,
Laurent
[1] https://rformassspectrometry.github.io/MsDataHub/
From: Bioc-devel on behalf of Vincent Carey
Sent: 22 May 2024 11:16
To: Hervé Pagès
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] Question relating to extending a class and inclusion
ExperimentHub
I would like to use something like `curl::has_internet()` in .onLoad() to first
check if there's is connectivity before calling createHubAccessors().
Am I missing something here? Does anyone have any experience with similar
issues?
Laurent
___
Thanks Ivan. I did not know about ` .Internal(printDeferredWarnings())`. It
does provide a solution for what I need.
Best,
Laurent
Le mer. 26 avr. 2023 à 06:23, Ivan Krylov a écrit :
> В Sun, 23 Apr 2023 13:33:16 -0400
> Laurent Gautier пишет:
>
> > When tracing what happens du
cloned the repo from git.bioconductor.org and it's also present there (with
all the figures)
Thank you anyway!
[1] https://github.com/lgatto/RforProteomics/tree/master/vignettes/figures
From: Oleksii Nikolaienko
Sent: 28 April 2023 16:53
To: Laurent Gatto
Cc
'RProtVis.Rmd' failed with diagnostics:
Cannot find the file(s): "figures/msanim1.gif"
--- failed re-building ‘RProtVis.Rmd’
Even though that figure does exists [1].
I am unable to reproduce locally and on Github [2]
Source: [3]
Any idea?
Laurent
[1] https://github.com/lgatto/RforProte
a suggestion about what I am missing?
Best,
Laurent
[[alternative HTML version deleted]]
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This is only a warning, and you can safely ignore it.
Best wishes,
Laurent
(Note that the message mentions the support forum, not the devel mailing list.)
From: Bioc-devel on behalf of TYLER H
WINTERMUTE via Bioc-devel
Sent: 15 March 2023 17:18
respective contributions in the manual pages.
Best wishes,
Laurent
From: Bioc-devel on behalf of Matteo Tiberti
Sent: 03 February 2023 09:08
To: bioc-devel@r-project.org
Subject: [Bioc-devel] name for new BioC package
dear maintainers,
I am currently
to join the discussion, please open an issue in the working
group github repo [3] and tag yourself. We plan our first round of discussions
Jan 2023.
Best wishes,
Laurent
[1]
http://workinggroups.bioconductor.org/currently-active-working-groups-committees.html#recommended-classes-and-methods
[2
Would it be possible to give Lisa Breckels write access to
the pRolocGUI git repo, as she will be taking over maintenance of the package.
Thank you in advance.
Laurent
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t; >
> >
> > Lori Shepherd
> >
> > Bioconductor Core Team
> >
> > Roswell Park Comprehensive Cancer Center
> >
> > Department of Biostatistics & Bioinformatics
> >
> > Elm & Carlton Streets
> >
> > Buffalo, New York 14263
> >
(on CRAN) or deprecated (on Bioconductor) are
available? This is likely to lead to serious confusion.
Laurent
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from different sources.
Best wishes,
Laurent
[1] https://github.com/RforMassSpectrometry
[2] http://bioconductor.org/developers/how-to/git/push-to-github-bioc/
From: Bioc-devel on behalf of Kelsey Chetnik
via Bioc-devel
Sent: 02 August 2021 17:16
Yes, that would be a sensible way, I think.
Laurent
From: Fabricio de Almeida
Sent: 01 July 2021 19:42
To: Laurent Gatto; bioc-devel@r-project.org
Subject: RE: Question on copyright in Bioc vignette
Hi, Laurent.
Thank you for your suggestion. How would
-use it (with credit). A licence would make that
straightforward.
Best wishes,
Laurent
From: Bioc-devel on behalf of Fabricio de
Almeida
Sent: 01 July 2021 19:20
To: bioc-devel@r-project.org
Subject: [Bioc-devel] Question on copyright in Bioc vignette
No worries at all, and thank you for following up.
Laurent
From: Bioc-devel on behalf of Marcel Ramos
Sent: 10 March 2021 18:39
To: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] bioconductor_docker:devel missing MAE and
GenomeInfoDb
Hi Laurent
Thank you Robert and Nitesh for your input.
The workshops at EuroBioc were using devel (as far as I can remember at least)
which is why I am using bioconductor_docker:devel. For now, I will (try to)
install these two packages from github.
Best wishes,
Laurent
for a different reason, much
later in the process.
Laurent
[1]
https://github.com/lgatto/QFeaturesScpWorkshop2021/runs/2070746544?check_suite_focus=true#step:8:157
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I just realised that the scp package
(http://bioconductor.org/packages/release/bioc/html/scp.html) DOI
(https://doi.org/doi:10.18129/B9.bioc.scp) is broken.
Any idea why?
Thanks in advance.
Laurent
___
Bioc-devel@r-project.org mailing list
functions
(xcmsSet and alike) to the new functions that make use of the MSnbase package
to represent the mass spec data [1].
Best wishes,
Laurent
[1] https://support.bioconductor.org/p/133388/#133400
From: Bioc-devel on behalf of Bruno pereira
Sent: 18
Thank you both - issue has just been opened.
Merci Hervé for pointing out the direct use of the `List()` constructor.
Laurent
From: Michael Lawrence
Sent: 21 October 2020 19:13
To: Pages, Herve
Cc: Laurent Gatto; bioc-devel@r-project.org
Subject: Re
to loose the *List classes in the individual DFrames.
Am I missing something? Is this something that is on the todo list, or that I
could help with?
Best wishes,
Laurent
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Thank you for these instructive, although somewhat disheartening clarifications.
Laurent
From: Henrik Bengtsson
Sent: 12 August 2020 19:01
To: Laurent Gatto
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] sapply and vapply
FWIW,
> sappl
)
Would you still recommend to use vapply() in such cases?
Thank you in advance.
Laurent
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FYI - I can reproduce this on linux with R Under development (unstable)
(2020-03-19 r78011)
From: Bioc-devel on behalf of Vincent Carey
Sent: 16 March 2020 23:52
To: bioc-devel
Subject: [Bioc-devel] proper way to define an S4 method for 'plot'
I just
the following two
options
- `doProcess(se)` returns a new SE object
- `doProcess(se)` adds a new assay to se
If you are interested about the broader context about this question, see
https://github.com/waldronlab/MultiAssayExperiment/issues/266
Thank you in advance for your input.
Laurent
ntext", or initial context, the code should from ?
Searching for "context" in the R-exts manual does not return much.
Best,
Laurent
Le sam. 14 déc. 2019 à 12:20, Simon Urbanek a
écrit :
> Laurent,
>
> the main point here is that ParseVector() just like any other R API has to
>
Le lun. 9 déc. 2019 à 09:57, Tomas Kalibera a
écrit :
> On 12/9/19 2:54 PM, Laurent Gautier wrote:
>
>
>
> Le lun. 9 déc. 2019 à 05:43, Tomas Kalibera a
> écrit :
>
>> On 12/7/19 10:32 PM, Laurent Gautier wrote:
>>
>> Thanks for the quick response Tomas.
&
Le lun. 9 déc. 2019 à 05:43, Tomas Kalibera a
écrit :
> On 12/7/19 10:32 PM, Laurent Gautier wrote:
>
> Thanks for the quick response Tomas.
>
> The same error is indeed happening when trying to have a zero-length
> variable name in an environment. The surprisin
>> e = ri.parse("list(''=123") R[write to console]: Error: attempt to use
>>> zero-length variable name
R[write to console]: Fatal error: unable to initialize the JIT
*** stack smashing detected ***: terminated
```
Le lun. 2 déc. 2019 à 06:37, Tomas Kalibera a
écrit :
&g
gth variable name
```
Should the parser be made to accept as valid what is otherwise possible
when using `[[<` ?
Best,
Laurent
Le sam. 30 nov. 2019 à 17:33, Laurent Gautier a écrit :
> I found the following code comment in `src/main/gram.c`:
>
> ```
>
> /* Memor
this be related to be issue ?
Le sam. 30 nov. 2019 à 14:04, Laurent Gautier a écrit :
> Hi,
>
> The behavior of
> ```
> SEXP R_ParseVector(SEXP, int, ParseStatus *, SEXP);
> ```
> defined in `src/include/R_ext/Parse.h` appears to be inconsistent
> depending on the string
`
Is there a reason for the difference in behavior, and is there a workaround ?
Thanks,
Laurent
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But it has been badly out-of-data in the past, not sure devel is available and
buggy (examples don't run, despite the Run button and outdated installation
instructions still using `source("https://bioconductor.org/biocLite.R;)`)
Laurent
From:
man pages (which can easily be overwhelming
for large packages) are readily available to read and search.
Laurent
From: Martin Morgan
Sent: 25 September 2019 23:10
To: Laurent Gatto; Ludwig Geistlinger; bioc-devel@r-project.org
Subject: Re: [Bioc-devel
I think this would be very useful. This is one of the reasons I create pkgdown
sites for my packages: manual pages, news and html vignettes are readily
available for all (including me) to browse.
Best wishes,
Laurent
From: Bioc-devel on behalf
:
> >>>>> Laurent Gautier
> >>>>> on Sun, 15 Sep 2019 15:01:09 -0400 writes:
>
> > In case a search engine leads someone with the same issue
> > here, I am documenting the point I reached:
>
> > I can reproduce the issue with a
In case a search engine leads someone with the same issue here, I am
documenting the point I reached:
I can reproduce the issue with a small example when forcing R to not load
any package at startup time (using an Renviron file):
```
package <- "utils"
lib.loc <- ""
ns <- loadNamespace(package,
ods*will reduce
>> the start-up time by a factor of up to two. But it can also be used to
>> customize R, e.g. for class use. Rscript also checks the environment
>> variable R_SCRIPT_DEFAULT_PACKAGES; if set, this takes precedence over
>> R_DEFAULT_PACKAGES.
>> Bill Dun
be used to
> customize R, e.g. for class use. Rscript also checks the environment
> variable R_SCRIPT_DEFAULT_PACKAGES; if set, this takes precedence over
> R_DEFAULT_PACKAGES.
> Bill Dunlap
> TIBCO Software
> wdunlap tibco.com
>
>
> On Sun, Sep 8, 2019 at 8:42 AM L
nd what
it is) earlier and with this make the task of troubleshooting easier.
Best,
Laurent
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I am not using the C API from a package but with an embedded R.
Why have it declared in the include/ if it cannot be accessed then?
Best,
Laurent
On Sun, Sep 8, 2019, 8:27 AM Tierney, Luke wrote:
> On Sat, 7 Sep 2019, Laurent Gautier wrote:
>
> > Hi,
> >
> >
>
Hi,
The function `Rf_findFun3` is declared in
`$(R CMD CONFIG HOME)/lib/R/include/Rinternals.h`
but appears to be missing from R's shared library (R.so).
Is this an oversight?
Best,
Laurent
[[alternative HTML version deleted]]
__
R-devel@r
No worries at all. Thank you for letting me know.
Laurent
From: Pages, Herve
Sent: 28 May 2019 22:24
To: Laurent Gatto; bioc-devel@r-project.org
Subject: Re: [Bioc-devel] index of Bioc repository unavailable
Hi Laurent,
This is temporary. We're
https://bioconductor.org/packages/3.10/data/annotation/src/contrib:
cannot open URL
'https://bioconductor.org/packages/3.10/data/annotation/src/contrib/PACKAGES'
chr [1:16400] "a4" "a4Base" "a4Classif" "a4Core" "a4Preproc" "a4Reporting" ...
m(se2)
> se2 <- readRDS("se2.rds")
> all.equal(se1, se2)
[1] "Attributes: < Component “assays”: Class definitions are not identical >"
Session information provided below.
Thank you in advance,
Laurent
R version 3.6.0 RC (2019-04-21 r76417)
Platform: x86_64-pc-linux-gn
paste0(paste(strsplit(x, "")[[1]][1:n], collapse = ""),
"...")
else x
}, USE.NAMES = FALSE)
})
to show
> x
DataFrame with 2 rows and 1 column
x
1 A veee...
2 A sho
paste0(paste(strsplit(x, "")[[1]][1:n], collapse = ""),
"...")
else x
})
})
With patch:
> DataFrame(a = 'foo', b = NA_character_)
DataFrame with 1 row and 2 columns
a b
foofoo
gt;> get("[")
> > .Primitive("[")
> >> get("+")
> > function (e1, e2) .Primitive("+")
> >
> > The other index operators, "[[", "[<-", "[[<-" are similar
> >
> &g
; NULL
> Warning message:
> In formals(fun) : argument is not a function
>
>
> Hope this helps,
>
> Rui Barradas
>
>
> Às 18:26 de 06/10/2018, Laurent Gautier escreveu:
> > Hi,
> >
> > A short code example showing the warning might the only thing needed
&g
ls(args(`sum`))
$...
$na.rm
[1] FALSE
> is.function(`sum`)
[1] TRUE
> is.primitive(`sum`)
[1] TRUE
> class(`[`)
[1] "function"
```
Is this a feature ?
Laurent
[[alternative HTML version deleted]]
__
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DIR}/NEWS.md > ${PKGDIR}/NEWS
(where ${PKGDIR} is the package directory)
Unsure whether this helps or adds further to the confusion.
Best wishes,
Laurent
[1] https://github.com/ComputationalProteomicsUnit/maker
On 25 September 2018 13:55, Shepherd, Lori wrote:
> It can be used current
e hook declined)
error: failed to push some refs to
'g...@git.bioconductor.org:packages/ProteomicsAnnotationHubData.git'
Any help in fixing this would be welcome.
Thank you in advance.
Laurent
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For those that have BiocStickers, what are your toughts on license and
requiring attributions, as they seem to limit reuse possibilities.
See
https://github.com/Bioconductor/BiocStickers/issues/54
for details.
Best wishes,
Laurent
___
Bioc-devel
On 20 March 2018 19:30, Turaga, Nitesh wrote:
> Hi Laurent,
>
> You cannot force push. Is you GitHub repo at a position where it needs
> to be synced to the Bioconductor repo?
>
> If so, I can force push for you and sync.
I was able to push from a cloned bioc repo, but can't t
On 20 March 2018 01:58, Turaga, Nitesh wrote:
> Hi Laurent,
>
> Are you sure you are using either of the private keys associated with
> these public keys? You have to make sure to use the correct private
> key.
Yes, I checked, and the keys are correct. Here's what I get in a
uld it be a configuration issue?
Thank you in advance.
Best wishes,
Laurent
--
Laurent Gatto | @lgatt0
http://cpu.sysbiol.cam.ac.uk/
http://lgatto.github.io/
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support forum rather than on the
developer mailing list.
https://support.bioconductor.org/
If you still have a problem with loading mzR, please follow up there.
Best wishes,
Laurent
> Regards,
>
> Murtaza Saifuddin Merchant
>
> MTech Chem
On 17 January 2018 18:26, Turaga, Nitesh wrote:
> The problem is not a separate branch from your primary repository. Its
> the branch coming from a “remote” which is not the primary repository
> (i.e Bioconductor).
>
> “rebase" is essentially doing what you do in two separate steps, so
> that
On 17 January 2018 17:40, Turaga, Nitesh wrote:
> Hi Laurent,
>
> After checking your package, it’s very hard to get rid of the
> duplicate commits at this stage of development. I don’t think it
> should effect the build process of your package.
>
> The only thing it migh
licated commits in github and bioconductor
histories.
Any idea how to address this within Bioconductor?
Thank you in advance.
Laurent
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s categorisation.
Best wishes,
Laurent
> Thank you for your suggestions.
>
>
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Cancer Institute
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
&
contains whole the process and codes in steps?
All the setup and more details are provided in
https://github.com/bioconductor/bioc_git_transition/
in particular the FAQ and all the scenarios at the bottom
https://github.com/Bioconductor/bioc_git_transition/blob/master/doc/faq
owizard 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
te. The RforProteomics vignette does explicitly
call library at the beginning of each section and explained that the
package was only a collection of analyses stemming from other packages,
but that wasn't enough apparently.
Laurent
> -Aaron
>
>
>
route we decided to go in the end, so no need
to move export() and import() for us at the moment.
Thanks again for your input.
Best wishes,
Laurent
> H.
>
>
> On 09/18/2017 11:28 PM, Laurent Gatto wrote:
>>
>> Out of curiosity, do you also have an import() function?
gy
>> Division of Public Health Sciences
>> Fred Hutchinson Cancer Research Center
>> 1100 Fairview Ave. N, M1-B514
>> P.O. Box 19024
>> Seattle, WA 98109-1024
>>
>> E-mail: hpa...@fredhutch.org
>> Phone: (206) 667-5791
>> Fax:(206) 667-1319
&
ytoplasm.
>Synonym: internal to cell
>Synonym: nucleocytoplasm
>Synonym: protoplasm
>Synonym: protoplast
>
> Also this name is consistent with what AmiGO is using:
>
>http://amigo.geneontology.org/amigo/term/GO:0005622
>
> So I actually don't think
,
Laurent
On 12 September 2017 16:35, Hervé Pagès wrote:
> Hi Laurent,
>
> The 2 Ontology,character methods defined in AnnotationDbi and
> rols do very different things. The 1st one expects a vector of
> GO IDs and returns the GO sub-ontologies that they belong to:
>
> >
to find an inherited method for function ‘Ontology’ for signature
‘"character"’
> getMethod("Ontology", "character")
Error in getMethod("Ontology", "character") :
no method found for function 'Ontology' and signature character
> getMethod(&q
Dear all,
It appears that at least two packages, AnnotationDbi and rols, define
the Ontology generic with the same signature
setGeneric("Ontology", function(object) standardGeneric("Ontology"))
Could it be moved to BiocGenerics, please?
Best wishes,
Laurent
--
Lau
On 30 August 2017 12:04, Turaga, Nitesh wrote:
> Hi Laurent,
>
> Please try again and let me know.
Thank you Nitesh, pushed successfully now.
Laurent
>> On Aug 29, 2017, at 5:51 PM, Laurent Gatto <lg...@cam.ac.uk> wrote:
>>
>>
>> On 29 August 2017
, there aren't any duplicated SHA1 tags, but some commit
messages are duplicated, and in some cases, the actual commit content
seems to be duplicated (for example re-generated Rd files).
Hope this helps.
Laurent
On 29 August 2017 20:53, Turaga, Nitesh wrote:
> Hi Laurent,
>
> We ar
tream/master works.
Any help greatly appreciated.
Laurent
--
Laurent Gatto | @lgatt0
http://cpu.sysbiol.cam.ac.uk/
http://lgatto.github.io/
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Dear Bioconductor admins,
When using the search box on www.bioconductor.org, I systematically get
the following error
A timeout or invalid search term resulted in an error.
Best wishes,
Laurent
--
Laurent Gatto | @lgatt0
http://cpu.sysbiol.cam.ac.uk/
http://lgatto.github.io
endencies, ... developers and users shouldn't notice the change at
all. The pwiz backend has been available for many years, but was just
not the default.
Let's see what the practice says...
Laurent
> On Tue, May 23, 2017 at 9:10 AM Laurent Gatto <lg...@cam.ac.uk> wrote:
>
or details. Please do
raise any concerns or problems in that issue.
Best wishes,
Laurent
--
Laurent Gatto | @lgatt0
http://cpu.sysbiol.cam.ac.uk/
http://lgatto.github.io/
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dardGeneric("header"))
and is used at least in mzR and MSnbase.
I guess that signature, as it is, wouldn't be a good for BiocGenerics.
Best wishes,
Laurent
> fixed
> info
> geno
>
> They are currently defined by both
> VariantAnnotation/SummarizedExperiment and
Dear all,
What is the equivalent of this URL
http://www.bioconductor.org/packages/3.5/bioc/VIEWS
for data/experiment packages?
Thank you in advance.
Laurent
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be helpful to
report these versions.
Best wishes,
Laurent
On 5 January 2017 16:40, Dickey, Aaron wrote:
> Howdy,
>
> I would like a bump to the mzR package per this issue. I don't
> currently have an error message... but I do have warnings (below) when
> running packages wi
a backup of any
files/dir you gitignore
2) rm -rf mzR
3) git clone g...@github.com:sneumann/mzR.git
4) use update_remotes.sh
Let me know if there's anything I can help with.
Best wishes,
Laurent
On 2 January 2017 22:12, Steffen Neumann wrote:
> Hi all,and a happy new year!
>
> I am exp
, but this
is not doing much to prevent it.
2017-01-01 19:42 GMT-05:00 Simon Urbanek <simon.urba...@r-project.org>:
>
> > On Jan 1, 2017, at 5:12 PM, Laurent Gautier <lgaut...@gmail.com> wrote:
> >
> >
> >
> > 2017-01-01 8:28 GMT-05:00 Prof Brian Ripley <rip...@stats.o
gt; AFAICS if you comply, there will not be a conflict.
>
> Also note that is only an issue if CSTACK_DEFNS is defined, not the
> default and not mentioned here.
>
>
>
>
> Thanks,
>> Simon
>>
>>
>>
>> On Dec 26, 2016, at 11:25 PM, Laurent Gautier
er/lastBuild/consoleText
Is there anything I can do here or is it a server side issue? Could it
be that libnetcdf or libnetcdf-dev is missing?
Thank you in advance.
Best wishes,
Laurent
--
Laurent Gatto | @lgatt0
http://cpu.sysbiol.cam.ac.uk/
http://lgatto.github.io/
k if that works for you.
>
> Thanks,
> Simon
>
>
>
> > On Dec 26, 2016, at 11:25 PM, Laurent Gautier <lgaut...@gmail.com>
> wrote:
> >
> > Hi,
> >
> > I was recently pointed out that a definition in Rinterface.h can be
> conflicting
On 23 December 2016 16:36, Laurent Gatto wrote:
> Dear all,
>
> I'm following up re my online references suggestion with my recent
> experience with Hadley's pkgdown package
>
> https://github.com/hadley/pkgdown
>
> It doesn't address the cross-package issue (which is
uintptr_t;
#endif
)
Is this expected ? Shouldn't R rely on the definition in stdint.h
rather than define its own ?
(report for the issue:
https://bitbucket.org/rpy2/rpy2/issues/389/failed-to-compile-with-python-360-on-32
)
Laurent
[[alternative HTML version deleted
/
Best wishes,
Laurent
On 23 December 2016 18:14, Laurent Gatto wrote:
> Dear Sean and Robert,
>
> On 23 December 2016 17:24, Robert M. Flight wrote:
>
>> Yes, this seems like a time where using a non-standard site directory
>> on Github is useful, or as Sean said,
cshttps://
> itsalocke.com/
> auto-deploying-documentation-better-change-tracking-artefacts/
>
> HTH
Thanks, Robert, I will explore this solution too.
Laurent
> Robert
>
> On Fri, Dec 23, 2016 at 1:14 PM Laurent Gatto <lg...@cam.ac.uk> wrote:
>
>
>
ws()!
I say not yet because there's a currenlty unused format argument to
news, so there's hope.
Laurent
> Best,
> Kasper
>
> On Fri, Dec 23, 2016 at 12:24 PM, Robert M. Flight <rfligh...@gmail.com
>> wrote:
>
> Yes, this seems like a time where using a non-standa
pendently of what git does?
Laurent
> -Robert
>
> On Fri, Dec 23, 2016 at 12:19 PM Sean Davis <seand...@gmail.com> wrote:
>
> Github allows you to set the branch for the docs directory if I
> recall. Perhaps a separate branch with a docs directory (not
> master)
that the docs directory (which is about 5.5M for
MSnbase) ends up on hedgehog. It is easy for it not to be part of the
package build artefact using .Rbuildignore, but I am not sure how to
easily push it to github but not hedgehog when using git-svn.
Laurent
On 23 December 2016 16:36, Laurent Gatto wrote
html_document2 with the nice floating table of contents...
Regarding the News tab, only NEWS.md (markdown format) are considered;
NEWS in Rd are ignored too.
Hope this helps.
Best wishes,
Laurent
On 16 March 2016 23:33, Andrzej Oleś wrote:
> Hi all,
>
> I had a discussion earlier today wi
, don't forget to provide the output of sessionInfo().
Best wishes,
Laurent
On 13 December 2016 15:19, Nadine Hoffmann wrote:
> Hello Bioconductor Team,
>
> I am using the software THqPCR for the first time and I have problems to
> get my files read. I attached a screenshot and also
d...
>
> [[alternative HTML version deleted]]
>
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--
Laurent Gatto | @lgatt0
http://cpu.sysbiol.cam.ac.uk/
http://lgatto.github.io/
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gt; updateObject(new("Spectrum2"))
updateObject(object = 'Spectrum')
Error: invalid version specification ‘Versioned; no version string’
> updateObject(new("ExpressionSet"))
ExpressionSet (storageMode: lockedEnvironment)
assayData: 0 features, 0 samples
element names: exprs
ptable solution for MSnbase, I
will submit an RMassBank patch that will sort the error (and other
things resulting from MSnbase improvements) out. What would be the best
way to submit a patch - email, a pull request to a github repo?
Best wishes,
Laurent
> On 07.10.2016 22:34, Laurent Ga
Dear Bioc team,
The isobar package doesn't build. Attached is a patch that fixes the
build errors and some namespace related warnings. There are still many
notes when checking, though.
Hope someone is happy to apply the patch.
Best wishes,
Laurent
Index: DESCRIPTION
o master for after a final package
check, but wait for the results of your intense torture tests before
committing to svn.
Laurent
> jo
>
>
>> On 7 Oct 2016, at 20:14, Rainer Johannes <johannes.rai...@eurac.edu> wrote:
>>
>> we could try to switch back from the C-co
ScanNum, precursorMz,
precursorIntensity,
precursorCharge,
collisionEnergy)
if (validObject(.Object))
.Object
})
Why is calling new("RmbSpectrum2") direclty re
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