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 <tsher...@jhu.edu> Date: Monday, October 29, 2018 at 3:29 PM To: Martin Morgan <mtmorgan.b...@gmail.com>, "bioc-devel@r-project.org" <bioc-devel@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.b...@gmail.com> Sent: Monday, October 29, 2018 3:23:31 PM To: Thomas Sherman; bioc-devel@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-boun...@r-project.org on behalf of tsher...@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 [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
