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

Thomas Sherman t@herm@4 @ending from jhu@edu
Mon Oct 29 20:29:52 CET 2018

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.


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:


    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,


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