I see, when you say
> experiencing. When I check the error online, it says:
>
> "001E# service=git-upload-pack
>
> 00000041ERR FATAL: unknown git/gitolite command: 'packages/powerTCR'
> FATAL: unknown git/gitolite command: 'packages/powerTCR'
> 001E# service=git-upload-pack
>
> 0041ERR FATAL: unknown git/gitolite command: 'packages/powerTCR'"
you mean that you point your browser to
https://git.bioconductor.org/packages/powerTCR
I see that message too; it is currently not possible to navigate to
package sources in this way on our system.
It looks like the recent commits are
powerTCR master$ git log -n 2
commit 6ba40e640fb779371cbe8b3a232f8b0b3d549d12
Author: LiNk-NY <marcel.ramospe...@roswellpark.org>
Date: Thu Sep 6 15:52:35 2018 +0000
additional updates from BiocInstaller to BiocManager
commit 8af9bbf7f788defc73021b0621efa29b5f2d2361
Merge: 97dadf9 f5e4d5f
Author: Hillary Koch <hillary.koc...@gmail.com>
Date: Thu Sep 6 09:37:03 2018 -0400
merge upstream
and from our 'build report'
http://bioconductor.org/checkResults/devel/bioc-LATEST/
clicking on the 'ERROR' for your package, e.g., on Linux
http://bioconductor.org/checkResults/devel/bioc-LATEST/powerTCR/malbec1-buildsrc.html
the page reports
Snapshot Date: 2018-09-11 16:46:14 -0400 (Tue, 11 Sep 2018)
URL: https://git.bioconductor.org/packages/powerTCR
Branch: master
Last Commit: 6ba40e6
Last Changed Date: 2018-09-06 11:52:35 -0400 (Thu, 06 Sep 2018)
so the checkout on the build machine is consistent (compare the 'Last
Commit:' field with the hash on the commit in the repository) with the
most recent commit.
It looks like you've pushed changes, but they have not fixed the problem.
In your vignettes directory you have
/powerTCR/vignettes$ ls
powerTCR_cache powerTCR_files powerTCR.html powerTCR.tex
powerTCR.fdb_latexmk powerTCR.fls powerTCR.Rmd
but you should have only the powerTCR.Rmd file committed, the others
should be removed.
Note that the log shows a commit from the core team to address use of
BiocManager (replacing BiocInstaller) so the right sequence of commands
will be along the lines of
git pull # update to current version
git rm -r vignettes/powerTCR_cache vignettes/powerTCR_files
powerTCR.html powerTCR.tex powerTCR.fdb_latexmk powerTCR.fls
git commit
after the git commit command, it can be helpful to change to a new
directory and make a local clone of your powerTCR package to make sure
it builds, e.g.,
cd /tmp
git clone /path/to/original/powerTCR
R CMD build powerTCR
R CMD check powerTCR_1.1.3.tar.gz
if that works out then change back to the original repository and git push.
Martin
On 09/12/2018 08:30 PM, Hillary Koch wrote:
Hi again,
I recently wrote about some build errors my bioconductor package is
experiencing. When I check the error online, it says:
"001E# service=git-upload-pack
00000041ERR FATAL: unknown git/gitolite command: 'packages/powerTCR'
FATAL: unknown git/gitolite command: 'packages/powerTCR'
001E# service=git-upload-pack
0041ERR FATAL: unknown git/gitolite command: 'packages/powerTCR'" >
I wrote about this a couple of days ago and received the response
"
Martin Morgan <mtmorgan.b...@gmail.com>
Sep 9, 2018, 12:47 PM (3 days ago)
to me, bioc-devel
I'd guess that your remote is incorrect; it should use ssh, and the
separation between the host 'git.bioconductor.org' and repository path
'packages/powerTCR' should be a colon, e.g.,
powerTCR master$ git remote -v
origin g...@git.bioconductor.org:packages/powerTCR (fetch)
origin g...@git.bioconductor.org:packages/powerTCR (push)
This could be corrected in various ways, one is
git remote remove origin
git remote add origin g...@git.bioconductor.org:packages/powerTCR"
I have looked into all of this again - I have an SSH key associated with
the package which BioConductor is aware of. When I check "git remote -v" in
master I see exactly
origin g...@git.bioconductor.org:packages/powerTCR (fetch)
origin g...@git.bioconductor.org:packages/powerTCR (push)
plus the fetch and push for the upstream branch which I created some time
ago.
I am not sure how to proceed here. Thanks in advance for the help!
Hillary
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