[Bioc-devel] git push access to MsCoreUtils repository

[Sebastian Gibb via Bioc-devel]

Dear Bioconductor team,

we (Laurent Gatto, Johannes Rainer, both CC) are maintainers of the MsCoreUtils
package.
Unfortunately Johannes Rainer and I can't push to the bioconductor git
repository:

$ git remote -v
origin  g...@github.com:rformassspectrometry/MsCoreUtils.git (fetch)
origin  g...@github.com:rformassspectrometry/MsCoreUtils.git (push)
upstreamg...@git.bioconductor.org:packages/MsCoreUtils.git (fetch)
upstreamg...@git.bioconductor.org:packages/MsCoreUtils.git (push)

$ git push upstream master
FATAL: W any packages/MsCoreUtils s.gibb DENIED by fallthru
(or you mis-spelled the reponame)
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.


Could you please add me and Johannes to this repository as well?

Kind regards,

Sebastian Gibb

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Re: [Bioc-devel] git permission denied to synapter repository

[Sebastian Gibb]

Dear Nitesh,

thank you very much. Now it works!

Best wishes,

Sebastian



On 2018-01-17 22:39:17, nitesh.tur...@roswellpark.org wrote:
> Hi Sebastian,
>
> You did not do anything wrong. Laurent is the only one listed on the package 
> so far. I will add you to it.
>
> Laurent, just a heads up, I’m adding Sebastian to the “synapter" package.
>
> Best,
>
> Nitesh
>
> > On Jan 17, 2018, at 4:07 PM, Sebastian Gibb <m...@sebastiangibb.de> wrote:
> >
> > Dear Bioconductor admins,
> >
> > I am the (co-)maintainer of the synapter package.
> >
> > I tried to push some changes the first time after the conversion to git and 
> > got
> > the following error:
> >
> > ```
> >> git push upstream master
> > FATAL: W any packages/synapter s.gibb DENIED by fallthru
> > (or you mis-spelled the reponame)
> > fatal: Could not read from remote repository.
> >
> > Please make sure you have the correct access rights
> > and the repository exists.
> > ```
> >
> > s.gibb was my svn username on bioc. AFAIK the access to my other 
> > repositories
> > (cleaver, topdownr) works as expected.
> >
> > Did I something wrong?
> >
> > Best wishes,
> >
> > Sebastian
> >
> > ___
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> > 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 
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[Bioc-devel] git permission denied to synapter repository

[Sebastian Gibb]

Dear Bioconductor admins,

I am the (co-)maintainer of the synapter package.

I tried to push some changes the first time after the conversion to git and got
the following error:

```
> git push upstream master
FATAL: W any packages/synapter s.gibb DENIED by fallthru
(or you mis-spelled the reponame)
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.
```

s.gibb was my svn username on bioc. AFAIK the access to my other repositories
(cleaver, topdownr) works as expected.

Did I something wrong?

Best wishes,

Sebastian

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Re: [Bioc-devel] EXTERNAL: Re: Git permission denied (publickey)

[Sebastian Gibb]

On 2017-10-10 22:48:43, martin.mor...@roswellpark.org wrote:
> On 10/10/2017 04:43 PM, Sebastian Gibb wrote:
> > Dear Biocondcutor admins,
> >
> > I am the maintainer of the cleaver package (and a co-maintainer of MSnbase,
> > Pbase, synapter). As many other user mentioned here I got the same 
> > "permission
> > denied (publickey)" error message. I already submit my mail address, svn
> > username and github id via the google form.
> >
> > My mail address: m...@sebastiangibb.de
> > Svn username: s.gibb
> > GitHub ID: sgibb
> > (public key is available via https://github.com/sgibb.keys )
> >
> > I tried:
> > git clone g...@git.bioconductor.org:packages/cleaver
> > Cloning into 'cleaver'...
> > Permission denied (publickey).
> > fatal: Could not read from remote repository.
> >
> > Please make sure you have the correct access rights
> > and the repository exists.
> >
> > My .ssh/config (same as for github but hostname differs):
> >
> > Host bioconductor.org
> >Hostname bioconductor.org
>
> I believe that should be git.bioconductor.org
Great, thanks! Sorry, such an obvious error!

Best wishes,

Sebastian

>
> You can also see the ssh transaction and (when successful) permissions with
>
> ssh -v g...@git.bioconductor.org/packages/cleaver
>
> Martin
>
> >User git
> >IdentityFile /home/sebastian/.ssh/sgibb@github:id_rsa
> >PreferredAuthentications publickey
> >
> > Anything else I could do?
> >
> > Best wishes,
> >
> > Sebastian
> >
> > On 2017-10-09 22:22:19, andrea@inra.fr wrote:
> >> Hello,
> >> A few days ago I submitted my GitHub id andreamrau (since GitHub knows my 
> >> SSH key) and my SVN id (a.rau) using the Git/SVN transition form, and I 
> >> still seem to be having difficulty accessing my packages coseq and 
> >> HTSFilter. I see the following message when I try to git clone one of my 
> >> packages:
> >>
> >> Permission denied (publickey).
> >> fatal: Could not read from remote repository
> >>
> >> Could you let me know if there's something I have done incorrectly with 
> >> the transition form?
> >>
> >> Thanks very much for the help,
> >> Andrea
> >>
> >>  [[alternative HTML version deleted]]
> >>
> >> ___
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> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
> > ___
> > 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 
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Re: [Bioc-devel] names, mcols and metadata are not changed in [- operator of class Vector

[Sebastian Gibb]

Hi Hervé,

thanks for the explanation. I never recognized that this happens with ordinary
vectors, too.

Of course, I see that it would be a bad style to overload [- for my own
class to behave like I want to.

So I need to update the metadata manually.

Kind regards,

Sebastian


On 2014-05-07 20:18:58, hpa...@fhcrc.org wrote:
 Hi Sebastian,

 This is the expected behavior and it's motivated by how [- behaves on
 ordinary vectors:

x - setNames(1:3, LETTERS[1:3])

 Then:

 x
A B C
1 2 3

 Replacing the first two elements:

x[2:1] - x[1:2]

 Then:

 x
A B C
2 1 3

 The names are preserved.

 So we need to think of [- as an operator that touches the values of
 a vector-like object without touching its structure or its attributes.
 People sometimes rely on this behavior to stuff the entire object with
 a given value:

x[] - some_value

 They wouldn't expect this to destroy the names or metadata cols that
 are on 'x'.

 Hope that makes sense,

 Cheers,
 H.


 On 05/07/2014 11:59 AM, Sebastian Gibb wrote:
  Dear all,
 
  today I observed an unexpected behaviour (at least for me) using the [-
  operator on classes that inherited Vector.
  I want to change the order of some elements inside the Vector (in my use 
  case it
  is an AAStringSet object). If I use an index in [- the names, the
  elementMetadata and the metadata are not replaced by their counterparts, 
  e.g.:
 
  ###
  library(IRanges)
 
  i - IRanges(1:3, 4:6)
  names(i) - LETTERS[1:3]
 
  i
  # IRanges of length 3
  # start end width names
  # [1] 1   4 4 A
  # [2] 2   5 4 B
  # [3] 3   6 4 C
 
  i[2:1] - i[1:2]
  i
  # IRanges of length 3
  # start end width names
  # [1] 2   5 4 A
  # [2] 1   4 4 B
  # [3] 3   6 4 C
 
 
  ## names should be B, A, C; the elementMetadata and metadata are in the 
  wrong
  ## order, too.
  ## expected output:
  # IRanges of length 3
  # start end width names
  # [1] 2   5 4 B
  # [2] 1   4 4 A
  # [3] 3   6 4 C
 
  ###
 
  I tried to figure out the reason for this and ended up with the 
  replaceROWS
  method (in {IRanges,S4Vectors}/R/Vector-class.R).
  In this method the mcols, metadata and names are just restored. To be 
  honest I
  do not really understand this function.
  Why is the new value first append to the original vector (`ans - c(x, 
  value)`)
  and subsequently extracted? Would a simple replace, e.g. `x[i] - value` 
  not be
  enough?
 
  In my opinion the last three lines should restore the original metadata
  *and* replace the corresponding metadata by their new counterparts.
 
  ### replaceROWS from IRanges/R/Vector-class.R
  setMethod(replaceROWS, Vector,
   function(x, i, value)
   {
   idx - seq_along(x)
   i - extractROWS(setNames(idx, names(x)), i)
   ## Assuming that objects of class 'class(x)' can be combined with 
  c().
   ans - c(x, value)
   idx[i] - length(x) + seq_len(length(value))
   ## Assuming that [ works on objects of class 'class(x)'.
   ans - ans[idx]
   ## Restore the original decoration.
   metadata(ans) - metadata(x)
   names(ans) - names(x)
   mcols(ans) - mcols(x)
   ans
   }
  )
  ###
 
  Kind regards,
 
  Sebastian
 
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 --
 Hervé Pagès

 Program in Computational Biology
 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...@fhcrc.org
 Phone:  (206) 667-5791
 Fax:(206) 667-1319

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Re: [Bioc-devel] Gviz AnnotationTrack fails when [-operator is defined

[Sebastian Gibb]

Dear Florian,

On 2014-05-05 16:17:41, florian.ha...@novartis.com wrote:
 Hm, this looks odd indeed. I am wondering whether this is some sort of
 name space problem. Does the same happen when you create your ³A² dummy
 class and the ³[³ method in a little dummy package with its own name
 space?
Your guess was right! I created a small dummy package
( https://github.com/sgibb/dummyA ). And after loading it with `library`
everything works like expected.
But if I load it with devtools' `load_all` it crashes with the same error:

Error in callNextMethod(x, i) :
  bad object found as method (class function)

Kind regards,

Sebastian

On 2014-05-05 16:17:41, florian.ha...@novartis.com wrote:
 Something seems to be messing up the methods table when you define
 the ³[³ method from the global environment.
 Any advice from the name space gurus on the list?
 Florian

 On 04/05/14 13:48, Sebastian Gibb sgibb.deb...@gmail.com wrote:

 Dear Florian, dear all,
 
 I want to use Gviz::AnnotationTrack to visualize my own class. This class
 overloads the [ operator. It seems that just the definition of my own
 [
 results in a method dispatching error:
 
 Error in callNextMethod(x, i) :
   bad object found as method (class ³function²)
 
 After defining [ even AnnotationTrack instances that are not using my
 class
 throw this error.
 
 I do not understand the error. Did I something wrong? Can somebody
 enlighten me?
 
 Please find a minimal reproducible example below.
 
 Kind regards,
 
 Sebastian
 
 ###
 library(Gviz)
 
 ## create dummy class
 setClass(A,
  slots = list(start = numeric, end = numeric),
  prototype = prototype(
   start = integer(),
   end = integer()))
 
 ## define a plotting function for A
 plotGVizA - function(obj) {
   aTrack - AnnotationTrack(start=obj@start, end=obj@end, name = a,
 chromosome = chr0, genome = all)
   plotTracks(aTrack, from = min(obj@start), to = max(obj@end))
 }
 
 ## define a plotting function without any A
 plotGViz - function() {
   aTrack - AnnotationTrack(start=c(1, 5), end=c(3, 10), name = a,
 chromosome = chr0, genome = all)
   plotTracks(aTrack, from = 1, to = 10)
 }
 
 ## create an object of class A
 a - new(A, start=c(1, 5), end=c(3, 10))
 
 ## works
 plotGViz()
 plotGVizA(a)
 
 ## define the [ operator for A
 setMethod([, A, function(x, i, j, ...) { return(c(x@start[i],
 x@end[i])) })
 
 ## crashes with the following error message:
 ## Error in callNextMethod(x, i) :
 ##  bad object found as method (class ³function²)
 plotGVizA(a)
 plotGViz()
 
 traceback()
 #12: stop(gettextf(bad object found as method (class %s),
 # dQuote(class(method))), domain = NA)
 #11: callNextMethod(x, i)
 #10: .local(x, i, ...)
 #9: GdObject[seqnames(GdObject) == chromosome(GdObject)]
 #8: .computeGroupRange(GdObject, hasAxis = hasAxis, hasTitle = hasTitle,
 #   title.width = title.width)
 #7: .local(GdObject, ...)
 #6: FUN(X[[1L]], ...)
 #5: FUN(X[[1L]], ...)
 #4: lapply(trackList, consolidateTrack, chromosome = chromosome,
 #   any(.needsAxis(trackList)), any(.needsTitle(trackList)),
 #   title.width, alpha = hasAlpha, ...)
 #3: lapply(trackList, consolidateTrack, chromosome = chromosome,
 #   any(.needsAxis(trackList)), any(.needsTitle(trackList)),
 #   title.width, alpha = hasAlpha, ...)
 #2: plotTracks(aTrack, from = 1, to = 10) at #4
 #1: plotGViz()
 
 sessionInfo()
 #R version 3.1.0 (2014-04-10)
 #Platform: x86_64-pc-linux-gnu (64-bit)
 #
 #locale:
 # [1] LC_CTYPE=en_US.UTF-8   LC_NUMERIC=C
 # [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
 # [5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8
 # [7] LC_PAPER=en_US.UTF-8   LC_NAME=C
 # [9] LC_ADDRESS=C   LC_TELEPHONE=C
 #[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
 #
 #attached base packages:
 #[1] parallel  grid  stats graphics  grDevices utils datasets
 #[8] methods   base
 #
 #other attached packages:
 #[1] XVector_0.4.0   IRanges_1.22.6  Gviz_1.8.0
 #[4] BiocGenerics_0.10.0 devtools_1.5vimcom.plus_0.9-93
 #[7] setwidth_1.0-3  colorout_1.0-2
 #
 #loaded via a namespace (and not attached):
 # [1] AnnotationDbi_1.26.0 BatchJobs_1.2
 # [3] BBmisc_1.6   Biobase_2.24.0
 # [5] BiocParallel_0.6.0   biomaRt_2.20.0
 # [7] Biostrings_2.32.0biovizBase_1.12.1
 # [9] bitops_1.0-6 brew_1.0-6
 #[11] BSgenome_1.32.0  cluster_1.15.2
 #[13] codetools_0.2-8  colorspace_1.2-4
 #[15] DBI_0.2-7dichromat_2.0-0
 #[17] digest_0.6.4 evaluate_0.5.5
 #[19] fail_1.2 foreach_1.4.2
 #[21] Formula_1.1-1GenomeInfoDb_1.0.2
 #[23] GenomicAlignments_1.0.1  GenomicFeatures_1.16.0
 #[25] GenomicRanges_1.16.3 Hmisc_3.14-4
 #[27] httr_0.3 iterators_1.0.7
 #[29] lattice_0.20-29  latticeExtra_0.6-26
 #[31] matrixStats_0.8.14   memoise_0.2.1
 #[33] munsell_0.4.2

[Bioc-devel] Gviz AnnotationTrack fails when [-operator is defined

[Sebastian Gibb]

Dear Florian, dear all,

I want to use Gviz::AnnotationTrack to visualize my own class. This class
overloads the [ operator. It seems that just the definition of my own [
results in a method dispatching error:

Error in callNextMethod(x, i) :
  bad object found as method (class “function”)

After defining [ even AnnotationTrack instances that are not using my class
throw this error.

I do not understand the error. Did I something wrong? Can somebody enlighten me?

Please find a minimal reproducible example below.

Kind regards,

Sebastian

###
library(Gviz)

## create dummy class
setClass(A,
 slots = list(start = numeric, end = numeric),
 prototype = prototype(
  start = integer(),
  end = integer()))

## define a plotting function for A
plotGVizA - function(obj) {
  aTrack - AnnotationTrack(start=obj@start, end=obj@end, name = a,
chromosome = chr0, genome = all)
  plotTracks(aTrack, from = min(obj@start), to = max(obj@end))
}

## define a plotting function without any A
plotGViz - function() {
  aTrack - AnnotationTrack(start=c(1, 5), end=c(3, 10), name = a,
chromosome = chr0, genome = all)
  plotTracks(aTrack, from = 1, to = 10)
}

## create an object of class A
a - new(A, start=c(1, 5), end=c(3, 10))

## works
plotGViz()
plotGVizA(a)

## define the [ operator for A
setMethod([, A, function(x, i, j, ...) { return(c(x@start[i], x@end[i])) })

## crashes with the following error message:
## Error in callNextMethod(x, i) :
##  bad object found as method (class “function”)
plotGVizA(a)
plotGViz()

traceback()
#12: stop(gettextf(bad object found as method (class %s),
# dQuote(class(method))), domain = NA)
#11: callNextMethod(x, i)
#10: .local(x, i, ...)
#9: GdObject[seqnames(GdObject) == chromosome(GdObject)]
#8: .computeGroupRange(GdObject, hasAxis = hasAxis, hasTitle = hasTitle,
#   title.width = title.width)
#7: .local(GdObject, ...)
#6: FUN(X[[1L]], ...)
#5: FUN(X[[1L]], ...)
#4: lapply(trackList, consolidateTrack, chromosome = chromosome,
#   any(.needsAxis(trackList)), any(.needsTitle(trackList)),
#   title.width, alpha = hasAlpha, ...)
#3: lapply(trackList, consolidateTrack, chromosome = chromosome,
#   any(.needsAxis(trackList)), any(.needsTitle(trackList)),
#   title.width, alpha = hasAlpha, ...)
#2: plotTracks(aTrack, from = 1, to = 10) at #4
#1: plotGViz()

sessionInfo()
#R version 3.1.0 (2014-04-10)
#Platform: x86_64-pc-linux-gnu (64-bit)
#
#locale:
# [1] LC_CTYPE=en_US.UTF-8   LC_NUMERIC=C
# [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
# [5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8
# [7] LC_PAPER=en_US.UTF-8   LC_NAME=C
# [9] LC_ADDRESS=C   LC_TELEPHONE=C
#[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
#
#attached base packages:
#[1] parallel  grid  stats graphics  grDevices utils datasets
#[8] methods   base
#
#other attached packages:
#[1] XVector_0.4.0   IRanges_1.22.6  Gviz_1.8.0
#[4] BiocGenerics_0.10.0 devtools_1.5vimcom.plus_0.9-93
#[7] setwidth_1.0-3  colorout_1.0-2
#
#loaded via a namespace (and not attached):
# [1] AnnotationDbi_1.26.0 BatchJobs_1.2
# [3] BBmisc_1.6   Biobase_2.24.0
# [5] BiocParallel_0.6.0   biomaRt_2.20.0
# [7] Biostrings_2.32.0biovizBase_1.12.1
# [9] bitops_1.0-6 brew_1.0-6
#[11] BSgenome_1.32.0  cluster_1.15.2
#[13] codetools_0.2-8  colorspace_1.2-4
#[15] DBI_0.2-7dichromat_2.0-0
#[17] digest_0.6.4 evaluate_0.5.5
#[19] fail_1.2 foreach_1.4.2
#[21] Formula_1.1-1GenomeInfoDb_1.0.2
#[23] GenomicAlignments_1.0.1  GenomicFeatures_1.16.0
#[25] GenomicRanges_1.16.3 Hmisc_3.14-4
#[27] httr_0.3 iterators_1.0.7
#[29] lattice_0.20-29  latticeExtra_0.6-26
#[31] matrixStats_0.8.14   memoise_0.2.1
#[33] munsell_0.4.2plyr_1.8.1
#[35] RColorBrewer_1.0-5   Rcpp_0.11.1
#[37] RCurl_1.95-4.1   R.methodsS3_1.6.1
#[39] Rsamtools_1.16.0 RSQLite_0.11.4
#[41] rtracklayer_1.24.0   scales_0.2.4
#[43] sendmailR_1.1-2  splines_3.1.0
#[45] stats4_3.1.0 stringr_0.6.2
#[47] survival_2.37-7  tools_3.1.0
#[49] VariantAnnotation_1.10.1 whisker_0.3-2
#[51] XML_3.98-1.1 zlibbioc_1.10.0

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[Bioc-devel] BiocStyle and knitr: option clash for package color

[Sebastian Gibb]

Dear BiocStyle-Maintainer,

I try to use BiocStyle (0.0.13) in a knitr vignette. It seems both knitr and 
BiocStyle include the color package with different options (knitr: without any 
option; BiocStyle with usenames,dvipsnames). That's why R CMD build fails:
...
* installing the package to re-build vignettes
* creating vignettes ... ERROR
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running ‘texi2dvi’ on ‘cleaver.tex’ failed.
LaTeX errors:
! LaTeX Error: Option clash for package color.
...

Please find some minimal working examples on: 
https://gist.github.com/sgibb/6057514

The following small patch should fix this problem (at least my knitr vignette 
is build correctly):

--- Bioconductor.sty2013-07-22 22:17:27.154142990 +0200
+++ Bioconductor-patched.sty2013-07-22 22:17:22.466143142 +0200
@@ -7,7 +7,8 @@
 %% \ExecuteOptions{pdftitle,pdfauthor}
 %% \ProcessOptions
 
-\RequirePackage[usenames,dvipsnames]{color}
+\PassOptionsToPackage{usenames,dvipsnames}{color}
+\RequirePackage{color}
 \definecolor{BiocBlue}{RGB}{24,129,194}
 \definecolor{BiocGreen}{RGB}{135,177,63}
 \RequirePackage[%


Kind regards,

Sebastian

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