[LON-CAPA-users] YUM problem with tre-common on CentOS 7
Raeburn, Stuart
raeburn at msu.edu
Tue Aug 20 14:37:16 EDT 2019
Donald,
The versions of tre and te-devel available from the EPEL 7 repo are newer than the corresponding packages available from the install.loncapa.org/centos/loncapa/7/ repo.
LONCAPA-prerequisites requires R, which results in a dependency chain:
R-devel -> R-core-devel -> tre-devel -> tre.
The 64-bit tre package from lon-capa-updates (tre-0.8.0-10.el7.x86_64) has no dependency on tre-common, whereas the 64-bit package from EPEL 7 (tre-0.8.0-18.20140228gitc2f5d13.el7.x86_64) does, which adds one final dependency to the chain: R-devel -> R-core-devel -> tre-devel -> tre -> tre-common
>
> I have not tried the exclude on the lon-capa repo, but assumed there was a reason the package exists
> there.
>
loncapa-updates-noarch contains tre-common because the LON-CAPA repositories for 32 bit CentOS 7 include the i386 rpm for tre-0.8.0-18, which (like its 64 bit counterpart) has a dependency on tre-common.
I think the solution will be for me to replace the 64-bit 0.8.0-10 packages for tre and tre-devel in lon-capa-updates with the 0.8.0-18 versions. I should be able to get to that this evening. After I have made that change you will want to run the "yum clean all" command (again).
For now, if you insure that you have the 0.8.0-10 versions of tre and tre-devel installed instead of the 0.8.0-18 versions, then there will be no dependency on tre-common (which you could remove). You would then want to temporarily disable updates of tre and tre-devel from EPEL7.
Stuart Raeburn
LON-CAPA Academic Consortium
_______________________________________
From: LON-CAPA-users <lon-capa-users-bounces at mail.lon-capa.org> on behalf of D G Teed <donald.teed at gmail.com>
Sent: Tuesday, August 20, 2019 8:22 AM
To: Discussion list for LON-CAPA users
Subject: [LON-CAPA-users] YUM problem with tre-common on CentOS 7
Hello,
I've just migrated our Redhat 6 Lon-Capa to CentOS 7.
It seems the site is working OK. When I did a yum update recently there is
a conflict with tre-common being provided by both epel and loncapa-updates
I tried exclude=tre-common within /etc/yum.repos.d/epel.repo
and did yum clean all followed by yum update. Same error as previously.
This package wasn't part of the R dependencies on the previous OS version so I can't compare to how it was satisfied on the previous server.
I think the problem is that tre comes from epel and lists a dependency and version found only
on epel of tre-common, while loncapa-updates provides tre-common but not the matching tre so
it isn't possible to make epel not provide tre packages.
# yum list tre-common
Loaded plugins: fastestmirror
Loading mirror speeds from cached hostfile
* base: mirror.calgah.com<https://urldefense.proofpoint.com/v2/url?u=http-3A__mirror.calgah.com&d=DwMGaQ&c=nE__W8dFE-shTxStwXtp0A&r=VsGo3jOm8tGLd6f-KlhT-g&m=wOaFS-i3n0r9lYv4k9rqgOYbY4-62QkPFQEY02KmLHo&s=sZ6tdCsXDERL_fv6KvAh-1yrLIZ3_yPFHIJ3tMAtd4o&e=>
* epel: epel.mirror.constant.com<https://urldefense.proofpoint.com/v2/url?u=http-3A__epel.mirror.constant.com&d=DwMGaQ&c=nE__W8dFE-shTxStwXtp0A&r=VsGo3jOm8tGLd6f-KlhT-g&m=wOaFS-i3n0r9lYv4k9rqgOYbY4-62QkPFQEY02KmLHo&s=Q80abozTNcYv_KzySeS4EVuoHt0pFAVNDZf-ts-Da5Q&e=>
* extras: mirror.its.dal.ca<https://urldefense.proofpoint.com/v2/url?u=http-3A__mirror.its.dal.ca&d=DwMGaQ&c=nE__W8dFE-shTxStwXtp0A&r=VsGo3jOm8tGLd6f-KlhT-g&m=wOaFS-i3n0r9lYv4k9rqgOYbY4-62QkPFQEY02KmLHo&s=3lgtWMlZcBS2PXj1QPEmmEP8qFyHi6Sb58e9--dYDWM&e=>
* updates: mirror.calgah.com<https://urldefense.proofpoint.com/v2/url?u=http-3A__mirror.calgah.com&d=DwMGaQ&c=nE__W8dFE-shTxStwXtp0A&r=VsGo3jOm8tGLd6f-KlhT-g&m=wOaFS-i3n0r9lYv4k9rqgOYbY4-62QkPFQEY02KmLHo&s=sZ6tdCsXDERL_fv6KvAh-1yrLIZ3_yPFHIJ3tMAtd4o&e=>
Installed Packages
tre-common.noarch 0.8.0-18.20140228gitc2f5d13.el7 @epel
Available Packages
tre-common.noarch 0.8.0-18.20140228gitc2f5d13.el7.centos loncapa-updates-noarch
# yum list tre
Loaded plugins: fastestmirror
Loading mirror speeds from cached hostfile
* base: mirror.its.dal.ca<https://urldefense.proofpoint.com/v2/url?u=http-3A__mirror.its.dal.ca&d=DwMGaQ&c=nE__W8dFE-shTxStwXtp0A&r=VsGo3jOm8tGLd6f-KlhT-g&m=wOaFS-i3n0r9lYv4k9rqgOYbY4-62QkPFQEY02KmLHo&s=3lgtWMlZcBS2PXj1QPEmmEP8qFyHi6Sb58e9--dYDWM&e=>
* epel: epel.mirror.constant.com<https://urldefense.proofpoint.com/v2/url?u=http-3A__epel.mirror.constant.com&d=DwMGaQ&c=nE__W8dFE-shTxStwXtp0A&r=VsGo3jOm8tGLd6f-KlhT-g&m=wOaFS-i3n0r9lYv4k9rqgOYbY4-62QkPFQEY02KmLHo&s=Q80abozTNcYv_KzySeS4EVuoHt0pFAVNDZf-ts-Da5Q&e=>
* extras: mirror.its.dal.ca<https://urldefense.proofpoint.com/v2/url?u=http-3A__mirror.its.dal.ca&d=DwMGaQ&c=nE__W8dFE-shTxStwXtp0A&r=VsGo3jOm8tGLd6f-KlhT-g&m=wOaFS-i3n0r9lYv4k9rqgOYbY4-62QkPFQEY02KmLHo&s=3lgtWMlZcBS2PXj1QPEmmEP8qFyHi6Sb58e9--dYDWM&e=>
* updates: mirror.its.dal.ca<https://urldefense.proofpoint.com/v2/url?u=http-3A__mirror.its.dal.ca&d=DwMGaQ&c=nE__W8dFE-shTxStwXtp0A&r=VsGo3jOm8tGLd6f-KlhT-g&m=wOaFS-i3n0r9lYv4k9rqgOYbY4-62QkPFQEY02KmLHo&s=3lgtWMlZcBS2PXj1QPEmmEP8qFyHi6Sb58e9--dYDWM&e=>
Installed Packages
tre.x86_64 0.8.0-18.20140228gitc2f5d13.el7 @epel
# yum update
Loaded plugins: fastestmirror
Loading mirror speeds from cached hostfile
epel/x86_64/metalink | 14 kB 00:00:00
* base: mirror.calgah.com<https://urldefense.proofpoint.com/v2/url?u=http-3A__mirror.calgah.com&d=DwMGaQ&c=nE__W8dFE-shTxStwXtp0A&r=VsGo3jOm8tGLd6f-KlhT-g&m=wOaFS-i3n0r9lYv4k9rqgOYbY4-62QkPFQEY02KmLHo&s=sZ6tdCsXDERL_fv6KvAh-1yrLIZ3_yPFHIJ3tMAtd4o&e=>
* epel: epel.mirror.constant.com<https://urldefense.proofpoint.com/v2/url?u=http-3A__epel.mirror.constant.com&d=DwMGaQ&c=nE__W8dFE-shTxStwXtp0A&r=VsGo3jOm8tGLd6f-KlhT-g&m=wOaFS-i3n0r9lYv4k9rqgOYbY4-62QkPFQEY02KmLHo&s=Q80abozTNcYv_KzySeS4EVuoHt0pFAVNDZf-ts-Da5Q&e=>
* extras: mirror.its.dal.ca<https://urldefense.proofpoint.com/v2/url?u=http-3A__mirror.its.dal.ca&d=DwMGaQ&c=nE__W8dFE-shTxStwXtp0A&r=VsGo3jOm8tGLd6f-KlhT-g&m=wOaFS-i3n0r9lYv4k9rqgOYbY4-62QkPFQEY02KmLHo&s=3lgtWMlZcBS2PXj1QPEmmEP8qFyHi6Sb58e9--dYDWM&e=>
* updates: mirror.calgah.com<https://urldefense.proofpoint.com/v2/url?u=http-3A__mirror.calgah.com&d=DwMGaQ&c=nE__W8dFE-shTxStwXtp0A&r=VsGo3jOm8tGLd6f-KlhT-g&m=wOaFS-i3n0r9lYv4k9rqgOYbY4-62QkPFQEY02KmLHo&s=sZ6tdCsXDERL_fv6KvAh-1yrLIZ3_yPFHIJ3tMAtd4o&e=>
Resolving Dependencies
--> Running transaction check
---> Package tre-common.noarch 0:0.8.0-18.20140228gitc2f5d13.el7 will be updated
--> Processing Dependency: tre-common = 0.8.0-18.20140228gitc2f5d13.el7 for package: tre-0.8.0-18.20140228gitc2f5d13.el7.x86_64
---> Package tre-common.noarch 0:0.8.0-18.20140228gitc2f5d13.el7.centos will be an update
--> Finished Dependency Resolution
Error: Package: tre-0.8.0-18.20140228gitc2f5d13.el7.x86_64 (@epel)
Requires: tre-common = 0.8.0-18.20140228gitc2f5d13.el7
Removing: tre-common-0.8.0-18.20140228gitc2f5d13.el7.noarch (@epel)
tre-common = 0.8.0-18.20140228gitc2f5d13.el7
Updated By: tre-common-0.8.0-18.20140228gitc2f5d13.el7.centos.noarch (loncapa-updates-noarch)
tre-common = 0.8.0-18.20140228gitc2f5d13.el7.centos
You could try using --skip-broken to work around the problem
You could try running: rpm -Va --nofiles --nodigest
[root at sirius ~]# yum clean all
Loaded plugins: fastestmirror
Cleaning repos: base epel extras loncapa-updates-basearch loncapa-updates-noarch updates
Cleaning up list of fastest mirrors
Other repos take up 115 M of disk space (use --verbose for details)
[root at sirius ~]# yum update
Loaded plugins: fastestmirror
Determining fastest mirrors
epel/x86_64/metalink | 14 kB 00:00:00
* base: mirror.its.dal.ca<https://urldefense.proofpoint.com/v2/url?u=http-3A__mirror.its.dal.ca&d=DwMGaQ&c=nE__W8dFE-shTxStwXtp0A&r=VsGo3jOm8tGLd6f-KlhT-g&m=wOaFS-i3n0r9lYv4k9rqgOYbY4-62QkPFQEY02KmLHo&s=3lgtWMlZcBS2PXj1QPEmmEP8qFyHi6Sb58e9--dYDWM&e=>
* epel: epel.mirror.constant.com<https://urldefense.proofpoint.com/v2/url?u=http-3A__epel.mirror.constant.com&d=DwMGaQ&c=nE__W8dFE-shTxStwXtp0A&r=VsGo3jOm8tGLd6f-KlhT-g&m=wOaFS-i3n0r9lYv4k9rqgOYbY4-62QkPFQEY02KmLHo&s=Q80abozTNcYv_KzySeS4EVuoHt0pFAVNDZf-ts-Da5Q&e=>
* extras: mirror.its.dal.ca<https://urldefense.proofpoint.com/v2/url?u=http-3A__mirror.its.dal.ca&d=DwMGaQ&c=nE__W8dFE-shTxStwXtp0A&r=VsGo3jOm8tGLd6f-KlhT-g&m=wOaFS-i3n0r9lYv4k9rqgOYbY4-62QkPFQEY02KmLHo&s=3lgtWMlZcBS2PXj1QPEmmEP8qFyHi6Sb58e9--dYDWM&e=>
* updates: mirror.its.dal.ca<https://urldefense.proofpoint.com/v2/url?u=http-3A__mirror.its.dal.ca&d=DwMGaQ&c=nE__W8dFE-shTxStwXtp0A&r=VsGo3jOm8tGLd6f-KlhT-g&m=wOaFS-i3n0r9lYv4k9rqgOYbY4-62QkPFQEY02KmLHo&s=3lgtWMlZcBS2PXj1QPEmmEP8qFyHi6Sb58e9--dYDWM&e=>
base | 3.6 kB 00:00:00
epel | 5.3 kB 00:00:00
extras | 3.4 kB 00:00:00
loncapa-updates-basearch | 951 B 00:00:00
loncapa-updates-noarch | 951 B 00:00:00
updates | 3.4 kB 00:00:00
(1/7): base/7/x86_64/group_gz | 166 kB 00:00:00
(2/7): epel/x86_64/group_gz | 88 kB 00:00:00
(3/7): epel/x86_64/updateinfo | 999 kB 00:00:00
(4/7): extras/7/x86_64/primary_db | 215 kB 00:00:00
(5/7): epel/x86_64/primary_db | 6.8 MB 00:00:00
(6/7): base/7/x86_64/primary_db | 6.0 MB 00:00:00
(7/7): updates/7/x86_64/primary_db | 7.4 MB 00:00:00
(1/2): loncapa-updates-noarch/7/primary | 32 kB 00:00:00
(2/2): loncapa-updates-basearch/7/x86_64/primary | 31 kB 00:00:00
loncapa-updates-basearch 81/81
loncapa-updates-noarch 65/65
Resolving Dependencies
--> Running transaction check
---> Package tre-common.noarch 0:0.8.0-18.20140228gitc2f5d13.el7 will be updated
--> Processing Dependency: tre-common = 0.8.0-18.20140228gitc2f5d13.el7 for package: tre-0.8.0-18.20140228gitc2f5d13.el7.x86_64
---> Package tre-common.noarch 0:0.8.0-18.20140228gitc2f5d13.el7.centos will be an update
--> Finished Dependency Resolution
Error: Package: tre-0.8.0-18.20140228gitc2f5d13.el7.x86_64 (@epel)
Requires: tre-common = 0.8.0-18.20140228gitc2f5d13.el7
Removing: tre-common-0.8.0-18.20140228gitc2f5d13.el7.noarch (@epel)
tre-common = 0.8.0-18.20140228gitc2f5d13.el7
Updated By: tre-common-0.8.0-18.20140228gitc2f5d13.el7.centos.noarch (loncapa-updates-noarch)
tre-common = 0.8.0-18.20140228gitc2f5d13.el7.centos
You could try using --skip-broken to work around the problem
You could try running: rpm -Va --nofiles --nodigest
What do you suggest I try to resolve that issue? I have not tried the exclude on the lon-capa repo, but assumed
there was a reason the package exists there.
Regards,
--Donald Teed
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