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-boun...@mail.lon-capa.org> on behalf of D G Teed <donald.t...@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@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@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 _______________________________________________ LON-CAPA-users mailing list LON-CAPA-users@mail.lon-capa.org http://mail.lon-capa.org/mailman/listinfo/lon-capa-users
