Cellprofiler-dateutil update fails on CentOS

I am running cellprofiler-2.1.1-2.x86_64 on CentOS-6.6.

yum update tries to update cellprofiler-dateutil-2.2-1 to version 2.2-2 but fails (see terminal output, below).

One can run # yum update --skip-broken, and skipping the dateutil update does not affect running CP, but it would be nice to fix. Has anyone else seen this?

Thanks!

root@localhost]# yum update
Loaded plugins: fastestmirror, refresh-packagekit, security
Setting up Update Process
Loading mirror speeds from cached hostfile

  • base: mirror.sanctuaryhost.com
  • epel: mirror.compevo.com
  • extras: mirror.ubiquityservers.com
  • updates: distro.ibiblio.org
    Resolving Dependencies
    –> Running transaction check
    —> Package cellprofiler-dateutil.x86_64 0:2.2-1 will be updated
    –> Processing Dependency: cellprofiler-dateutil = 2.2-1 for package: cellprofiler-2.1.1-2.x86_64
    —> Package cellprofiler-dateutil.x86_64 0:2.2-2 will be an update
    –> Finished Dependency Resolution
    Error: Package: cellprofiler-2.1.1-2.x86_64 (@cellprofiler)
    Requires: cellprofiler-dateutil = 2.2-1
    Removing: cellprofiler-dateutil-2.2-1.x86_64 (@cellprofiler)
    cellprofiler-dateutil = 2.2-1
    Updated By: cellprofiler-dateutil-2.2-2.x86_64 (cellprofiler)
    cellprofiler-dateutil = 2.2-2
    You could try using --skip-broken to work around the problem
    You could try running: rpm -Va --nofiles --nodigest

[root@localhost]# rpm -qa cellprofiler
cellprofiler-2.1.1-2.x86_64

[root@localhost]# rpm -qa cellprofiler-dateutil
cellprofiler-dateutil-2.2-1.x86_64

Thanks for reporting. I filed a bug report here: github.com/CellProfiler/CellPro … ssues/1359
We’ll try and report back here if/when there is a fix.

-David

Hi Rob,
cellprofiler-dateutil-2.2-2 is needed for the trunk build of CellProfiler. I put it into the repository so that it could be picked up by that version and unfortunately, I think it gives the error you saw. I’m not so much of an expert in this area, so I’m not sure how to put a later version of a dependency in the repo (the old version is still there) without causing this error. There are several conflicting requirements:

  • We want a reproducible binary for CellProfiler 2.1.1, so we want to distribute an exact set of its dependencies including cellprofiler-dateutil-2.1.1
  • We want to maintain a single RPM repository
  • We want to be able to upgrade versions of dependencies as necessary

So, I think we’re stuck with the issue. Would it work for you to remove the CellProfiler repo from your list until you want to update it?

–Lee

Hi Lee,

Thanks for your reply. It’s helpful to understand why I’m getting the error message when I update my system.

Removing the repo is one way to go but I would rather just disable it so that I can re-enable when your new version is released (see example of terminal output, below).

Thanks again,

Rob

[root@localhost robert]# cat /etc/yum.repos.d/cellprofiler.repo
[cellprofiler]
name=CellProfiler for CentOS 6
baseurl=http://www.cellprofiler.org/linux/centos6/
enabled=1
gpgcheck=0

/** change enabled=1 to enabled=0 using nano (or vim, etc.), then # cat to confirm the change was made **/
[root@localhost robert]# nano /etc/yum.repos.d/cellprofiler.repo
[root@localhost robert]# cat /etc/yum.repos.d/cellprofiler.repo
[cellprofiler]
name=CellProfiler for CentOS 6
baseurl=http://www.cellprofiler.org/linux/centos6/
enabled=0
gpgcheck=0

/** run # yum update to confirm cellprofiler.repo is ignored **/
[root@localhost robert]# yum update
Loaded plugins: fastestmirror, refresh-packagekit, security
Setting up Update Process
Loading mirror speeds from cached hostfile