[Bioc-devel] Error in .get_entry_index(name, stop_if_missing)

[Zhezhen Wang]

Hi I had the following error while checking the package 
https://github.com/xyang2uchicago/BioTIP

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getCluster_methods
> ### Title: Clustering Network Nodes
> ### Aliases: getCluster_methods
>
> ### ** Examples
>
> test = list('state1' = matrix(sample(1:10,6),3,3),'state2' =
+ matrix(sample(1:10,6),3,3),'state3' = matrix(sample(1:10,6),3,3))
> #assign colnames and rownames to the matrix
>
> for(i in names(test)){
+ colnames(test[[i]]) = 1:3
+ row.names(test[[i]]) = 1:3}
>
> #using 'rw' or 'natural' method
> igraphL <- getNetwork(test, fdr=1)
[1] "state1:3 nodes"
[1] "state2:3 nodes"
[1] "state3:3 nodes"
> #[1] "state1:3 nodes"
> #[1] "state2:3 nodes"
> #[1] "state3:3 nodes"
>
> cl <- getCluster_methods(igraphL)
>
> #using 'km', 'pam' or 'hcm'
> cl <- getCluster_methods(test, method = 'pam', cutoff=2)
Error in .get_entry_index(name, stop_if_missing) :
  Entry TSDistances not in registry.
Calls: getCluster_methods ... TSDatabaseDistances -> dist ->  -> f 
-> .get_entry_index
Execution halted

It seems the problem is because the required library 'TSdist' not load 
successfully. However, import(TSdist) is written in both DESCRIPTION and 
NAMESPACE.

Zhezhen

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Re: [Bioc-devel] Import BSgenome class without attaching BiocGenerics (and others)?

[Pages, Herve]

Hi Aditya,

It feels that a coercion method from BSgenome to GRanges should rather 
be defined in the BSgenome package itself. Patch/PR welcome on GitHub. 
More generally speaking, coercion methods should be defined in a place 
that is "as close as possible" to the "from" or "to" classes rather than 
in a package that doesn't own any of the 2 classes involved.

Is this what you have in mind for this coercion?

   > as(seqinfo(BSgenome.Celegans.UCSC.ce10), "GRanges")
   GRanges object with 7 ranges and 0 metadata columns:
seqnames ranges strand
   
   chrI chrI 1-15072423  *
  chrIIchrII 1-15279345  *
 chrIII   chrIII 1-13783700  *
  chrIVchrIV 1-17493793  *
   chrV chrV 1-20924149  *
   chrX chrX 1-17718866  *
   chrM chrM1-13794  *
 ---
 seqinfo: 7 sequences (1 circular) from ce10 genome

Thanks,
H.


On 9/6/19 03:39, Bhagwat, Aditya wrote:
> Dear Bioc devel,
> 
> Is it possible to import the BSgenome class without attaching BiocGenerics 
> (to keep a clean namespace during the development of 
> multicrispr  >).
> 
> BSgenome <- methods::getClassDef('BSgenome', package = 'BSgenome')
> 
> (Posted earlier on BioC 
> support  > and redirected here following Martin's suggestion)
> 
> Thankyou :-)
> 
> Aditya
> 
>   [[alternative HTML version deleted]]
> 
> ___
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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
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E-mail: hpa...@fredhutch.org
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[Bioc-devel] RGL warning

[Zhezhen Wang]

Hi

I am having the following warnings and not sure what to update.

Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE

The package github link is here : https://github.com/xyang2uchicago/BioTIP

Zhezhen

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[Bioc-devel] Change package name

[Lulu Chen]

Dear all,

Could the package name be changed after released?

I have a package which has been in Bioconductor for more than one year. We
want to publish a paper about it recently. My advisor wants to use a new
name which can better reflect the objective of the package.

Thanks for any help!
Best,
Lulu

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Re: [Bioc-devel] Failing to build vignette because of problems with ImageMagick

[Christian Mertes]

Thanks a lot for the info! So from my understanding we dont use any
trimming or editing function from ImageMagick directly. I think this is
rather knitr based since we just include png files in the vignette.

I guess it was an hickup since now the error is gone over night.

Best regards,

Christian

On 9/9/19 4:34 PM, Kasper Daniel Hansen wrote:
> You don't declare any systems requirements for ImageMagick (doing so
> will probably not solve your problem, but you really should).
>
> Alternatively you could look into using the tools provided by the
> magick package, which wraps ImageMagick.
>
> But it looks like you're editing PNG files for your vignette. I would
> really recommend not doing so. It introduces a system dependency which
> is just going to increase headaches on your end, for (perhaps) no real
> tangible benefits. If you're trimming PNGs, you should be able to
> achieve the same effect when using the png device(s) in R, and that
> will make everything more portable anyway.
>
> On Mon, Sep 9, 2019 at 9:42 AM Christian Mertes  > wrote:
>
> Dear BioC team,
>
> I just noticed that our package is failing on the bioconductor build
> system during the build of the vignette on Windows and on MacOS
> platforms.
>
> From the error I would guess its a problem with the installation
> of the
> ImageMagick package. Please correct me if Im wrong.
>
> It goes through on travis and appveyor. Any suggestions?
>
> Here are some links to the build logs:
>
> http://bioconductor.riken.jp/checkResults/3.9/bioc-LATEST/OUTRIDER/
> https://travis-ci.org/gagneurlab/OUTRIDER
> https://ci.appveyor.com/project/c-mertes/OUTRIDER
>
> Best,
>
> Christian
>
> PS: the error message on the bioc build system:
>
> 
> ##
> 
> ##
> ###
> ### Running command:
> ###
> ###   chmod a+r OUTRIDER -R &&
> C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD build
> --keep-empty-dirs --no-resave-data OUTRIDER
> ###
> 
> ##
> 
> ##
>
>
> * checking for file 'OUTRIDER/DESCRIPTION' ... OK
> * preparing 'OUTRIDER':
> * checking DESCRIPTION meta-information ... OK
> * cleaning src
> * installing the package to build vignettes
> * creating vignettes ... ERROR
> --- re-building 'OUTRIDER.Rnw' using knitr
> Invalid Parameter - /deVsOutlier-1.png"
> Warning in shell(paste(c(cmd, args), collapse = " ")) :
>   'convert "figure/deVsOutlier-1.png" -trim
> "figure/deVsOutlier-1.png"' execution failed with error code 4
> 229 genes did not passed the filter due to zero counts. This is
> 22.9% of the genes.
> Sat Sep 07 01:16:53 2019: SizeFactor estimation ...
> Sat Sep 07 01:16:53 2019: Controlling for confounders ...
> Using estimated q with: 23
> Sat Sep 07 01:16:53 2019: Using the autoencoder implementation for
> controlling.
> Sat Sep 07 01:17:52 2019: Used the autoencoder implementation for
> controlling.
> Sat Sep 07 01:17:52 2019: P-value calculation ...
> Sat Sep 07 01:17:52 2019: Zscore calculation ...
> Invalid Parameter - /quick_guide-1.png"
> Warning in shell(paste(c(cmd, args), collapse = " ")) :
>   'convert "figure/quick_guide-1.png" -trim
> "figure/quick_guide-1.png"' execution failed with error code 4
> Quitting from lines 222-232 (OUTRIDER.Rnw)
> Error: processing vignette 'OUTRIDER.Rnw' failed with diagnostics:
> no lines available in input
> --- failed re-building 'OUTRIDER.Rnw'
>
> SUMMARY: processing the following file failed:
>   'OUTRIDER.Rnw'
>
> Error: Vignette re-building failed.
> Execution halted
>
> -- 
>
> Christian Mertes
> PhD Student / Lab Administrator
> Gagneur lab
>
> Computational Genomics
> I12 - Bioinformatics Department
> Technical University Munich
> Boltzmannstr. 3
> 85748 Garching, Germany
>
> Mail: mer...@in.tum.de 
> Phone: +49-89-289-19416
> http://gagneurlab.in.tum.de
>
>
>         [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org  mailing
> list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>
>
> -- 
> Best,
> Kasper

-- 

Christian Mertes
PhD Student / Lab Administrator
Gagneur lab
 
Computational Genomics
I12 - Bioinformatics Department
Technical University Munich
Boltzmannstr. 3
85748 Garching, Germany

Mail: mer...@in.tum.de
Phone: +49-89-289-19416
http://gagneurlab.in.tum.de


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Re: [Bioc-devel] Reset to a previous commit

[Turaga, Nitesh]

Hi Simon,

I take this back actually. I think the best way forward is just undo the code 
changes, and add a new version number to it ( 1.9.3) and push. 

Step 1,

Since your version 1.9.2 is already on Bioconductor, first sync your 
GitHub with that version.

Step 2,

Undo the code changes, and add a new version 1.9.3 to it.

Step 3,

You should be able to just do a regular push to Bioconductor here on 
out.

Best,

Nitesh 

> On Sep 10, 2019, at 8:51 AM, Turaga, Nitesh  
> wrote:
> 
> Hi Simon,
> 
> Bioconductor's git system doesn't allow force push (This is a feature) .  It 
> only allows a force push by administrators (Bioconductor Core team). Please 
> send me a link to your GitHub repo which is at 1.9.0, and I will sync it for 
> you.
> 
> I've updated the link where the instructions are outdated. Thank you for 
> bringing this to our attention. 
> 
> Best,
> 
> Nitesh 
> 
>> On Sep 10, 2019, at 3:42 AM, 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  
>>> 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 

Re: [Bioc-devel] Reset to a previous commit

[Turaga, Nitesh]

Hi Simon,

Bioconductor's git system doesn't allow force push (This is a feature) .  It 
only allows a force push by administrators (Bioconductor Core team). Please 
send me a link to your GitHub repo which is at 1.9.0, and I will sync it for 
you.

I've updated the link where the instructions are outdated. Thank you for 
bringing this to our attention. 

Best,

Nitesh 

> On Sep 10, 2019, at 3:42 AM, 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" 
>>  
>> 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  
>> 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
> profit from that.
> 
 As Lori mentioned at the end of her email (see below), we can't make
 the tensorflow Python module available on our Windows builders at the
 moment because we need to update Python to Python 3 on these machines
 first (AFAIK tensorflow is only available for Python 3 on Windows).
 This is something that we are currently working on.
 
 As for the Mac builders, we have tensorflow there but unfortunately
 it's an old version because recent versions of are broken on El
 Capitan (this is the Mac OS version that, for 

[Bioc-devel] Fwd: Update InterMineR maintainer

[Turaga, Nitesh]

Begin forwarded message:

From: ni41435_ca 
mailto:nitesh.tur...@roswellpark.org>>
Subject: Re: Update InterMineR maintainer
Date: September 10, 2019 at 8:08:40 AM EDT
To: Rachel Lyne mailto:rac...@intermine.org>>

Lower case 'i'  vs upper case in the package name 'I'.

It's a typo. "Git" is case sensitive.

Best,

Nitesh

On Sep 10, 2019, at 8:03 AM, Rachel Lyne 
mailto:rac...@intermine.org>> wrote:



git remote -v:


origing...@github.com:intermine/intermineR.git 
(fetch)
origing...@github.com:intermine/intermineR.git 
(push)
upstream
g...@git.bioconductor.org:packages/intermineR.git
 (fetch)
upstream
g...@git.bioconductor.org:packages/intermineR.git
 (push)


ssh -T g...@git.bioconductor.org
For this command I get R W next to the InterMineR package,

R  packages/ImpulseDE2
R  packages/InPAS
R  packages/InTAD
R  packages/IntEREst
R Wpackages/InterMineR
R  packages/InteractionSet
R  packages/IntramiRExploreR
R  packages/IrisSpatialFeatures
R  packages/IsoCorrectoR
R  packages/IsoCorrectoRGUI
R  packages/IsoGeneGUI


Rachel.




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 
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[Bioc-devel] Fwd: Update InterMineR maintainer

[Turaga, Nitesh]

Forwarding to Bioc-devel for issue tracking.

Begin forwarded message:

From: Rachel Lyne mailto:rac...@intermine.org>>
Subject: Re: Update InterMineR maintainer
Date: September 10, 2019 at 8:03:55 AM EDT
To: "Turaga, Nitesh" 
mailto:nitesh.tur...@roswellpark.org>>



git remote -v:


origin
g...@github.com:intermine/intermineR.git
 (fetch)
origin
g...@github.com:intermine/intermineR.git
 (push)
upstream
g...@git.bioconductor.org:packages/intermineR.git
 (fetch)
upstream
g...@git.bioconductor.org:packages/intermineR.git
 (push)


ssh -T g...@git.bioconductor.org
For this command I get R W next to the InterMineR package,

 R  packages/ImpulseDE2
 R  packages/InPAS
 R  packages/InTAD
 R  packages/IntEREst
 R Wpackages/InterMineR
 R  packages/InteractionSet
 R  packages/IntramiRExploreR
 R  packages/IrisSpatialFeatures
 R  packages/IsoCorrectoR
 R  packages/IsoCorrectoRGUI
 R  packages/IsoGeneGUI


Rachel.



On 10/09/2019 12:58, Turaga, Nitesh wrote:

Can you please send me the results of this command 
(http://bioconductor.org/developers/how-to/git/faq/, question number 14).

It will help me debug.

Best,

Nitesh



On Sep 10, 2019, at 5:52 AM, Rachel Lyne 
 wrote:

Hi Nitesh,

I have made all the necessary changes and updated the BioCredentials account 
with my ssh key and github user name.  However when I try and push the changes 
to the bioconductor git I get the following error:

FATAL: W any packages/intermineR r.lyne 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.

Do you know what could be causing this error?

Thanks,

Rachel.








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.
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Re: [Bioc-devel] Reset to a previous commit

[Simon Dirmeier]

Hi,

this is the way described in [1].

Cheers,

S

On 10.09.19 13:51, Neumann, Steffen wrote:

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"
 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
  > >> profit from that.
  > >>
  > > As Lori mentioned at the end of her email (see below), we
can't make
  > > the tensorflow Python module available on our Windows
builders at the
  > > moment because we need to update Python to Python 3 on
these machines
  > > first (AFAIK tensorflow is only available for Python 3 on
Windows).
  > 

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] Reset to a previous commit

[Simon Dirmeier]

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" 
>  
> 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  
> 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
>  > >> profit from that.
>  > >>
>  > > As Lori mentioned at the end of her email (see below), we can't make
>  > > the tensorflow Python module available on our Windows builders at the
>  > > moment because we need to update Python to Python 3 on these machines
>  > > first (AFAIK tensorflow is only available for Python 3 on Windows).
>  > > This is something that we are currently working on.
>  > >
>  > > As for the Mac builders, we have tensorflow there but unfortunately
>  > > it's an old version because recent versions of are broken on El
>  > > Capitan (this is the Mac OS version that, for various reasons, we are
>  > > stuck with at the moment). This prevents us from installing the
>  > > tensorflow_probability module which requires a recent version of
>  > > tensorflow.
>  > >
>  > > The tensorflow and