[Bioc-devel] Issue with 'configure' not being executable

[Martin Morgan]

I can’t provide much more help than googling, but it seems like git can be configured to not commit permissions; query and set from within the repository

  git config core.filemode
  git config core.filemode true

from https://stackoverflow.com/a/10516406/547331 and maybe updating the permissions flag following https://stackoverflow.com/a/21071387/547331 . I’d ‘test’ this by making and commiting changes to your local repository, then cloning from your local repository to a temporary location

  cd /tmp
  git clone path/to/R_package
  ls -l R_package/configure*

(also, and FWIW and sorry in advance for being presumptuous, but it is very unusual to run as root; you can do all kinds of very bad [to yourself] things, with simple typos)

Martin

From: Thomas Sherman <tsherma4 using jhu.edu>
Date: Monday, October 29, 2018 at 3:29 PM
To: Martin Morgan <mtmorgan.bioc using gmail.com>, "bioc-devel using r-project.org" <bioc-devel using r-project.org>
Subject: Re: [Bioc-devel] Issue with 'configure' not being executable

When I run the same command locally, this is what I see - is there a reason the permissions would be different between the remote and local?

R_Package$ ls -l configure*
-rwxrwxrwx 1 root root 248755 Oct 29 14:03 configure
-rwxrwxrwx 1 root root   3748 Oct 29 14:03 configure.ac

________________________________
From: Martin Morgan <mtmorgan.bioc using gmail.com>
Sent: Monday, October 29, 2018 3:23:31 PM
To: Thomas Sherman; bioc-devel using r-project.org
Subject: Re: [Bioc-devel] Issue with 'configure' not being executable

This is what I see in a recent checkout of your package

CoGAPS master$ ls -l configure*
-rw-r--r--  1 ma38727  ROSWELL\Domain Users  248755 Oct 27 21:24 configure
-rw-r--r--  1 ma38727  ROSWELL\Domain Users    3748 Oct 27 21:23 configure.ac

The '-rw' means that the files can be read / written by the owner of the file; if it were executable this would be '-rwx'

On non-Windows I think you would change the execute status

  chmod u+x configure

and then commit. This https://stackoverflow.com/a/21694391/547331 might help on Windows.

Martin

On 10/29/18, 3:15 PM, "Bioc-devel on behalf of Thomas Sherman" <bioc-devel-bounces using r-project.org on behalf of tsherma4 using jhu.edu> wrote:

    Hello,


    The latest build for our package (https://github.com/FertigLab/CoGAPS) failed with the error -


    ERROR: 'configure' exists but is not executable -- see the 'R Installation and Administration Manual'


    I've run into this before with our CI service, but the issue was fixed there by modifying TMPDIR based on the recommendation here: http://mazamascience.com/WorkingWithData/?p=1185 .


    I'm not sure how to fix this issue for the bioconductor build system, so I've temporarily removed the configuration step.


    Any help is much appreciated,

    Tom



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