[Bioc-devel] persistent build errors in bioconductor package

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 at 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 at 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

[Bioc-devel] persistent build errors in bioconductor package

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