[Bioc-devel] BioC packages NuPoP and nuCpos - Bioc-devel

Fri, May 24, 2019 5:51 AM #

Hi,

   We have made minor revision of the NuPoP package such that the revised version does not pass character strings from R to Fortran. This revised package has been tested working properly. We would like to replace the NuPoP package at Bioconductor.org by the attached one.  Please advise if anything else we should do or correct. Thanks for help.

Sincerely,
Jiping
------------------------------------------------------
Ji-Ping Wang, Ph.D.
Professor
Department of Statistics and Molecular BioSciences
Northwestern University 
-------------------------------------------------------

?On 5/22/19, 1:10 AM, "Prof Brian Ripley" <ripley at stats.ox.ac.uk> wrote:

These now give in R-patched and R-devel (and BioC 3.9 and 3.10)
    
    NuPoP.Rcheck/NuPoP-Ex.Rout:  passing a char vector to .Fortran is not 
    portable
    nuCpos.Rcheck/nuCpos-Ex.Rout:  passing a char vector to .Fortran is not 
    portable
    
    This come from the NEWS item
    
         ? The use of a character vector with .Fortran() is formally
           deprecated and gives a non-portability warning.  (It has long
           been strongly discouraged in ?Writing R Extensions?.)
    
    (It is even less portable than we had previously thought.)  Please avoid 
    it (and it is liable to be removed before too long): the preferred way 
    to do that is to use .Call with a C wrapper calling the Fortran code.
    
    -- 
    Brian D. Ripley,                  ripley at stats.ox.ac.uk
    Emeritus Professor of Applied Statistics, University of Oxford
    


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Shepherd, Lori

Fri, May 24, 2019 6:02 AM #

We do not manually replace Bioconductor packages for maintainers.  Bioconductor packages are maintained in git and you will have to push up the changes.


Please see the following documentation:

http://bioconductor.org/developers/how-to/git/


Feel free to comment back here with any further questions or if you have trouble connecting the the bioconductor git repository of your packages.


Cheers,


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

From: Bioc-devel <bioc-devel-bounces at r-project.org> on behalf of Jiping Wang <jzwang at northwestern.edu>
Sent: Friday, May 24, 2019 8:51:22 AM
To: bioc-devel at r-project.org
Cc: Prof Brian Ripley; Liqun Xi
Subject: [WARNING: UNSCANNABLE EXTRACTION FAILED]Re: [Bioc-devel] BioC packages NuPoP and nuCpos

Hi,

   We have made minor revision of the NuPoP package such that the revised version does not pass character strings from R to Fortran. This revised package has been tested working properly. We would like to replace the NuPoP package at Bioconductor.org by the attached one.  Please advise if anything else we should do or correct. Thanks for help.

Sincerely,
Jiping
------------------------------------------------------
Ji-Ping Wang, Ph.D.
Professor
Department of Statistics and Molecular BioSciences
Northwestern University
-------------------------------------------------------


?On 5/22/19, 1:10 AM, "Prof Brian Ripley" <ripley at stats.ox.ac.uk> wrote:

    These now give in R-patched and R-devel (and BioC 3.9 and 3.10)

    NuPoP.Rcheck/NuPoP-Ex.Rout:  passing a char vector to .Fortran is not
    portable
    nuCpos.Rcheck/nuCpos-Ex.Rout:  passing a char vector to .Fortran is not
    portable

    This come from the NEWS item

         ? The use of a character vector with .Fortran() is formally
           deprecated and gives a non-portability warning.  (It has long
           been strongly discouraged in ?Writing R Extensions?.)

    (It is even less portable than we had previously thought.)  Please avoid
    it (and it is liable to be removed before too long): the preferred way
    to do that is to use .Call with a C wrapper calling the Fortran code.

    --
    Brian D. Ripley,                  ripley at stats.ox.ac.uk
    Emeritus Professor of Applied Statistics, University of Oxford




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.

Jiping Wang

Fri, May 24, 2019 2:30 PM #

Hi,

   I believe I have set up all github and credential stuff (see screenshot for the latter). But
I cannot get access to git.bioconductor for some reason. Could you help? Thanks.

Jiping Wang

From: "Shepherd, Lori" <Lori.Shepherd at RoswellPark.org>
Date: Friday, May 24, 2019 at 8:02 AM
To: jiping/wang User <jzwang at northwestern.edu>, "bioc-devel at r-project.org" <bioc-devel at r-project.org>
Cc: Prof Brian Ripley <ripley at stats.ox.ac.uk>, Liqun Xi <liqunxi02 at gmail.com>
Subject: Re: BioC packages NuPoP and nuCpos

We do not manually replace Bioconductor packages for maintainers.  Bioconductor packages are maintained in git and you will have to push up the changes.

Please see the following documentation:

http://bioconductor.org/developers/how-to/git/<https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_developers_how-2Dto_git_&d=DwMGaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=MzPN0f82008-zQrz9tigmiha_-r6wh9au957srxLM7E&m=IvFeB5UVW_g7OYb5Jb9AR1WskbptTOEDRcmCnZM52oc&s=GM7pVU79-OExb1ApfvoG9nIt5af-WhziYOKJDaCHCNk&e=>

Feel free to comment back here with any further questions or if you have trouble connecting the the bioconductor git repository of your packages.

Cheers,

Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

From: Bioc-devel <bioc-devel-bounces at r-project.org> on behalf of Jiping Wang <jzwang at northwestern.edu>
Sent: Friday, May 24, 2019 8:51:22 AM
To: bioc-devel at r-project.org
Cc: Prof Brian Ripley; Liqun Xi
Subject: [WARNING: UNSCANNABLE EXTRACTION FAILED]Re: [Bioc-devel] BioC packages NuPoP and nuCpos

Hi,

   We have made minor revision of the NuPoP package such that the revised version does not pass character strings from R to Fortran. This revised package has been tested working properly. We would like to replace the NuPoP package at Bioconductor.org by the attached one.  Please advise if anything else we should do or correct. Thanks for help.

Sincerely,
Jiping
------------------------------------------------------
Ji-Ping Wang, Ph.D.
Professor
Department of Statistics and Molecular BioSciences
Northwestern University
-------------------------------------------------------


On 5/22/19, 1:10 AM, "Prof Brian Ripley" <ripley at stats.ox.ac.uk> wrote:

    These now give in R-patched and R-devel (and BioC 3.9 and 3.10)

    NuPoP.Rcheck/NuPoP-Ex.Rout:  passing a char vector to .Fortran is not
    portable
    nuCpos.Rcheck/nuCpos-Ex.Rout:  passing a char vector to .Fortran is not
    portable

    This come from the NEWS item

         ? The use of a character vector with .Fortran() is formally
           deprecated and gives a non-portability warning.  (It has long
           been strongly discouraged in ?Writing R Extensions?.)

    (It is even less portable than we had previously thought.)  Please avoid
    it (and it is liable to be removed before too long): the preferred way
    to do that is to use .Call with a C wrapper calling the Fortran code.

    --
    Brian D. Ripley,                  ripley at stats.ox.ac.uk
    Emeritus Professor of Applied Statistics, University of Oxford


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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Jiping Wang

Tue, May 28, 2019 7:22 AM #

Hi,

  I have been trying to update the NuPop Package to solve the passing character to fortran subroutine. I have revised the package, but I was advised to set up the updating pipeline through github. I have followed the instructions, and I now I have access to github (and can do clone etc). I also have input information to bioCredential (please see screen shot attached).


debug1: client_input_channel_req: channel 0 rtype exit-status reply 0

Hi jipingw! You've successfully authenticated, but GitHub does not provide shell access.

But when I tried to connect to Bioconductor, I got error message.


bash-3.2$    ssh -T git at git.bioconductor.org

git at git.bioconductor.org: Permission denied (publickey).

I have sent quite a few messages to bioc-devel at r-project.org bioc-devel at r-project.org<mailto:bioc-devel at r-project.org>, asking for assistance, but have heard no reply.
Could someone help me on this? Why did I keep getting this error message. Thanks.

Jiping Wang



From: jiping/wang User <jzwang at northwestern.edu>
Date: Friday, May 24, 2019 at 4:30 PM
To: "Shepherd, Lori" <Lori.Shepherd at RoswellPark.org>, "bioc-devel at r-project.org" <bioc-devel at r-project.org>
Subject: Re: BioC packages NuPoP and nuCpos

Hi,

   I believe I have set up all github and credential stuff (see screenshot for the latter). But
I cannot get access to git.bioconductor for some reason. Could you help? Thanks.

Jiping Wang


From: "Shepherd, Lori" <Lori.Shepherd at RoswellPark.org>
Date: Friday, May 24, 2019 at 8:02 AM
To: jiping/wang User <jzwang at northwestern.edu>, "bioc-devel at r-project.org" <bioc-devel at r-project.org>
Cc: Prof Brian Ripley <ripley at stats.ox.ac.uk>, Liqun Xi <liqunxi02 at gmail.com>
Subject: Re: BioC packages NuPoP and nuCpos


We do not manually replace Bioconductor packages for maintainers.  Bioconductor packages are maintained in git and you will have to push up the changes.



Please see the following documentation:

http://bioconductor.org/developers/how-to/git/<https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_developers_how-2Dto_git_&d=DwMGaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=MzPN0f82008-zQrz9tigmiha_-r6wh9au957srxLM7E&m=IvFeB5UVW_g7OYb5Jb9AR1WskbptTOEDRcmCnZM52oc&s=GM7pVU79-OExb1ApfvoG9nIt5af-WhziYOKJDaCHCNk&e=>



Feel free to comment back here with any further questions or if you have trouble connecting the the bioconductor git repository of your packages.



Cheers,



Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

From: Bioc-devel <bioc-devel-bounces at r-project.org> on behalf of Jiping Wang <jzwang at northwestern.edu>
Sent: Friday, May 24, 2019 8:51:22 AM
To: bioc-devel at r-project.org
Cc: Prof Brian Ripley; Liqun Xi
Subject: [WARNING: UNSCANNABLE EXTRACTION FAILED]Re: [Bioc-devel] BioC packages NuPoP and nuCpos

Hi,

   We have made minor revision of the NuPoP package such that the revised version does not pass character strings from R to Fortran. This revised package has been tested working properly. We would like to replace the NuPoP package at Bioconductor.org by the attached one.  Please advise if anything else we should do or correct. Thanks for help.

Sincerely,
Jiping
------------------------------------------------------
Ji-Ping Wang, Ph.D.
Professor
Department of Statistics and Molecular BioSciences
Northwestern University
-------------------------------------------------------


On 5/22/19, 1:10 AM, "Prof Brian Ripley" <ripley at stats.ox.ac.uk> wrote:

    These now give in R-patched and R-devel (and BioC 3.9 and 3.10)

    NuPoP.Rcheck/NuPoP-Ex.Rout:  passing a char vector to .Fortran is not
    portable
    nuCpos.Rcheck/nuCpos-Ex.Rout:  passing a char vector to .Fortran is not
    portable

    This come from the NEWS item

         ? The use of a character vector with .Fortran() is formally
           deprecated and gives a non-portability warning.  (It has long
           been strongly discouraged in ?Writing R Extensions?.)

    (It is even less portable than we had previously thought.)  Please avoid
    it (and it is liable to be removed before too long): the preferred way
    to do that is to use .Call with a C wrapper calling the Fortran code.

    --
    Brian D. Ripley,                  ripley at stats.ox.ac.uk
    Emeritus Professor of Applied Statistics, University of Oxford


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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