[Bioc-devel] updating pathwayPCA: "permission denied (publickey)"

Gabriel Odom godom @end|ng |rom ||u@edu
Mon Mar 20 21:25:22 CET 2023

Thank you Prof. MacDonald.
The solution ended up being slightly different than we had anticipated, but I'm including it below should any other users have similar difficulties.

TL;DR: RStudio Terminal can't find my SSH key (despite being listed in the RStudio Global Options), but Git Bash can. Solution: push upstream via Git Bash.

Long version: I use Git via the Terminal in RStudio rather than through more traditional means. As of last year, the home directory (~/) on Windows for an RStudio Terminal is different than the home directory for the rest of the computer. This issue is documented here (https://community.rstudio.com/t/git-bash-uses-different-home-directory-in-rstudio-2022-12-0-on-windows/155508), but has not yet been resolved.
For me, this means that I had the correct RSA key according to Git Bash (~/ = C:/Users/godom/) and RStudio Global Options (~/ = C:/Users/godom/), but not for the RStudio Terminal which I used in my attempts to perform a git push (~/ = C:/Users/godom/Documents/, which obviously doesn't have the expected .ssh/ folder).

-----Original Message-----
From: Bioc-devel <bioc-devel-bounces using r-project.org> On Behalf Of James W. MacDonald
Sent: Thursday, February 9, 2023 3:50 PM
To: Gabriel Odom <godom using fiu.edu>; bioc-devel using r-project.org
Subject: Re: [Bioc-devel] updating pathwayPCA: "permission denied (publickey)"

Note: This message originated from outside the FIU Faculty/Staff email system.

That looks like you have the wrong RSA key. You should be able to check which key you are using by logging in here: https://urldefense.com/v3/__https://git.bioconductor.org/BiocCredentials/login/__;!!FjuHKAHQs5udqho!LGpeGB2VKDnOCR9x6ZTjbGZGzrsTdPAf9rpYI4UGgwNWl2StQ8BMlhIRUBnu9TX2pHK5nP0VaNJhbbiRsI8$

-----Original Message-----
From: Bioc-devel <bioc-devel-bounces using r-project.org> On Behalf Of Gabriel Odom
Sent: Thursday, February 9, 2023 1:56 PM
To: bioc-devel using r-project.org
Subject: [Bioc-devel] updating pathwayPCA: "permission denied (publickey)"

Dear BioC-Devel folks,

My package, pathwayPCA, had an error in the vignettes which I've just fixed.
It's been a few years since my last bug fix, and I don't know what I'm doing wrong.
When I use "git push upstream master",  I see "mailto:git using git.bioconductor.org: Permission denied (publickey)."
Using "git remote -v" shows "upstream        mailto:git using git.bioconductor.org:packages/pathwayPCA.git (push)" (and pull).
Am I missing something simple?


Gabriel J. Odom, PhD, ThD
Assistant Professor
Department of Biostatistics
Stempel College of Public Health
Florida International University
Office: (305) 348-5486
Email: Gabriel.odom using fiu.edu

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