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

[Jiping Wang]

Hi,

I have followed all instructions to set up the github account and ssh key etc.
Now I can ssh to github to clone etc, but I cannot access the biodonctor through git.
I have set up the bio credentials (please see screen shot attached). Could you someone help on this issue?
I need to update the R package NuPoP on Bioconductor? Thanks.

Jiping Wang
------------------------------------------------------
Ji-Ping Wang, Ph.D.
Professor
Department of Statistics
Northwestern University
-------------------------------------------------------


From: jiping/wang User <jzwang using northwestern.edu>
Date: Friday, May 24, 2019 at 4:16 PM
To: "Shepherd, Lori" <Lori.Shepherd using RoswellPark.org>
Cc: "bioc-devel using bioconductor.org" <bioc-devel using bioconductor.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

Jipings-MacBook-Pro-2:NuPoP jon$ ssh -T git using git.bioconductor.org
git using git.bioconductor.org: Permission denied (publickey).


From: jiping/wang User <jzwang using northwestern.edu>
Date: Friday, May 24, 2019 at 2:50 PM
To: "Shepherd, Lori" <Lori.Shepherd using RoswellPark.org>
Subject: Re: BioC packages NuPoP and nuCpos

Hi Lori,

 I tried hard to follow your suggestion and I am still in trouble. I set up my github account and repository and ssh key.
I also input all information for Git Credentials. But when I run the following commands, I always got into the errors
about the access rights. Could you give me some hints which might be wrong here? (I have no problem to clone from my github directory).
Thanks.

jiping


Jipings-MacBook-Pro-2:NuPoP jon$ git remote add upstream git using git.bioconductor.org:packages/NuPoP

fatal: remote upstream already exists.

Jipings-MacBook-Pro-2:NuPoP jon$ git fetch -all

error: did you mean `--all` (with two dashes ?)

Jipings-MacBook-Pro-2:NuPoP jon$ git fetch --all

Fetching origin

Fetching upstream

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

fatal: Could not read from remote repository.



Please make sure you have the correct access rights

and the repository exists.

error: Could not fetch upstream


From: "Shepherd, Lori" <Lori.Shepherd using RoswellPark.org>
Date: Friday, May 24, 2019 at 8:02 AM
To: jiping/wang User <jzwang using northwestern.edu>, "bioc-devel using r-project.org" <bioc-devel using r-project.org>
Cc: Prof Brian Ripley <ripley using stats.ox.ac.uk>, Liqun Xi <liqunxi02 using 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 using r-project.org> on behalf of Jiping Wang <jzwang using northwestern.edu>
Sent: Friday, May 24, 2019 8:51:22 AM
To: bioc-devel using 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 using 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 using stats.ox.ac.uk
    Emeritus Professor of Applied Statistics, University of Oxford


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