrote:
> > > >
> > > > > Dear Martin,
> > > > >
> > > > > > On 11 Oct 2017, at 13:05, Martin Morgan <martin.morgan@rosw
> > ellp
> > > > > > ark.org> wrote:
> > > > > >
> > > > > > On 10/11/2017 03:48 AM, Rainer Johannes wrote:
> > > > > > > Hi,
> > > > > > > would it be possible to increase the allowed build and
> > check
> > > > > > > times for mzR on Windows? Building mzR takes very long
> > due to
> > > > > > > the compilation of the included proteowizard (and boost?)
> > > > > > > code so there is not much we can do to speed that up.
> > > > > >
> > > > > > what's the role of proteowizard in mzR? is it required in
> > its
> > > > > > entirety, or can it be more selectively included? I agree
> > that
> > > > > > mzR is often problematic because of the excessive
> > compilation
> > > > > > time.
> > > > > >
> > > > >
> > > > > mzR uses Rcpp modules to directly call/use the C++ code from
> > > > > proteowizard to read mzML, mzXML and other MS file formats.
> > > > > Regarding
> > > > > selective includes: I believe Steffen Neumann and Laurent
> > Gatto
> > > > > spent
> > > > > already a great deal of time to reduce the amount of code
> > that
> > > > > needs
> > > > > to be included for mzR to compile/work. I think there is not
> > much
> > > > > more
> > > > > that can be done here, unfortunately.
> > > >
> > > > Steffen (he should get the credit for this) has indeed tried to
> > be
> > > > as
> > > > selective as possible, yes. There might be more to be done, but
> > I
> > > > don't
> > > > think we could gain anything really substantial.
> > >
> > > probably we have been down this road before but is another option
> > to 
> > > pre-compile and distribute the Windows binaries?
> > >
> > > Martin
> > >
> > > >
> > > > Laurent
> > > >
> > > > > jo
> > > > >
> > > > > > Martin
> > > > > >
> > > > > > > On linux and macOS all is fine, but we get TIMEOUT errors
> > on
> > > > > > > a regular basis on Windows (I guess because it has to be
> > > > > > > compiled for i386 and x86_64). The problem is that a
> > failing
> > > > > > > mzR causes all packages depending on it (like MSnbase and
> > > > > > > xcms) to fail too.
> > > > > > > cheers, jo
> > > > > > > ___

Re: [Bioc-devel] Vignette for xcms fails to build on tokay1

[Neumann, Steffen]

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,
> > and have started to convert the xcmsDirect vignette to Rmd.
> > Now, we have the same kind of build error on the xcmsMsn vignette,
> > http://bioconductor.org/checkResults/devel/bioc-LATEST/xcms/tokay1-
> > buildsrc.html
> > 
> > I think that just 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 ?
> 
> This generally looks like a transient problem we see, maybe related
> to 
> disk latency associated with large files (e.g., plots) produced
> during 
> the vignette processing, but we really don't have a clear handle on
> this.
> 
> Martin
> 
> > 
> > Yours,
> > Steffen
> > 
> > 
> > On Sun, 2017-07-30 at 19:42 +, Neumann, Steffen wrote:
> > > 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-
> > > outp
> > > ut-file-quot-td4664111.html
> > > 
> > > Back in 2015, but both referring to SPB:
> > > https://github.com/Bioconductor/packagebuilder/issues/2
> > > https://github.com/Bioconductor/packagebuilder/issues/26
> > > 
> > > And from 2016 without any resolution:
> > > https://github.com/r-hub/rhub/issues/58
> > > 
> > > Yours,
> > > Steffen
> > > 
> > > 
> > > 
> > > On Thu, 2017-07-27 at 10:23 +, Rainer Johannes wrote:
> > > > Dear all,
> > > > 
> > > > one of the xcms vignettes fails to build on tokay1 recently
> > > > with
> > > > the
> > > > error message:
> > > > 
> > > > Warning: running command
> > > > '"C:\PROGRA˜1\MIKTEX˜1.9\miktex\bin\x64\texify.exe" --quiet --
> > > > pdf
> > > > "xcmsDirect.tex" --max-iterations=20 -I
> > > > "C:/Users/biocbuild/bbs-
> > > > 3.6-
> > > > bioc/R/share/texmf/tex/latex" -I "C:/Users/biocbuild/bbs-3.6-
> > > > bioc/R/share/texmf/bibtex/bst"' had status 1
> > > > Error in find_vignette_product(name, by = "texi2pdf", engine =
> > > > engine) :
> > > >    Failed to locate the 'texi2pdf' output file (by engine
> > > > 'utils::Sweave') for vignette with name 'xcmsDirect'. The
> > > > following
> > > > files exist in directory '.': 'FlowChart.graffle',
> > > > 'FlowChart.pdf',
> > > > 'benchmarking.Rmd-notrun', 'biomed-central.csl', 'example.tsv',
> > > > 'new_functionality.R', 'new_functionality.Rmd',
> > > > 'new_functionality.html', 'new_functionality.org',
> > > > 'references.bib',
> > > > 'xcms.bib', 'xcms.org<http://xcms.org>', 'xcmsDirect-005.pdf',
> > > > 'xcmsDirect.Rnw', 'xcmsDirect.tex', 'xcmsInstall.Rnw',
> > > > 'xcmsMSn.Rnw',
> > > > 'xcmsPreprocess.Rnw-notrun'
> > > > Calls:  -> find_vignette_product
> > > > Execution halted
> > > > 
> > > > is this some problem with tokay1 or is it related to the
> > > > vignette
> > > > (I
> > > > have no problems building this vignette in my Windows build
> > > > machine)?
> > > > 
> > > > thanks, jo
> > > > 
> > > > 
> > > > [[alternative HTML version deleted]]
> > > > 
> > > > ___
> > > > Bioc-devel@r-project.org mailing list
> > > > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > > 
> > > -- 
> > > 
> > > IPB HalleAG Massenspektrometrie &
> > > Bioinformatik
> > > Dr. Steffen Neumann  http://www.IPB-Halle.DE
> > > Weinberg 3   http://msbi.bic-gh.de
> > > 06120 Halle  Tel. +49 (0) 345 5582 - 1470
> > >   

Re: [Bioc-devel] Vignette for xcms fails to build on tokay1

[Neumann, Steffen]

Hi BioC, 

since that build error we have updated xcms to 2.99.6,
and have started to convert the xcmsDirect vignette to Rmd.
Now, we have the same kind of build error on the xcmsMsn vignette,
http://bioconductor.org/checkResults/devel/bioc-LATEST/xcms/tokay1-buildsrc.html

I think that just 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 +, Neumann, Steffen wrote:
> 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-outp
> ut-file-quot-td4664111.html
> 
> Back in 2015, but both referring to SPB:
> https://github.com/Bioconductor/packagebuilder/issues/2
> https://github.com/Bioconductor/packagebuilder/issues/26
> 
> And from 2016 without any resolution:
> https://github.com/r-hub/rhub/issues/58
> 
> Yours,
> Steffen
> 
> 
> 
> On Thu, 2017-07-27 at 10:23 +, Rainer Johannes wrote:
> > Dear all,
> > 
> > one of the xcms vignettes fails to build on tokay1 recently with
> > the
> > error message:
> > 
> > Warning: running command
> > '"C:\PROGRA˜1\MIKTEX˜1.9\miktex\bin\x64\texify.exe" --quiet --pdf
> > "xcmsDirect.tex" --max-iterations=20 -I "C:/Users/biocbuild/bbs-
> > 3.6-
> > bioc/R/share/texmf/tex/latex" -I "C:/Users/biocbuild/bbs-3.6-
> > bioc/R/share/texmf/bibtex/bst"' had status 1
> > Error in find_vignette_product(name, by = "texi2pdf", engine =
> > engine) :
> >   Failed to locate the 'texi2pdf' output file (by engine
> > 'utils::Sweave') for vignette with name 'xcmsDirect'. The following
> > files exist in directory '.': 'FlowChart.graffle', 'FlowChart.pdf',
> > 'benchmarking.Rmd-notrun', 'biomed-central.csl', 'example.tsv',
> > 'new_functionality.R', 'new_functionality.Rmd',
> > 'new_functionality.html', 'new_functionality.org',
> > 'references.bib',
> > 'xcms.bib', 'xcms.org<http://xcms.org>', 'xcmsDirect-005.pdf',
> > 'xcmsDirect.Rnw', 'xcmsDirect.tex', 'xcmsInstall.Rnw',
> > 'xcmsMSn.Rnw',
> > 'xcmsPreprocess.Rnw-notrun'
> > Calls:  -> find_vignette_product
> > Execution halted
> > 
> > is this some problem with tokay1 or is it related to the vignette
> > (I
> > have no problems building this vignette in my Windows build
> > machine)?
> > 
> > thanks, jo
> > 
> > 
> > [[alternative HTML version deleted]]
> > 
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> 
> -- 
> 
> IPB HalleAG Massenspektrometrie & Bioinformatik
> Dr. Steffen Neumann  http://www.IPB-Halle.DE
> Weinberg 3   http://msbi.bic-gh.de
> 06120 Halle  Tel. +49 (0) 345 5582 - 1470
>   +49 (0) 345 5582 - 0
> sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
-- 

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Weinberg 3   http://msbi.bic-gh.de
06120 Halle  Tel. +49 (0) 345 5582 - 1470
  +49 (0) 345 5582 - 0
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Re: [Bioc-devel] Vignette for xcms fails to build on tokay1

[Neumann, Steffen]

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-output-file-quot-td4664111.html

Back in 2015, but both referring to SPB:
https://github.com/Bioconductor/packagebuilder/issues/2
https://github.com/Bioconductor/packagebuilder/issues/26

And from 2016 without any resolution:
https://github.com/r-hub/rhub/issues/58

Yours,
Steffen



On Thu, 2017-07-27 at 10:23 +, Rainer Johannes wrote:
> Dear all,
> 
> one of the xcms vignettes fails to build on tokay1 recently with the
> error message:
> 
> Warning: running command
> '"C:\PROGRA˜1\MIKTEX˜1.9\miktex\bin\x64\texify.exe" --quiet --pdf
> "xcmsDirect.tex" --max-iterations=20 -I "C:/Users/biocbuild/bbs-3.6-
> bioc/R/share/texmf/tex/latex" -I "C:/Users/biocbuild/bbs-3.6-
> bioc/R/share/texmf/bibtex/bst"' had status 1
> Error in find_vignette_product(name, by = "texi2pdf", engine =
> engine) :
>   Failed to locate the 'texi2pdf' output file (by engine
> 'utils::Sweave') for vignette with name 'xcmsDirect'. The following
> files exist in directory '.': 'FlowChart.graffle', 'FlowChart.pdf',
> 'benchmarking.Rmd-notrun', 'biomed-central.csl', 'example.tsv',
> 'new_functionality.R', 'new_functionality.Rmd',
> 'new_functionality.html', 'new_functionality.org', 'references.bib',
> 'xcms.bib', 'xcms.org', 'xcmsDirect-005.pdf',
> 'xcmsDirect.Rnw', 'xcmsDirect.tex', 'xcmsInstall.Rnw', 'xcmsMSn.Rnw',
> 'xcmsPreprocess.Rnw-notrun'
> Calls:  -> find_vignette_product
> Execution halted
> 
> is this some problem with tokay1 or is it related to the vignette (I
> have no problems building this vignette in my Windows build machine)?
> 
> thanks, jo
> 
> 
>   [[alternative HTML version deleted]]
> 
> ___
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Dr. Steffen Neumann  http://www.IPB-Halle.DE
Weinberg 3   http://msbi.bic-gh.de
06120 Halle  Tel. +49 (0) 345 5582 - 1470
  +49 (0) 345 5582 - 0
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Re: [Bioc-devel] R CMD check without WARNING: g++ and STL issue for xcms and mzR

[Neumann, Steffen]

Hi,

just a quick report, I followed this up to r-devel,
and a fix adding -O2 back to default CXXFLAGS 
has been committed (r72549, see [1]) to R by Martyn Plummer, 
thus "fixing" the abort() related WARNING in mzR/xcms 
once this gets into the R version used on malbec2.

Yours,
Steffen

[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 whitelisting functionality if the
> > cause is beyond the package's control.
> > 
> > In this case I doubt it is a handler for SIGABRT,
> > since that would not go away with -O2, or would it ?
> > 
> > For now, just adding -O2 on Linux would fix this issue.
> The code is compiled on the user machine, so twiddling with the
> build 
> system masks the problem from the developer while leaving the user 
> vulnerable.
> 
> Calling abort() is certainly a serious problem, abruptly ending the
> user 
> session.
> 
> Optimization could either eliminate a dead code path, or it could 
> compile the call to abort in a way that R no longer recognizes it --
> R 
> is doing the equivalent of nm *.o |grep abort.
> 
> It would be appropriate to ignore the warning about abort() if it
> were 
> never reached; one would only know this by careful code analysis
> rather 
> than adjusting optimization flags.
> 
> Rsamtools re-defines abort (before including offending headers), and 
> avoids the warning (and crash), with the equivalent of
> 
>    PKG_CFLAGS=-D__builtin_abort=_samtools_abort
> 
> where _samtools_abort is my own implementation to signal an R error 
> telling the user that an unrecoverable error has occurred and they 
> should stop what they are doing. Unfortunately this requires 
> -U_FORTIFY_SOURCE and doesn't actually address the reason for the
> abort, 
> and is hardly ideal.
> 
> I don't think the developer can set the optimization flag in a way
> that 
> overrides the R or user setting (the PKG_CXXFLAGS is inserted before
> the 
> R flags). And it doesn't address the underlying problem anyway.
> 
> Kasper's pragmatic approach (it's a very unlikely situation, and 
> difficult to fix, so live with the warning) seems like it would often
> be 
> a reasonable one.
> 
> FWIW this little bit of C++ seems to be enough to include abort
> 
> tmp.cpp:
> ---
> #include 
> 
> int foo(int argc, const char *argv[]) {
>  std::list l1, l2;
>  std::list::iterator it;
> 
>  it = l1.begin();
>  l1.splice (it, l2); // mylist1: 1 10 20 30 2 3 4
> 
>  return 0;
> }
> ---
> 
> Test with
> 
>    rm -f tmp.o && R CMD SHLIB tmp.cpp && nm tmp.o | grep abort
> 
> with compiler settings in
> 
> ~/.R/Makevars
> -
> CXXFLAGS = -g -O0
> -
> 
> 
> Martin
> 
> > 
> > 
> > Yours,
> > Steffen
> > 
> > 
> > On Mi, 2017-04-12 at 10:07 -0400, Vincent Carey wrote:
> > > 
> > > 
> > > Suppose you had a handler for SIGABRT in your code.  Could CMD
> > > check
> > > check for that and, if found, refrain from warning?  That is
> > > somewhat
> > > involved and goes beyond Bioc but it seems a principled way of
> > > dealing with operations in binary infrastructure whose behavior
> > > we
> > > cannot control.  The problem will surely arise in other settings.
> > > Could BiocCheck prototype the approach?
> > > 
> > > On Wed, Apr 12, 2017 at 9:12 AM, Kasper Daniel Hansen
> > >  > > n...@gmail.com> wrote:
> > > > 
> > > > 
> > > > I think "we" have to appreciate that the warning about
> > > > abort/etc
> > > > and others
> > > > is really hard to deal with when you're including (large)
> > > > external
> > > > source
> > > > as you do in mzR and for example affxparser /
> > > > Rgraphviz.  Generally
> > > > fixing
> > > > those in external code requires a lot of effort, and the
> > > > further
> > > > effort to
> > > > document that the included sources in the package are different
> > > > from the
> > > > official sources.  I have had warnings about this in affxparser
> > > > for
> > > > a long,
> > > > long time and no-one has bothered me over it.
> > > > 
> > > > What might be nice is (somehow) setting a fl

[Rd] Default R-3.4.0 RC CXXFLAGS without -O2 on x86_64-linux-gnu with g++-5.4.0 causes WARNING from stl_list.h

[Neumann, Steffen]

Hi r-devel,

a recent install of R-3.4.0 RC (2017-04-13 r72510) 
on Linux (Ubuntu 16.04.1 LTS) x86_64-linux-gnu 
with g++ (Ubuntu 5.4.0-6ubuntu1~16.04.4) 5.4.0 20160609
(see 
http://bioconductor.org/checkResults/devel/bioc-LATEST/malbec2-NodeInfo.html 
for more) 
results in CXXFLAGS not containing "-O2" as optimisation flag,
there is only " -Wall", while CFLAGS are happy with "-g -O2
-Wall"

This has an influence in at least one place
https://stat.ethz.ch/pipermail/bioc-devel/2017-April/010733.html
where we have WARNINGS in R CMD check from "Found ‘abort’, 
possibly from ‘abort’ (C)" in packages xcms/mzR.
The abort() call is not coming from XCMS, but rather 
from the C++ code in the STL:

[...]
# 1770 "/usr/include/c++/5/bits/stl_list.h"
void _M_check_equal_allocators(list& __x) {
 if (_M_get_Node_allocator())
   __builtin_abort();
}

If we compile with -O2 optimisation, this getting rid of 
the abort() symbol, as shown 
in https://github.com/sneumann/xcms/issues/150#issuecomment-293545521

Martin Morgan created a minimum example that shows that 
the symbol is indeed deep down in the STL (see below and in:
https://stat.ethz.ch/pipermail/bioc-devel/2017-April/010837.html )

This raises several questions:

1) is there any way to avoid the WARNING / abort() inside 
   the STL list implementation ? Or just live with it ?

2) If not, is there a reason why the Bioconductor build farm 
   Ubuntu machine is not using -O2 as default CXXFLAG ?
   BioC admins are trying to have a vanilla R installation with defaults. 
   According to Herve Pages, CXXFLAGS without -O2 is default 
   since R-3.4 beta, but I don't know enough about the package 
   build logic to point to a particular R commit. 

3) I thought about cheating the system and add -O2 
   in the package CXXFLAGS, but Martin Morgan 
   recommends packages shouldn't mess and override system build defaults
   to mask and paper over the actual issue having a nasty abort() 
   lurking somewhere.
   But I couldn't add PKG_CXXFLAGS=-O2 in first place, since that 
   triggers the different WARNING that -O2 is not portable. 

=> Any help and input would be highly appreciated. 

Thanks in advance, 
yours,
Steffen


tmp.cpp by Martin Morgan (also in above linked mail thread)
---
#include 

int foo(int argc, const char *argv[]) {
 std::list l1, l2;
 std::list::iterator it;

 it = l1.begin();
 l1.splice (it, l2); // mylist1: 1 10 20 30 2 3 4

 return 0;
}
---

Test with

   rm -f tmp.o && R CMD SHLIB tmp.cpp && nm tmp.o | grep abort

with compiler settings in ~/.R/Makevars with/without -O2 
-
CXXFLAGS = -g -O0
-





--
IPB HalleAG Massenspektrometrie &
Bioinformatik
Dr. Steffen Neumann  http://www.IPB-Halle.DE
Weinberg 3                   Tel. +49 (0) 345 5582 - 1470
06120 Halle                       +49 (0) 345 5582 - 0           
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Re: [Bioc-devel] R CMD check without WARNING: g++ and STL issue for xcms and mzR

[Neumann, Steffen]

Hi,

certainly these are good suggestions, but I would tend 
to simply add some whitelisting functionality if the 
cause is beyond the package's control. 

In this case I doubt it is a handler for SIGABRT, 
since that would not go away with -O2, or would it ?

For now, just adding -O2 on Linux would fix this issue. 

Yours,
Steffen


On Mi, 2017-04-12 at 10:07 -0400, Vincent Carey wrote:
> 
> Suppose you had a handler for SIGABRT in your code.  Could CMD check
> check for that and, if found, refrain from warning?  That is somewhat
> involved and goes beyond Bioc but it seems a principled way of
> dealing with operations in binary infrastructure whose behavior we
> cannot control.  The problem will surely arise in other settings. 
> Could BiocCheck prototype the approach?
> 
> On Wed, Apr 12, 2017 at 9:12 AM, Kasper Daniel Hansen  n...@gmail.com> wrote:
> > 
> > I think "we" have to appreciate that the warning about abort/etc
> > and others
> > is really hard to deal with when you're including (large) external
> > source
> > as you do in mzR and for example affxparser / Rgraphviz.  Generally
> > fixing
> > those in external code requires a lot of effort, and the further
> > effort to
> > document that the included sources in the package are different
> > from the
> > official sources.  I have had warnings about this in affxparser for
> > a long,
> > long time and no-one has bothered me over it.
> > 
> > What might be nice is (somehow) setting a flag saying this should
> > be
> > ignored in the check process, but of course we don't want that flag
> > to be
> > set by the developer, because usually, 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
> > 
> > On Wed, Apr 12, 2017 at 7:22 AM, Neumann, Steffen <sneumann@ipb-hal
> > le.de>
> > wrote:
> > 
> > > 
> > > Hi Martin and malbec2 admin(s):
> > > 
> > > Some more digging revealed that malbec2
> > > http://bioconductor.org/checkResults/devel/bioc-
> > > LATEST/malbec2-NodeInfo.html
> > > is using "CFLAGS=-g -O2 -Wall" but only "CXXFLAGS=-Wall"
> > > while e.g. tokay2 uses "CXXFLAGS=-O2 -Wall -mtune=core2"
> > > 
> > > The -O2 optimisation is getting rid of the abort() symbol,
> > > as shown in https://github.com/sneumann/xcms/issues/150#
> > > issuecomment-293545521
> > > 
> > > => Is there a way to get -O2 back on the BioC build machines ?
> > >     This should fix our WARNING. Bonus: will fix the same issue
> > > in
> > mzR :-)
> > > 
> > > 
> > > Yours,
> > > Steffen
> > > 
> > > 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 abort() call is not coming from XCMS, but rather
> > > > > from the C++ code in the STL, and we have no idea
> > > [...]
> > > > 
> > > > 
> > > > > 
> > > > > 
> > > > > We are tracking this in:
> > > > > https://github.com/sneumann/xcms/issues/150
> > > [...]
> > > > 
> > > > 
> > > > I don't think Bioconductor can help with this; maybe the Rcpp
> > or R-
> > > 
> > > > 
> > > > devel mailing lists?
> > > --
> > > 3rd Leibniz Plant Biochemistry Symposium, 22.-23. of June 2017
> > > http://www.ipb-halle.de/en/public-relations/3rd-leibniz-plant-bio
> > chemis
> > > 
> > > try-symposium/
> > > --
> > > IPB Halle                    AG Massenspektrometrie &
> > > Bioinformatik
> > > Dr. Steffen Neumann          http://www.IPB-Halle.DE
> > > Weinberg 3                   Tel. +49 (0) 345 5582 - 1470
> > > 06120 Halle                       +49 (0) 345 5582 - 0
> > > sneumann(at)IPB-Halle.DE     Fax. +49 (0) 345 5582 - 1409
> > > 
> > > --
> > > 3rd Leibniz Plant Biochemistry Symposium, 22.-23. of June 2017
> > > http://www.i

Re: [Bioc-devel] R CMD check without WARNING: g++ and STL issue for xcms and mzR

[Neumann, Steffen]

Hi Martin and malbec2 admin(s):

Some more digging revealed that malbec2 
http://bioconductor.org/checkResults/devel/bioc-LATEST/malbec2-NodeInfo.html
is using "CFLAGS=-g -O2 -Wall" but only "CXXFLAGS=-Wall"
while e.g. tokay2 uses "CXXFLAGS=-O2 -Wall -mtune=core2"

The -O2 optimisation is getting rid of the abort() symbol,
as shown in https://github.com/sneumann/xcms/issues/150#issuecomment-293545521

=> Is there a way to get -O2 back on the BioC build machines ? 
   This should fix our WARNING. Bonus: will fix the same issue in mzR :-)

Yours,
Steffen

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 abort() call is not coming from XCMS, but rather
> > from the C++ code in the STL, and we have no idea
[...]
> 
> > 
> > We are tracking this in:
> > https://github.com/sneumann/xcms/issues/150
[...]
> 
> I don't think Bioconductor can help with this; maybe the Rcpp or R-
> devel mailing lists?
-- 
3rd Leibniz Plant Biochemistry Symposium, 22.-23. of June 2017
http://www.ipb-halle.de/en/public-relations/3rd-leibniz-plant-biochemis
try-symposium/
--
IPB HalleAG Massenspektrometrie &
Bioinformatik
Dr. Steffen Neumann  http://www.IPB-Halle.DE
Weinberg 3                   Tel. +49 (0) 345 5582 - 1470
06120 Halle                       +49 (0) 345 5582 - 0           
sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409

-- 
3rd Leibniz Plant Biochemistry Symposium, 22.-23. of June 2017
http://www.ipb-halle.de/en/public-relations/3rd-leibniz-plant-biochemis
try-symposium/
--
IPB HalleAG Massenspektrometrie &
Bioinformatik
Dr. Steffen Neumann  http://www.IPB-Halle.DE
Weinberg 3                   Tel. +49 (0) 345 5582 - 1470
06120 Halle                       +49 (0) 345 5582 - 0           
sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409

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[Bioc-devel] R CMD check without WARNING: g++ and STL issue for xcms and mzR

[Neumann, Steffen]

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/sneumann/xcms/issues/150

In a nutshell, the standard tenplate library (STL) that comes 
with g++-5.4.0 has a snippet:

https://github.com/gcc-mirror/gcc/blob/1cb6c2eb3b8361d850be8e8270c59727
0a1a7967/libstdc%2B%2B-v3/include/bits/stl_list.h#L1825

...
# 1770 "/usr/include/c++/5/bits/stl_list.h"
void _M_check_equal_allocators(list& __x) {
 if (_M_get_Node_allocator())
   __builtin_abort();
}

You can also check this by looking at the compiler output 
after the preprocess step:

g++ -I/usr/share/R/include -DNDEBUG  -fpic  -g -O2 -fstack-
protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -g  -c massifquant/TrMgr.cpp -E | less

The same applies to mzR, where the same stl_list.h is included
in two files (Found ‘abort’, possibly from ‘abort’ (C)
Objects: ‘./boost/libs/regex/src/instances.o’,
  ‘./boost/libs/regex/src/winstances.o’)

=> Since we don't want to patch the STL, we have no idea 
   how to fix that WARNING. Is there a way to get an exception, 
   or patch/whitelist this call in R CMD check ?

Yours, 
Steffen Neumann

-- 
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06120 Halle                       +49 (0) 345 5582 - 0           
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[Bioc-devel] BiocStyle on windows with spaces in path names

[Neumann, Steffen]

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 causes MiKTeX to fail with 
! LaTeX Error: File 
`C:/ProgramFiles/R/R-3.1.0/library/BiocStyle/sty/Bioconductor.sty' not found.
(This is with BiocStyles-1.3.15) 

What is the recommended solution here ? Installing R to a non-standard location 
?
Use texlive instead of miktex (does that make a difference ?) Or something else 
?

Yours,
Steffen





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