[Bioc-devel] credentials/authors for MTseeker, biscuiteer, and data packages corresponding to each

[Tim Triche, Jr.]

Hi Nitesh,

I'm the actual maintainer of MTseeker and the person who currently gets
emails about biscuiteer.  However, Jacob Morrison is the person who
actually maintains biscuiteer.  At some point my credentials for bioc-git
seem to have become interchanged with jacob's, and when I went to fix this,
it appears that my email suddenly replaced that of all my co-authors on
MTseeker and biscuiteer.  This is a bit of a problem since we are different
people.

How do I go about fixing this?  I am the maintainer (and currently fixing
up) the MTseeker package and its companion MTseekerData; Jacob handles
biscuiteer and biscuiteerData.  I'd just like to ensure that the two are as
intended; we have discussed, but not yet implemented, a "rebroadcaster"
email address for each package, and were wondering if that's a better way
forwards regardless.

Thanks,

--t

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[Bioc-devel] rstan related build error on tokay2

[Simo Kitanovski]

Dear all,

I have noticed that 3 packages that depend on rstan (genphen, IgGeneUsage and 
banocc)
seem to have build errors only on tokay2. The error messages are the same:

/Compiling model ... Error: C++14 standard requested but CXX14 is not 
defined Execution halted/

This error and the solution have been documented by the rstan community [1]. 
Would you
mind checking whether these instructions have been followed when rstan was 
installed on
tokay2. Alternative solutions are also welcome.

[1]:https://github.com/stan-dev/rstan/wiki/Installing-RStan-from-source-on-Windows#configuration

Best,
Simo


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[Bioc-devel] Announcement: Update to Rhdf5lib

[Mike Smith]

Dear all,

This is a heads up that I've updated the version of HDF5 distributed in
Rhdf5lib to 1.10.6.

The change was principally motivated to allow the use of the S3 virtual
file driver allowing read access to HDF5 files stored in S3 buckets.  As
such the library compilation now uses the --enable-ros3-vfd flag if the
appropriate system libraries are installed.  Pre-compiled Windows binaries
are included and have been built with both the Rtool 3.5 and 4.0 toolchains.

Ideally the change should be transparent to users and packages, and all my
tests have found no required changes.  However those tests are not
exhaustive, and I will be keeping a close eye on the build system in case
something unexpected happens.  Those who maintain packages that link with
Rhdf5lib may wish to bump their version numbers to ensure the new version
is used.

Please let me know if you see any errors that may be related to this.

Best regards,
Mike

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Re: [Bioc-devel] Access issues to package fcoex

[Turaga, Nitesh]

Thanks for the information. This helped me resolve your issue quickly.

Please try again now.

Best,

Nitesh 

> On Apr 15, 2020, at 12:28 PM, Tiago Lubiana Alves 
>  wrote:
> 
> Thanks Nitesh,
> 
> Adding more information about the issue:
> 
> 1 - My remotes seem to be set up correctly. 
> 
> $ git remote -v 
>   
> 
> origin  g...@github.com:csbl-usp/fcoex.git (fetch)
>   
> origin  g...@github.com:csbl-usp/fcoex.git (push) 
>   
> upstreamg...@git.bioconductor.org:packages/fcoex.git (fetch)  
>
> upstreamg...@git.bioconductor.org:packages/fcoex.git (push) 
> 
> 
> 2 - Push to origin works, push to remote does not. 
> 
> $ git push origin master  
> 
> Everything up-to-date 
> 
>  
> $ git push upstream master
> 
> FATAL: W any packages/fcoex lubianat 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.
> 
>  
> 3 - I only have read access to the fcoex package. 
> $ ssh -T g...@git.bioconductor.org
>  Rpackages/fcoex
> 
> 4 - The same command shows write access to the other packages I maintain.
> $ ssh -T g...@git.bioconductor.org
>  R W  packages/FCBF
>  (...)
>  R W  packages/PubScore
> 
> 5 - I am the maintainer of all 3 packages above. 
> 
> For fcoex and PubScore, the original repo was sent from the csbl-usp (my 
> laboratory) account: 
> - fcoex submission issue 
> - PubScore submission issue
> 
> For FCBF, the original repo was from the lubianat (my personal) account: 
> - FCBF submission issue
> 
> But I am nevertheless listed as the maintainer for all 3, with the same 
> e-mail:
> - fcoex :  Maintainer: Tiago Lubiana 
> - FCBF: Maintainer: Tiago Lubiana  (which I 
> have recently updated)
> - PubScore:  Maintainer: Tiago Lubiana 
> 
> 6 - I have an ssh config file with the content: 
> 
> host git.bioconductor.org
> HostName git.bioconductor.org
> IdentityFile ~/.ssh/id_rsa.pub
> User git
> 
> 9- The public ssh-key was copied and added to BiocCredentials, and should be 
> functional.
> 
> xclip -sel clip < ~/.ssh/id_rsa.pub 
> When adding it to https://git.bioconductor.org/BiocCredentials/add_sshkey/ I 
> get the error Ssh key with this Sshkey already exists. This is expected, as I 
> had added it before.
> 
> 
> If there is anything else that would be important to check, please let me 
> know and I will add. 
> 
> I am not super savvy with git too, and I already apologize for any basic 
> mistakes.
> I am sorry for the trouble and thank you very much for your time and help.
> 
> Tiago
> 
> Tiago Lubiana, 
> MSc in Bioinformatics, University of São Paulo
> Computational Systems Biology Laboratory (CSBL)
> 
> 
> 
> 
> On Thu, Apr 9, 2020 at 2:01 PM Turaga, Nitesh  
> wrote:
> We need more information,
> 
> http://bioconductor.org/developers/how-to/git/faq/ 
> 
> #13 and #14 in the FAQ are relevant to you.
> 
> Nitesh
> 
> > On Apr 9, 2020, at 12:39 PM, Tiago Lubiana Alves 
> >  wrote:
> > 
> > Hello all,
> > 
> > I have recently made a few change to a package that I mantain, but I seem
> > to be currently unable to update the fcoex package.
> > 
> > Even though I am the maintainer (
> > http://bioconductor.org/packages/3.11/bioc/html/fcoex.html)  I do not have
> > access to it according to BiocCredentials:
> > 'tiago.lubiana.al...@usp.br' has access to the following packages:FCBF
> > PubScore
> > 
> > (and only those two) .
> > 
> > I believe that might be the reason why I am getting the error message when
> > I run git push upstream master:
> > 
> > FATAL: W any packages/fcoex lubianat 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 why this might be occurring?
> > 
> > Thank you for your time,
> > Tiago
> > 
> > Tiago Lubiana,
> > MSc in Bioinformatics, University of São Paulo
> > *Computational Systems Biology Laboratory (CSBL)*
> > 
> >   [[alternative 

Re: [Bioc-devel] Access issues to package fcoex

[Tiago Lubiana Alves]

Thanks Nitesh,

Adding more information about the issue:


*1 - My remotes seem to be set up correctly. *
*$ git remote -v *


origin  g...@github.com:csbl-usp/fcoex.git (fetch)

origin  g...@github.com:csbl-usp/fcoex.git (push)

upstreamg...@git.bioconductor.org:packages/fcoex.git (fetch)

upstreamg...@git.bioconductor.org:packages/fcoex.git (push)



*2 - Push to origin works, push to remote does not. *
*$ git push origin master  *

Everything up-to-date


*$ git push upstream master  *

FATAL: W any packages/fcoex lubianat 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.


*3 - I only have read access to the fcoex package. *

*$ ssh -T g...@git.bioconductor.org *
 R   packages/fcoex

*4 - The same command shows write access to the other packages I maintain.*

*$ ssh -T g...@git.bioconductor.org * R W
packages/FCBF
 (...)
 R W packages/PubScore

*5 - I am the maintainer of all 3 packages above. *

For fcoex and PubScore, the original repo was sent from the csbl-usp
 (my laboratory) account:
- fcoex submission issue

- PubScore submission issue


For FCBF, the original repo was from the lubianat
 (my personal) account:
- FCBF submission issue


But I am nevertheless listed as the maintainer for all 3, with the same
e-mail:
- fcoex  :
 Maintainer:
Tiago Lubiana 
- FCBF :
Maintainer:
Tiago Lubiana  (which I have recently
updated)
- PubScore 
:  Maintainer: Tiago Lubiana 

*6 - I have an ssh config file with the content: *

host git.bioconductor.org
HostName git.bioconductor.org
IdentityFile ~/.ssh/id_rsa.pub
User git

*9- The public ssh-key was copied and added to BiocCredentials, and should
be functional.*

*xclip -sel clip < ~/.ssh/id_rsa.pub *
When adding it to https://git.bioconductor.org/BiocCredentials/add_sshkey/ I
get the error Ssh key with this Sshkey already exists. This is expected, as
I had added it before.


If there is anything else that would be important to check, please let me
know and I will add.

I am not super savvy with git too, and I already apologize for any basic
mistakes.
I am sorry for the trouble and thank you very much for your time and help.

Tiago

Tiago Lubiana,
MSc in Bioinformatics, University of São Paulo
*Computational Systems Biology Laboratory (CSBL)*




On Thu, Apr 9, 2020 at 2:01 PM Turaga, Nitesh 
wrote:

> We need more information,
>
> http://bioconductor.org/developers/how-to/git/faq/
>
> #13 and #14 in the FAQ are relevant to you.
>
> Nitesh
>
> > On Apr 9, 2020, at 12:39 PM, Tiago Lubiana Alves <
> tiago.lubiana.al...@usp.br> wrote:
> >
> > Hello all,
> >
> > I have recently made a few change to a package that I mantain, but I seem
> > to be currently unable to update the fcoex package.
> >
> > Even though I am the maintainer (
> > http://bioconductor.org/packages/3.11/bioc/html/fcoex.html)  I do not
> have
> > access to it according to BiocCredentials:
> > 'tiago.lubiana.al...@usp.br' has access to the following packages:FCBF
> > PubScore
> >
> > (and only those two) .
> >
> > I believe that might be the reason why I am getting the error message
> when
> > I run git push upstream master:
> >
> > FATAL: W any packages/fcoex lubianat 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 why this might be occurring?
> >
> > Thank you for your time,
> > Tiago
> >
> > Tiago Lubiana,
> > MSc in Bioinformatics, University of São Paulo
> > *Computational Systems Biology Laboratory (CSBL)*
> >
> >   [[alternative HTML version deleted]]
> >
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[Bioc-devel] Got timeout for machv2 BUILD

[Jianhong Ou, Ph.D.]

Hi,

Hope you are doing well.

I got timeout for my package motifStack in machv2. The ellapsedTime is 2403.0 
seconds while in tokay2 is 82.1 seconds and in malbec2 is 126.1 seconds. I have 
limited information how to debug.
Could you share your suggestion? Thank you.



Yours Sincerely,

Jianhong Ou

Email: jianhong...@duke.edu
Bioinformatician II
Department of Cell Biology
Duke University School of Medicine
Durham, NC, 27710

Confidentiality Notice:\ This e-mail message, including ...{{dropped:12}}

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