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

Mon, Oct 29, 2018 1:28 PM

git config core.filemode true


seems to have fixed it, thank you so much.


Also, thanks for pointing out that root was the owner, I must've run sudo git clone ... but I can't think of a reason why I would've done that.

From: Martin Morgan <mtmorgan.bioc at gmail.com>
Sent: Monday, October 29, 2018 3:44:32 PM
To: Thomas Sherman; bioc-devel at r-project.org
Subject: Re: [Bioc-devel] Issue with 'configure' not being executable

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 at jhu.edu>
Date: Monday, October 29, 2018 at 3:29 PM
To: Martin Morgan <mtmorgan.bioc at gmail.com>, "bioc-devel at r-project.org" <bioc-devel at 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 at gmail.com>
Sent: Monday, October 29, 2018 3:23:31 PM
To: Thomas Sherman; bioc-devel at 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 at r-project.org on behalf of tsherma4 at 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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Thread (6 messages)

Thomas Sherman Issue with 'configure' not being executable Oct 29 Thomas Sherman Issue with 'configure' not being executable Oct 29 Martin Morgan Issue with 'configure' not being executable Oct 29 Thomas Sherman Issue with 'configure' not being executable Oct 29 Martin Morgan Issue with 'configure' not being executable Oct 29 Thomas Sherman Issue with 'configure' not being executable Oct 29