Re: [Bioc-devel] Git Transition Plan

[Angerer, Philipp]

hi, do you know by now when the beta will start? i’m honestly a bit tired of 
SVN and would like to participate 


Von: "Turaga, Nitesh"  
An: bioc-devel@r-project.org 
Gesendet: Donnerstag, 1. Juni 2017 14:19:59 
Betreff: Re: [Bioc-devel] Git Transition Plan 

Hi Nathan, 

We¹ve been working on a few things for the beta phase of the transition. 

1. Getting the experiment data packages on board 
2. Making sure manifests are in order along with their commit history. 
3. Writing documentation for our new workflows for developers/maintainers. 

The beta process has not started but, we expect it to be in play very 
soon. 

New package submissions are still going through SVN. We will make sure to 
send out an email/ post in the support group NEWS, and inform all the 
users as soon as that happens. 

You did not miss anything. 

Best, 

Nitesh 




>Hi Nitesh and all, 
> 
>Can you give any status update on the SVN-to-git transition? I haven't 
>seen any news since this exchange in March -- is the announced public 
>beta in progress or ongoing? Are new package submissions going straight 
>into git at this point? 
> 
>Or did I miss something? 
> 
>Thanks, 
> 
>Nathan 
> 
> 
>On 04/01/2017 09:14 AM, Martin Morgan wrote: 
>> On 03/29/2017 03:55 PM, Henrik Bengtsson wrote: 
>>> Thanks. I have a few thoughts and questions in order to plan ahead: 
>>> 
 - Our plan is to make a 'clean' transition from SVN to git, 
 approximately one month after the next Bioconductor release. 
 Developers or users will not have access to the SVN system after the 
 date of transition. 
>>> 
>>> In order to preserve commit authorship, what's your plan for mapping 
>>> SVN username to Git 'user.email' and 'user.name'? The 'user.email' is 
>>> what GitHub uses to associate commits and contributions to GitHub 
>>> accounts. 
>> 
>> The svn administrators kept a comprehensive (but not complete) record 
>> of svn id, real user name, and contact email at the time the svn id 
>> was create. We use this to map between svn commits and git user name 
>> and email address. 
>> 
>> The information is not entirely consistent, with some fields for some 
>> records 'missing' (e.g., my record doesn't contain my real name) and 
>> of course out of date (e.g., my email address). 
>> 
>> Our intention is NOT to re-write history, but to map the information 
>> that we have to the git repositories. So my svn commits appear without 
>> a proper name, and with an outdated email address. Of course, new 
>> commits after the transition will contain whatever info git provides. 
>> 
>>> 
>>> BTW, using obsolete email addresses may prevent people from being 
>>> associated with those email addresses on GitHub and other online 
>>> services that require authentication of authorship claims (which go 
>>> out via those email addresses). 
>>> 
>>> When I SVN-to-Git exported my Bioconductor packages a few years ago, I 
>>> could handle manually because there were not too many contributors in 
>>> the SVN logs and I reached out to each of them and asked what email 
>>> addresses they would prefer to have in the Git commits. That approach 
>>> is obviously not feasible to automate for all Bioconductor packages. 
>>> Maybe this can be handled optionally by each package maintainers by 
>>> adding a .gitauthors file to the package root (or possibly via a 
>>> global Bioc one that everyone can commit to), e.g. 
>>> ```r 
>>> hb = Henrik Bengtsson  
>>> j...@foo.com = John Doe  
>>> ``` 
>>> and then Bioc can use this mapping when exporting to Git? 
>>> 
>>> Finally, will people like me who already done the SVN-to-Git migration 
>>> be able to use that instead of the Bioc generated one? (I assume not, 
>>> but worth asking) 
>> 
>> No, we'll make a git snapshots of svn at the time of transition, and 
>> these git repositories will be the cannonical version -- developers 
>> will need to sync with these as they see fit. 
>> 
>> Martin 
>> 
>>> 
>>> Thanks, 
>>> 
>>> Henrik 
>>> 
>>> On Wed, Mar 29, 2017 at 9:51 AM, Turaga, Nitesh 
>>>  wrote: 
 Dear Bioconductor Developers, 
 
 More news about the Git transition plan. We are coming close to our 
 transition date and have made significant progress in getting our 
 new server ready for the Bioconductor community. 
 
 1. Overall plan: 
 
 - Bioconductor hosts each package as a distinct repository at 
 git.bioconductor.org. From 
 Bioconductor's perspective, this is the canonical location. Nightly 
 builds will be based on these repositories, release branches will be 
 created in these repositories, etc. The naming convention for 
 branches remains the same. 
 
 - Developers clone or otherwise sync their code base to these 
 repositories. Each developer will be able to push to and pull from 
 (e.g., during branching 

Re: [Bioc-devel] transitioning scater/scran to SingleCellExperiment

[Angerer, Philipp]

Hi Aaron, 



I guess this would be a question for the SummarizedExperiment developers, 
though personally, I never liked ExpressionSet's inclination to slap names on 
everything. 



Too bad we’re bound to SummarizedExperiment’s “rows” and “cols”. Since they 
always refer to features and samples, respectively: Why not name them that? 

There’s already too many APIs in too many programming languages that 
confusingly have one or the other convention – if whe know which is which, why 
not name them after that knowledge? 
BQ_BEGIN


It probably wouldn't be a good idea to store distances as expression matrices. 
However, if there is a need for it, we can add a new slot for distance 
matrices. I think SC3 has a similar requirement, so perhaps this would be more 
generally useful than I first thought. You can post an issue on the github 
repository to remind Davide or me to do it. 
BQ_END


Distance matrices (cell×cell) can’t only come from cell×gene matrices. You can 
e.g. use dynamic time warping to create them from cell×gene×time arrays. 
BQ_BEGIN


Finally, I'm not sure what advantages those ergonomics provide. Indeed, if 
every package defines its own plot() S4 method for SingleCellExperiment, they 
will clobber each other in the dispatch table, resulting in some interesting 
results dependent on package loading order. If you have destiny-specific data 
and methods, best to keep them separate rather than stuffing them into the SCE 
object. 
BQ_END


I wrote that I could e.g. create a plot_dm method, which plots a diffusion map 
stored in a SCE. 

Also I didn’t mean the plot method with ergonomics. I meant fortify , names , $ 
, and [[ . Those would be very useful, as you could just do things like the 
following, and have autocompletion: 
sce$Predicate1 <- sce$SampleMeta1 > 40 # `$` accesses counts (by gene) and 
rowData. `$<-` sets rowData 
qplot(Gene1, Gene2, colour = Predicate1, data = sce) # fortify creates a 
data.frame containing cbind(t(counts), rowData) 


Just as you can do now with DiffusionMap objects. 

Also I’m not sure if i got rowData and the “t” right in the above code ;) I 
meant cbind(counts as cell×gene, sampleMeta as cell×n_meta) 

Best, 
Phil 

 


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85764 Neuherberg

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Re: [Bioc-devel] transitioning scater/scran to SingleCellExperiment

[Angerer, Philipp]

Hi Aaron and Martin, 



In any case, a distance matrix calculated from such an array would be fine, as 
long as the dimensions are equal to the number of cells. The question is 
whether it is needed by enough packages to warrant a slot in the base SCE 
class; I will discuss this with Davide and Vlad. 



Yeah, that was my point. since it’s cumbersome and non-natural to have 3D data 
in there, a distance matrix would fit better. 
BQ_BEGIN


The SingleCellExperiment package makes no statement on whether downstream 
users/packages want to (or not) use the tidy-verse or ggplot2. It simply 
provides the minimal class and methods; convenience wrappers are left to the 
discretion of each package developer. scater, for example, implements a few 
dplyr verbs for SCE objects. 
BQ_END


Of course, but only fortify is ggplot2-specific. But anyway; Martin pointed 
out: 
BQ_BEGIN


FWIW, SummarizedExperiment (hence SingleCellExperimet) uses $ (and $<-; also [[ 
and [[<-) to access (with auto-completion) colData. And it wouldn't be a good 
idea to have $ access one element (counts) and $<- modify another (rowData), or 
to mix what $ and [[ access. 

Martin 
BQ_END


Ah, I see! names and .DollarNames.SummarizedExperiment are also defined! Well, 
that’s good enough i think, although this seems cumbersome: 
assays(sce)$log_counts[ 'Actb' , ] 


Cheers, Phil 

 


Helmholtz Zentrum Muenchen

Deutsches Forschungszentrum fuer Gesundheit und Umwelt (GmbH)

Ingolstaedter Landstr. 1

85764 Neuherberg

www.helmholtz-muenchen.de

Aufsichtsratsvorsitzende: MinDir'in Baerbel Brumme-Bothe

Geschaeftsfuehrer: Prof. Dr. Guenther Wess, Heinrich Bassler, Dr. Alfons Enhsen

Registergericht: Amtsgericht Muenchen HRB 6466

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Re: [Bioc-devel] transitioning scater/scran to SingleCellExperiment

[Angerer, Philipp]

Hi! 

As I told you at the HCA hackathon, I’m interested in switching over destiny! I 
think the class is a really cool idea and seems very well thought out. 

Interestingly the design decisions coverged very well with [ 
https://github.com/theislab/scanpy#readme | scanpy ] ’s [ 
https://www.pydoc.io/pypi/scanpy-0.2.3/autoapi/data_structs/ann_data/index.html#data_structs.ann_data.AnnData
 | AnnData ] class that I helped Alex design. Scanpy makes heavy use of HDF5 
serialization. I think we should quickly converge on a serialization format 
(keys and so on) so that AnnData and SingleCellExperiment can have 
interoperability via HDF5! 

The only point of criticism is that you, while staying specific to single cell 
data, named the dimensions “rows” and “columns” instead of e.g. “samples” and 
“variables”. Alex and me came to the conclusion that ExpressionSet ’s way of 
returning a named vector for dims is a good idea, and having the dimensions 
named for their roles reduces confusion. 

I have “two” “questions” regarding destiny, with some feature requests hiding 
in the second one: 1. 


destiny accepts either an expression matrix or a distance matrix (both with 
optional metadata). 

Currently the signature is this: 
DiffusionMap(data = ExpressionSet | data.frame | matrix | Matrix,
 distance = NULL | "euclidean" | "cosine" | "rankcor" ) 
DiffusionMap(data = NULL | data.frame , # Metadata distance = matrix | dist 
| symmetricMatrix) 


The idea is that both when providing expressions and when providing a distance 
matrix, you should be able to provide metadata. I’m not super happy with my 
approach, since the current methods of providing metadata differ. 

However, ExpressionSet and SingleCellExperiment are both specific for 
expression data. I think neither can hold dist objects as data. 

Is it valid and a good idea to neither store counts not exprs, but e.g. 
SingleCellExperiment(assays = list(dists = some_mat)) ? It wouldn’t be sliced 
properly, for example, and it being symmetric would mean that column and row 
metadata is the same… 

Is it a good idea to require assays to have certain names (e.g. “exprs” or 
“dists” here)? 2. 


The reducedDim methods would be able to store and retrieve diffusion components 
in a SingleCellExperiment , while destiny’s dataset method stores the original 
data used to create a DiffusionMap . 

What do you think is the best approach? Just conversions between the two 
classes? Or also deprecate DiffusionMap objects and create a diffusion_map 
function that returns a SingleCellExperiment object with the reduced dimensions 
and all the necessary metadata for further methods like e.g. DPT? 

I think for the latter, SingleCellExperiment isn’t quite cool enough yet :P. 
I’d like to have the full ergonomics of DiffusionMap : 

* A names method (returning gene and per-cell-metadata names) 
* Gene/per-cell-metadata access by $ and [[ . 
* A fortify method that makes everything available in ggplot2. (E.g. 
ggplot(dm, aes(DC1, DC2, colour = Condition)) works!) 



I can do without the remaining methods (or provide them in destiny), as they 
are are neither general purpose enough for SingleCellExperiment nor really 
necessary, e.g. I can add an alias plot(a_dm_object) → plot_dm(a_sce_object) . 

Cheers, Philipp 
Von: "Aaron Lun"  
An: "bioc-devel"  
Gesendet: Montag, 31. Juli 2017 10:38:03 
Betreff: Re: [Bioc-devel] transitioning scater/scran to SingleCellExperiment 

Dear developers, 

Both scater and scran will be migrating to the SingleCellExperiment 
class (https://bioconductor.org/packages/SingleCellExperiment) in the 
next BioC release. This is based on a SummarizedExperiment and provides 
a more modern user interface, as well as supporting different matrix 
representations (e.g., dgCMatrix, HDF5Matrix). 

We note that there are a number of Bioconductor packages that depend 
on/import/suggest scater or scran, which we have listed below: 

scDD 
scone 
SIMLR 
splatter 
Glimma 
SC3 
phenopath 
switchde 

To the maintainers of these packages, we advise switching from SCESet to 
SingleCellExperiment as soon as possible; the former will be deprecated 
in the next release cycle. There are several things to note here: 

- The SCESet previously contained a number of slots relating to 
distances and clustering results. These are no longer present in the 
SingleCellExperiment, in line with the minimalist design philosophy of 
that package. If these are necessary, we suggest extending the 
SingleCellExperiment class in your own packages(*). 

- For packages that depend directly on methods in scater or scran, a 
number of methods have been removed. This aims to simplify the analysis 
workflow and code maintenance by reducing redundancy. Please ensure that 
your package does not need those missing methods by CHECKing it against 
the experimental versions(**) of these two packages: 

https://github.com/LTLA/scran 

Re: [Bioc-devel] New pre-receive hook on git.bioconductor.org

[Angerer, Philipp]

hi, sadly my duplicate commits are authored by Herve Pages and already in the 
repo , so i can’t work at all on my package (destiny). 

$ git push 
Zähle Objekte: 12, Fertig. 
Delta compression using up to 8 threads. 
Komprimiere Objekte: 100% (12/12), Fertig. 
Schreibe Objekte: 100% (12/12), 1.14 KiB | 1.14 MiB/s, Fertig. 
Total 12 (delta 9), reused 0 (delta 0) 
remote: Error: duplicate commits. 
remote: 
remote: There are duplicate commits in your commit history, These cannot be 
remote: pushed to the Bioconductor git server. Please make sure that this is 
remote: resolved. 
remote: 
remote: Take a look at the documentation to fix this, 
remote: 
https://bioconductor.org/developers/how-to/git/sync-existing-repositories/, 
remote: particularly, point #8 (force Bioconductor master to Github master). 
remote: 
remote: For more information, or help resolving this issue, contact 
remote: . Provide the error, the package name and 
remote: any other details we might need. 
remote: 
remote: Use 
remote: 
remote: git show 72261dcfd1d1e7adf73f16bb4e6d9e38eecccbf9 
remote: git show b3fb272fc4517faab44a3792825a07460eadc345 
remote: 
remote: to see body of commits. 
remote: 
To git.bioconductor.org:packages/destiny 
! [remote rejected] RELEASE_3_5 -> RELEASE_3_5 (pre-receive hook declined) 
error: Fehler beim Versenden einiger Referenzen nach 
'g...@git.bioconductor.org:packages/destiny' 
$ git show 72261dcfd1d1e7adf73f16bb4e6d9e38eecccbf9 
commit 72261dcfd1d1e7adf73f16bb4e6d9e38eecccbf9 
Author: Herve Pages  
Date: Mon Apr 24 19:45:44 2017 + 

Creating branch for BioC 3.5 release 

git-svn-id: 
file:///home/git/hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/destiny@129128
 bc3139a8-67e5-0310-9ffc-ced21a209358 
$ git show b3fb272fc4517faab44a3792825a07460eadc345 
commit b3fb272fc4517faab44a3792825a07460eadc345 
Author: Herve Pages  
Date: Mon Apr 24 19:25:24 2017 + 

bump x.y.z versions to even y prior to creation of 3_5 branch 

git-svn-id: 
file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/destiny@129126
 bc3139a8-67e5-0310-9ffc-ced21a209358 

diff --git a/DESCRIPTION b/DESCRIPTION 
index 9a01095..2368e6d 100644 
--- a/DESCRIPTION 
+++ b/DESCRIPTION 
@@ -1,7 +1,7 @@ 
Package: destiny 
Type: Package 
Title: Creates diffusion maps 
-Version: 2.2.11 
+Version: 2.4.0 
Date: 2014-12-19 
Authors@R: c( 


Von: "Nitesh Turaga"  
An: "bioc-devel"  
Gesendet: Dienstag, 29. August 2017 18:15:38 
Betreff: [Bioc-devel] New pre-receive hook on git.bioconductor.org 

Hi Maintainers, 

We have added a new pre-receive hook on our 
git.bioconductor.org system today. We now prevent 
large-files (>5MB) from being committed. We also prevent ‘duplicate' commits. 

A duplicate commit is when two commits have the same content, but different 
SHA1 signatures. This can happen, for instance, when you clone 
git.bioconductor.org and then merge with your 
local git development repository or 
github.com/Bioconductor-mirror 
repository. The best way to approach this issue is in the documentation, 
http://bioconductor.org/developers/how-to/git/abandon-changes#force-bioconductor--to-github-,
 including the option to cherry-pick local commits into the master branch 
synced from git.bioconductor.org. 

Please let us know if you have any questions. 

Best, 

Nitesh 


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Aufsichtsratsvorsitzende: MinDir'in Baerbel Brumme-Bothe

Geschaeftsfuehrer: Prof. Dr. Guenther Wess, Heinrich Bassler, Dr. Alfons Enhsen

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Re: [Bioc-devel] New pre-receive hook on git.bioconductor.org

[Angerer, Philipp]

hi nitesh, 

thank you, it worked now! 

best, philipp 


Von: "Nitesh Turaga" <nitesh.tur...@roswellpark.org> 
An: "Philipp Angerer" <philipp.ange...@helmholtz-muenchen.de> 
CC: "bioc-devel" <bioc-devel@r-project.org> 
Gesendet: Mittwoch, 30. August 2017 14:04:50 
Betreff: Re: [Bioc-devel] New pre-receive hook on git.bioconductor.org 

Hi Philipp, 

Please try again. 

Best, 

Nitesh 


> On Aug 30, 2017, at 4:33 AM, Angerer, Philipp 
> <philipp.ange...@helmholtz-muenchen.de> wrote: 
> 
> hi, sadly my duplicate commits are authored by Herve Pages and already in the 
> repo, so i can’t work at all on my package (destiny). 
> 
> $ git push 
> Zähle Objekte: 12, Fertig. 
> Delta compression using up to 8 threads. 
> Komprimiere Objekte: 100% (12/12), Fertig. 
> Schreibe Objekte: 100% (12/12), 1.14 KiB | 1.14 MiB/s, Fertig. 
> Total 12 (delta 9), reused 0 (delta 0) 
> remote: Error: duplicate commits. 
> remote: 
> remote: There are duplicate commits in your commit history, These cannot be 
> remote: pushed to the Bioconductor git server. Please make sure that this is 
> remote: resolved. 
> remote: 
> remote: Take a look at the documentation to fix this, 
> remote: 
> https://bioconductor.org/developers/how-to/git/sync-existing-repositories/, 
> remote: particularly, point #8 (force Bioconductor master to Github master). 
> remote: 
> remote: For more information, or help resolving this issue, contact 
> remote: <bioc-devel@r-project.org>. Provide the error, the package name and 
> remote: any other details we might need. 
> remote: 
> remote: Use 
> remote: 
> remote: git show 72261dcfd1d1e7adf73f16bb4e6d9e38eecccbf9 
> remote: git show b3fb272fc4517faab44a3792825a07460eadc345 
> remote: 
> remote: to see body of commits. 
> remote: 
> To git.bioconductor.org:packages/destiny 
> ! [remote rejected] RELEASE_3_5 -> RELEASE_3_5 (pre-receive hook declined) 
> error: Fehler beim Versenden einiger Referenzen nach 
> 'g...@git.bioconductor.org:packages/destiny' 
> $ git show 72261dcfd1d1e7adf73f16bb4e6d9e38eecccbf9 
> commit 72261dcfd1d1e7adf73f16bb4e6d9e38eecccbf9 
> Author: Herve Pages <hpa...@fhcrc.org> 
> Date: Mon Apr 24 19:45:44 2017 + 
> 
> Creating branch for BioC 3.5 release 
> 
> git-svn-id: 
> file:///home/git/hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/destiny@129128
>  bc3139a8-67e5-0310-9ffc-ced21a209358 
> $ git show b3fb272fc4517faab44a3792825a07460eadc345 
> commit b3fb272fc4517faab44a3792825a07460eadc345 
> Author: Herve Pages <hpa...@fhcrc.org> 
> Date: Mon Apr 24 19:25:24 2017 + 
> 
> bump x.y.z versions to even y prior to creation of 3_5 branch 
> 
> git-svn-id: 
> file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/destiny@129126
>  bc3139a8-67e5-0310-9ffc-ced21a209358 
> 
> diff --git a/DESCRIPTION b/DESCRIPTION 
> index 9a01095..2368e6d 100644 
> --- a/DESCRIPTION 
> +++ b/DESCRIPTION 
> @@ -1,7 +1,7 @@ 
> Package: destiny 
> Type: Package 
> Title: Creates diffusion maps 
> -Version: 2.2.11 
> +Version: 2.4.0 
> Date: 2014-12-19 
> Authors@R: c( 
> 
> Von: "Nitesh Turaga" <nitesh.tur...@roswellpark.org> 
> An: "bioc-devel" <bioc-devel@r-project.org> 
> Gesendet: Dienstag, 29. August 2017 18:15:38 
> Betreff: [Bioc-devel] New pre-receive hook on git.bioconductor.org 
> 
> Hi Maintainers, 
> 
> We have added a new pre-receive hook on our 
> git.bioconductor.org<http://git.bioconductor.org> system today. We now 
> prevent large-files (>5MB) from being committed. We also prevent ‘duplicate' 
> commits. 
> 
> A duplicate commit is when two commits have the same content, but different 
> SHA1 signatures. This can happen, for instance, when you clone 
> git.bioconductor.org<http://git.bioconductor.org> and then merge with your 
> local git development repository or 
> github.com/Bioconductor-mirror<http://github.com/Bioconductor-mirror> 
> repository. The best way to approach this issue is in the documentation, 
> http://bioconductor.org/developers/how-to/git/abandon-changes#force-bioconductor--to-github-,
>  including the option to cherry-pick local commits into the master branch 
> synced from git.bioconductor.org<http://git.bioconductor.org>. 
> 
> Please let us know if you have any questions. 
> 
> Best, 
> 
> Nitesh 
> 
> 
> 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, cop

[Bioc-devel] jupyter installation on merida1

[Angerer, Philipp]

Dear BioConductor maintainers, 

The buildbots almost seem able to build my package’s vignettes again, but the 
jupyter installation on merida1 still [ 
http://bioconductor.org/checkResults/release/bioc-LATEST/destiny/merida1-buildsrc.html
 | doesn’t seem quite right ] : 
* creating vignettes ... ERROR 
--- re-building ‘DPT.ipynbmeta’ using nbconvert 
Warning in system2("jupyter", shQuote(args), carg, carg, wait = TRUE, env = 
env,  : 
running command 'PYTHONPATH=.:.: 'jupyter' 'nbconvert' [...] 'DPT.ipynb' 2>&1' 
had status 126 
Call failed. Output: 
sh: /usr/local/bin/jupyter: /usr/local/opt/python3/bin/python3.6: bad 
interpreter: No such file or directory 


Exit status 126 means “The thing you tried to execute is not executable or 
doesn’t exist”. The message looks like sh tries to find the binary referenced 
in the shebang of /usr/local/bin/jupyter, and fails. I assume jupyter has been 
installed with an interpreter that no longer exists, and now its shebang points 
into the void? I guess the following is true for your system: 
$ head -n1 /usr/local/bin/jupyter 
#!/usr/local/opt/python3/bin/python3.6 
$ ls /usr/local/opt/python3/bin/python3.6 
No such file or directory (os error 2) 


Anyway, it would be amazing if someone could fix jupyter’s installation on that 
system (until jupyter nbconvert --help works). The vignette engine trying to 
use it (nbconvertR) [ https://cran.rstudio.com/web/packages/nbconvertR/INSTALL 
| has extensive INSTALL instructions ] that might help! 


Thank you so much, 
Philipp 

Helmholtz Zentrum München


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Re: [Bioc-devel] jupyter installation on merida1

[Angerer, Philipp]

Dear maintainers,

Is there any progress with this? Any way I can help?

Thank you,
Philipp

- Ursprüngliche Mail -
Von: "Philipp Angerer" 
An: "bioc-devel" 
Gesendet: Mittwoch, 4. Dezember 2019 10:58:44
Betreff: [Bioc-devel] jupyter installation on merida1

Dear BioConductor maintainers, 

The buildbots almost seem able to build my package’s vignettes again, but the 
jupyter installation on merida1 still doesn’t seem quite right: 
http://bioconductor.org/checkResults/release/bioc-LATEST/destiny/merida1-buildsrc.html

* creating vignettes ... ERROR
--- re-building ‘DPT.ipynbmeta’ using nbconvert
Warning in system2("jupyter", shQuote(args), carg, carg, wait = TRUE, env = 
env, :
running command 'PYTHONPATH=.:.: 'jupyter' 'nbconvert' [...] 'DPT.ipynb' 2>&1' 
had status 126
Call failed. Output:
sh: /usr/local/bin/jupyter: /usr/local/opt/python3/bin/python3.6: bad 
interpreter: No such file or directory

Exit status 126 means “The thing you tried to execute is not executable or 
doesn’t exist”. The message looks like sh tries to find the binary referenced 
in the shebang of /usr/local/bin/jupyter, and fails. I assume jupyter has been 
installed with an interpreter that no longer exists, and now its shebang points 
into the void? I guess the following is true for your system:

$ head -n1 /usr/local/bin/jupyter
#!/usr/local/opt/python3/bin/python3.6
$ ls /usr/local/opt/python3/bin/python3.6
No such file or directory (os error 2)

Anyway, it would be amazing if someone could fix jupyter’s installation on that 
system (until jupyter nbconvert --help works). The vignette engine trying to 
use it (nbconvertR) has extensive INSTALL instructions that might help: 
https://cran.rstudio.com/web/packages/nbconvertR/INSTALL

Thank you so much,
Philipp

Helmholtz Zentrum München

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Re: [Bioc-devel] Git mirror out of sync

[Angerer, Philipp via Bioc-devel]

great, thanks! 


Von: "Martin Morgan" <martin.mor...@roswellpark.org> 
An: "Angerer, Philipp" <philipp.ange...@helmholtz-muenchen.de>, "bioc-devel" 
<bioc-devel@r-project.org> 
Gesendet: Donnerstag, 11. August 2016 12:54:50 
Betreff: Re: [Bioc-devel] Git mirror out of sync 

On 08/09/2016 04:18 AM, Angerer, Philipp via Bioc-devel wrote: 
> Hi, 
> 
> destiny ’s git mirror has been out of sync for quite some time. 
> 
> The currently latest SVN revision has bumped the version to 1.3.4 , but git 
> master is still on 1.3.0 . 
> 

This should be back on track now, please let us know if problems occur 
again. 

Martin 

> Thanks for looking at it, 
> Philipp 
> 
> 
> 
> 
> Helmholtz Zentrum Muenchen 
> 
> Deutsches Forschungszentrum fuer Gesundheit und Umwelt (GmbH) 
> 
> Ingolstaedter Landstr. 1 
> 
> 85764 Neuherberg 
> 
> www.helmholtz-muenchen.de 
> 
> Aufsichtsratsvorsitzende: MinDir'in Baerbel Brumme-Bothe 
> 
> Geschaeftsfuehrer: Prof. Dr. Guenther Wess, Dr. Alfons Enhsen, Renate 
> Schlusen (komm.) 
> 
> Registergericht: Amtsgericht Muenchen HRB 6466 
> 
> USt-IdNr: DE 129521671 
> 
> 
> [[alternative HTML version deleted]] 
> 
> ___ 
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> 


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[Bioc-devel] Git mirror out of sync

[Angerer, Philipp via Bioc-devel]

Hi, 

destiny ’s git mirror has been out of sync for quite some time. 

The currently latest SVN revision has bumped the version to 1.3.4 , but git 
master is still on 1.3.0 . 

Thanks for looking at it, 
Philipp 

 


Helmholtz Zentrum Muenchen

Deutsches Forschungszentrum fuer Gesundheit und Umwelt (GmbH)

Ingolstaedter Landstr. 1

85764 Neuherberg

www.helmholtz-muenchen.de

Aufsichtsratsvorsitzende: MinDir'in Baerbel Brumme-Bothe

Geschaeftsfuehrer: Prof. Dr. Guenther Wess, Dr. Alfons Enhsen, Renate Schlusen 
(komm.)

Registergericht: Amtsgericht Muenchen HRB 6466

USt-IdNr: DE 129521671


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Re: [Bioc-devel] Git mirror out of sync

[Angerer, Philipp via Bioc-devel]

hi, it happened 
again:https://github.com/Bioconductor-mirror/destinyout of 
sync… 


Von: "Angerer, Philipp via Bioc-devel" <bioc-devel@r-project.org> 
An: "Martin Morgan" <martin.mor...@roswellpark.org> 
CC: "bioc-devel" <bioc-devel@r-project.org> 
Gesendet: Donnerstag, 11. August 2016 13:05:58 
Betreff: Re: [Bioc-devel] Git mirror out of sync 

great, thanks! 


Von: "Martin Morgan" <martin.mor...@roswellpark.org> 
An: "Angerer, Philipp" <philipp.ange...@helmholtz-muenchen.de>, "bioc-devel" 
<bioc-devel@r-project.org> 
Gesendet: Donnerstag, 11. August 2016 12:54:50 
Betreff: Re: [Bioc-devel] Git mirror out of sync 

On 08/09/2016 04:18 AM, Angerer, Philipp via Bioc-devel wrote: 
> Hi, 
> 
> destiny ’s git mirror has been out of sync for quite some time. 
> 
> The currently latest SVN revision has bumped the version to 1.3.4 , but git 
> master is still on 1.3.0 . 
> 

This should be back on track now, please let us know if problems occur 
again. 

Martin 

> Thanks for looking at it, 
> Philipp 
> 
> 
> 
> 
> Helmholtz Zentrum Muenchen 
> 
> Deutsches Forschungszentrum fuer Gesundheit und Umwelt (GmbH) 
> 
> Ingolstaedter Landstr. 1 
> 
> 85764 Neuherberg 
> 
> www.helmholtz-muenchen.de 
> 
> Aufsichtsratsvorsitzende: MinDir'in Baerbel Brumme-Bothe 
> 
> Geschaeftsfuehrer: Prof. Dr. Guenther Wess, Dr. Alfons Enhsen, Renate 
> Schlusen (komm.) 
> 
> Registergericht: Amtsgericht Muenchen HRB 6466 
> 
> USt-IdNr: DE 129521671 
> 
> 
> [[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 
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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. 




Helmholtz Zentrum Muenchen 

Deutsches Forschungszentrum fuer Gesundheit und Umwelt (GmbH) 

Ingolstaedter Landstr. 1 

85764 Neuherberg 

www.helmholtz-muenchen.de 

Aufsichtsratsvorsitzende: MinDir'in Baerbel Brumme-Bothe 

Geschaeftsfuehrer: Prof. Dr. Guenther Wess, Dr. Alfons Enhsen 

Registergericht: Amtsgericht Muenchen HRB 6466 

USt-IdNr: DE 129521671 


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Helmholtz Zentrum Muenchen

Deutsches Forschungszentrum fuer Gesundheit und Umwelt (GmbH)

Ingolstaedter Landstr. 1

85764 Neuherberg

www.helmholtz-muenchen.de

Aufsichtsratsvorsitzende: MinDir'in Baerbel Brumme-Bothe

Geschaeftsfuehrer: Prof. Dr. Guenther Wess, Dr. Alfons Enhsen

Registergericht: Amtsgericht Muenchen HRB 6466

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Re: [Bioc-devel] tokay1 (windows) build server cannot use the nbconvertR vignette engine

[Angerer, Philipp via Bioc-devel]

Although, since you (Philipp) are the maintainer of the nbconvertR package, you 
may want to create an INSTALL file in that package. It's up to you. 

Dan 




Haha, yeah. Thanks, Dan! 

I’m already in the process of submitting nbconvertR 1.1, which only uses 
jupyter (Using ipython nbconvert is deprecated). 

That nbconvertR version also clarifies that the nbconvert python package (which 
depends on jupyter) needs to be installed, and contains install instructions in 
README.md. 

Best, Philipp 

 


Helmholtz Zentrum Muenchen

Deutsches Forschungszentrum fuer Gesundheit und Umwelt (GmbH)

Ingolstaedter Landstr. 1

85764 Neuherberg

www.helmholtz-muenchen.de

Aufsichtsratsvorsitzende: MinDir'in Baerbel Brumme-Bothe

Geschaeftsfuehrer: Prof. Dr. Guenther Wess, Dr. Alfons Enhsen

Registergericht: Amtsgericht Muenchen HRB 6466

USt-IdNr: DE 129521671


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[Bioc-devel] tokay1 (windows) build server cannot use the nbconvertR vignette engine

[Angerer, Philipp via Bioc-devel]

Hi, 

Looking at my package’s build report, the devel version isn’t built anymore on 
windows: 
http://bioconductor.org/checkResults/devel/bioc-LATEST/destiny/tokay1-buildsrc.html
 

The release version is built just fine with moscato2: 
http://bioconductor.org/checkResults/release/bioc-LATEST/destiny/moscato2-buildsrc.html
 

It would be really nice if this could be fixed. Usually running “jupyter 
nbconvert --help” successfully means that nbconvertR will work. 

Best, Philipp 

 


Helmholtz Zentrum Muenchen

Deutsches Forschungszentrum fuer Gesundheit und Umwelt (GmbH)

Ingolstaedter Landstr. 1

85764 Neuherberg

www.helmholtz-muenchen.de

Aufsichtsratsvorsitzende: MinDir'in Baerbel Brumme-Bothe

Geschaeftsfuehrer: Prof. Dr. Guenther Wess, Dr. Alfons Enhsen

Registergericht: Amtsgericht Muenchen HRB 6466

USt-IdNr: DE 129521671


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[Bioc-devel] destiny git mirror and SVN desynced

[Angerer, Philipp via Bioc-devel]

hi, 

for my package “destiny”, the master and release-3.4 branches aren’t in sync 
between SVN and the gihub mirror. 

release-3.4 is just 2 commits behind, but the master branch has diverged. (a 
few commits have different hashs and a few are missing on the github mirror) 

this has been really unstable so far. do you plan to offer upstream 
repositories soon? 

best regards, philipp 

 


Helmholtz Zentrum Muenchen

Deutsches Forschungszentrum fuer Gesundheit und Umwelt (GmbH)

Ingolstaedter Landstr. 1

85764 Neuherberg

www.helmholtz-muenchen.de

Aufsichtsratsvorsitzende: MinDir'in Baerbel Brumme-Bothe

Geschaeftsfuehrer: Prof. Dr. Guenther Wess, Dr. Alfons Enhsen

Registergericht: Amtsgericht Muenchen HRB 6466

USt-IdNr: DE 129521671


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Re: [Bioc-devel] destiny git mirror and SVN desynced

[Angerer, Philipp via Bioc-devel]

hmm, this is bad. now the release branch is OK, but there seems to be problem. 

when i do git svn rebase , i get this history: 


and a git reset origin/master sends me here: 


so the git mirror and the SVN seem to have permanently desynced… 

best, philipp 


Von: "Martin Morgan" <martin.mor...@roswellpark.org> 
An: "Angerer, Philipp" <philipp.ange...@helmholtz-muenchen.de>, "bioc-devel" 
<bioc-devel@r-project.org> 
Gesendet: Mittwoch, 14. Dezember 2016 16:02:04 
Betreff: Re: [Bioc-devel] destiny git mirror and SVN desynced 

On 12/14/2016 09:27 AM, Angerer, Philipp via Bioc-devel wrote: 
> hi, 
> 
> for my package “destiny”, the master and release-3.4 branches aren’t in sync 
> between SVN and the gihub mirror. 
> 
> release-3.4 is just 2 commits behind, but the master branch has diverged. (a 
> few commits have different hashs and a few are missing on the github mirror) 
> 
> this has been really unstable so far. do you plan to offer upstream 
> repositories soon? 

yes; the current situation is unsatisfactory. 

Currently the cannonical repository is svn. The build system (and hence 
packages seen by the user) don't care about the mirror. Also, the mirror 
is in many ways confusing -- not the official repository, and not the 
developer repository. 

> 
> best regards, philipp 
> 
> 
> 
> 
> Helmholtz Zentrum Muenchen 
> 
> Deutsches Forschungszentrum fuer Gesundheit und Umwelt (GmbH) 
> 
> Ingolstaedter Landstr. 1 
> 
> 85764 Neuherberg 
> 
> www.helmholtz-muenchen.de 
> 
> Aufsichtsratsvorsitzende: MinDir'in Baerbel Brumme-Bothe 
> 
> Geschaeftsfuehrer: Prof. Dr. Guenther Wess, Dr. Alfons Enhsen 
> 
> Registergericht: Amtsgericht Muenchen HRB 6466 
> 
> USt-IdNr: DE 129521671 
> 
> 
> [[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 
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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. 

 


Helmholtz Zentrum Muenchen

Deutsches Forschungszentrum fuer Gesundheit und Umwelt (GmbH)

Ingolstaedter Landstr. 1

85764 Neuherberg

www.helmholtz-muenchen.de

Aufsichtsratsvorsitzende: MinDir'in Baerbel Brumme-Bothe

Geschaeftsfuehrer: Prof. Dr. Guenther Wess, Dr. Alfons Enhsen

Registergericht: Amtsgericht Muenchen HRB 6466

USt-IdNr: DE 129521671

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