[Bioc-devel] persistent build errors in bioconductor package

[Martin Morgan]

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.ramosperez using 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.koch01 using 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.bioc using 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  git using git.bioconductor.org:packages/powerTCR (fetch)
> origin  git using git.bioconductor.org:packages/powerTCR (push)
> 
> This could be corrected in various ways, one is
> 
>     git remote remove origin
>     git remote add origin git using 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  git using git.bioconductor.org:packages/powerTCR (fetch)
> origin  git using 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
> 
> 	[[alternative HTML version deleted]]
> 
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