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 at northwestern.edu> Date: Friday, May 24, 2019 at 4:16 PM To: "Shepherd, Lori" <Lori.Shepherd at RoswellPark.org> Cc: "bioc-devel at bioconductor.org" <bioc-devel at 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 at git.bioconductor.org git at git.bioconductor.org: Permission denied (publickey). From: jiping/wang User <jzwang at northwestern.edu> Date: Friday, May 24, 2019 at 2:50 PM To: "Shepherd, Lori" <Lori.Shepherd at 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 at 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 at 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 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
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
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