Multiple dependency issues during RedHat's yum update

Question

As soon as I login I tried sudo yum update and it shows following errors. How do I solve this updates issue?

[ec2-user@ip-172-31-16-247 ~]$ sudo yum update

Loaded plugins: priorities, update-motd, upgrade-helper
amzn-main/latest           | 2.1 kB  00:00
  amzn-updates/latest          | 2.3 kB  00:00
  737 packages excluded due to repository priority protections
Resolving Dependencies
--> Running transaction check
---> Package aws-cfn-bootstrap.noarch 0:1.4-11.6.amzn1 will be updated
---> Package aws-cfn-bootstrap.noarch 0:1.4-12.7.amzn1 will be an update
---> Package aws-cli.noarch 0:1.10.46-1.40.amzn1 will be updated
---> Package aws-cli.noarch 0:1.10.56-1.41.amzn1 will be an update
---> Package bind-libs.x86_64 32:9.8.2-0.37.rc1.45.amzn1 will be updated
---> Package bind-libs.x86_64 32:9.8.2-0.37.rc1.47.amzn1 will be an update
---> Package bind-utils.x86_64 32:9.8.2-0.37.rc1.45.amzn1 will be updated
---> Package bind-utils.x86_64 32:9.8.2-0.37.rc1.47.amzn1 will be an update
---> Package curl.x86_64 0:7.40.0-8.58.amzn1 will be updated
---> Package curl.x86_64 0:7.40.0-8.59.amzn1 will be an update
---> Package db4.x86_64 0:4.7.25-18.11.amzn1 will be obsoleted
--> Processing Dependency: libdb-4.7.so()(64bit) for package: apr-util- 1.4.1-4.17.amzn1.x86_64
--> Processing Dependency: libdb-4.7.so()(64bit) for package: python27- libs-2.7.12-2.120.amzn1.x86_64
--> Processing Dependency: libdb-4.7.so()(64bit) for package: cyrus-sasl- lib-2.1.23-13.16.amzn1.x86_64
--> Processing Dependency: libdb-4.7.so()(64bit) for package: rpm-4.11.2- 2.73.amzn1.x86_64
--> Processing Dependency: libdb-4.7.so()(64bit) for package: ruby20-libs- 2.0.0.648-1.29.amzn1.x86_64
--> Processing Dependency: libdb-4.7.so()(64bit) for package: rpm-build- 4.11.2-2.73.amzn1.x86_64
--> Processing Dependency: libdb-4.7.so()(64bit) for package: iproute- 4.4.0-3.23.amzn1.x86_64
--> Processing Dependency: libdb-4.7.so()(64bit) for package: subversion- libs-1.9.4-2.55.amzn1.x86_64
--> Processing Dependency: libdb-4.7.so()(64bit) for package: pam-1.1.8- 12.33.amzn1.x86_64
--> Processing Dependency: libdb-4.7.so()(64bit) for package: subversion- 1.9.4-2.55.amzn1.x86_64
--> Processing Dependency: libdb-4.7.so()(64bit) for package: sendmail- 8.14.4-8.12.amzn1.x86_64
--> Processing Dependency: libdb-4.7.so()(64bit) for package: pam_ccreds- 10-4.9.amzn1.x86_64
--> Processing Dependency: libdb-4.7.so()(64bit) for package: libserf- 1.3.7-1.7.amzn1.x86_64
--> Processing Dependency: libdb-4.7.so()(64bit) for package: rpm-libs- 4.11.2-2.73.amzn1.x86_64
--> Processing Dependency: libdb-4.7.so()(64bit) for package: cyrus-sasl- 2.1.23-13.16.amzn1.x86_64
--> Processing Dependency: libdb-4.7.so()(64bit) for package: rpm-python27- 4.11.2-2.73.amzn1.x86_64
--> Processing Dependency: libdb-4.7.so()(64bit) for package: python26- 2.6.9-2.88.amzn1.x86_64
--> Processing Dependency: libdb-4.7.so()(64bit) for package: rpm-build- libs-4.11.2-2.73.amzn1.x86_64
---> Package db4-utils.x86_64 0:4.7.25-18.11.amzn1 will be obsoleted
---> Package dracut.noarch 0:004-336.28.amzn1 will be updated
---> Package dracut.noarch 0:004-409.31.amzn1 will be an update

amzn-updates/latest/filelists_db       | 3.3 MB  00:00
  epel/x86_64/filelists_db         | 7.2 MB  00:00 
---> Package kernel.x86_64 0:4.4.19-29.55.amzn1 will be installed
---> Package kernel-devel.x86_64 0:4.4.19-29.55.amzn1 will be installed
---> Package kernel-headers.x86_64 0:4.4.15-25.57.amzn1 will be updated
---> Package kernel-headers.x86_64 0:4.4.19-29.55.amzn1 will be an update
---> Package kernel-tools.x86_64 0:4.4.15-25.57.amzn1 will be updated
---> Package kernel-tools.x86_64 0:4.4.19-29.55.amzn1 will be an update
---> Package libcurl.x86_64 0:7.40.0-8.58.amzn1 will be updated
---> Package libcurl.x86_64 0:7.40.0-8.59.amzn1 will be an update
---> Package libdb4.x86_64 0:4.8.30-13.el7 will be obsoleting
---> Package libdb4-utils.x86_64 0:4.8.30-13.el7 will be obsoleting
---> Package libevent.x86_64 0:2.0.18-1.11.amzn1 will be updated
---> Package libevent.x86_64 0:2.0.21-4.19.amzn1 will be an update
---> Package libgcrypt.x86_64 0:1.5.3-12.18.amzn1 will be updated
---> Package libgcrypt.x86_64 0:1.5.3-12.19.amzn1 will be an update
---> Package mysql-config.x86_64 0:5.5.46-1.10.amzn1 will be updated
---> Package mysql-config.x86_64 0:5.5.51-1.11.amzn1 will be an update
---> Package python26.x86_64 0:2.6.9-2.86.amzn1 will be updated
---> Package python26.x86_64 0:2.6.9-2.88.amzn1 will be an update
--> Processing Dependency: libdb-4.7.so()(64bit) for package: python26- 2.6.9-2.88.amzn1.x86_64
---> Package python26-libs.x86_64 0:2.6.9-2.86.amzn1 will be updated
---> Package python26-libs.x86_64 0:2.6.9-2.88.amzn1 will be an update
---> Package python27.x86_64 0:2.7.10-4.122.amzn1 will be updated
---> Package python27.x86_64 0:2.7.12-2.120.amzn1 will be an update
---> Package python27-boto.noarch 0:2.39.0-1.0.amzn1 will be updated
---> Package python27-boto.noarch 0:2.42.0-1.1.amzn1 will be an update
---> Package python27-botocore.noarch 0:1.4.36-1.56.amzn1 will be updated
---> Package python27-botocore.noarch 0:1.4.46-1.58.amzn1 will be an update
---> Package python27-devel.x86_64 0:2.7.10-4.122.amzn1 will be updated
---> Package python27-devel.x86_64 0:2.7.12-2.120.amzn1 will be an update
---> Package python27-libs.x86_64 0:2.7.10-4.122.amzn1 will be updated
---> Package python27-libs.x86_64 0:2.7.12-2.120.amzn1 will be an update
--> Processing Dependency: libdb-4.7.so()(64bit) for package: python27- libs-2.7.12-2.120.amzn1.x86_64
--> Processing Dependency: /usr/bin/db_stat for package: rpm-4.11.2- 2.73.amzn1.x86_64
--> Processing Conflict: libdb4-4.8.30-13.el7.x86_64 conflicts filesystem <

3
--> Finished Dependency Resolution

Error: Package: python26-2.6.9-2.88.amzn1.x86_64 (amzn-updates)
    Requires: libdb-4.7.so()(64bit)
    Removing: db4-4.7.25-18.11.amzn1.x86_64 (installed)
     libdb-4.7.so()(64bit)
    Obsoleted By: libdb4-4.8.30-13.el7.x86_64 (epel)
    ~libdb-4.8.so()(64bit)

Error: Package: rpm-4.11.2-2.73.amzn1.x86_64 (installed)
    Requires: /usr/bin/db_stat
    Removing: db4-utils-4.7.25-18.11.amzn1.x86_64 (installed)
     Not found
    Obsoleted By: libdb4-utils-4.8.30-13.el7.x86_64 (epel)
     Not found

Error: Package: iproute-4.4.0-3.23.amzn1.x86_64 (installed)
    Requires: libdb-4.7.so()(64bit)
    Removing: db4-4.7.25-18.11.amzn1.x86_64 (installed)
     libdb-4.7.so()(64bit)
    Obsoleted By: libdb4-4.8.30-13.el7.x86_64 (epel)
    ~libdb-4.8.so()(64bit)

Error: Package: ruby20-libs-2.0.0.648-1.29.amzn1.x86_64 (installed)
    Requires: libdb-4.7.so()(64bit)
    Removing: db4-4.7.25-18.11.amzn1.x86_64 (installed)
     libdb-4.7.so()(64bit)
    Obsoleted By: libdb4-4.8.30-13.el7.x86_64 (epel)
    ~libdb-4.8.so()(64bit)

Error: Package: rpm-build-4.11.2-2.73.amzn1.x86_64 (@amzn-main)
    Requires: libdb-4.7.so()(64bit)
    Removing: db4-4.7.25-18.11.amzn1.x86_64 (installed)
     libdb-4.7.so()(64bit)
    Obsoleted By: libdb4-4.8.30-13.el7.x86_64 (epel)
    ~libdb-4.8.so()(64bit)

Error: Package: rpm-python27-4.11.2-2.73.amzn1.x86_64 (installed)
    Requires: libdb-4.7.so()(64bit)
    Removing: db4-4.7.25-18.11.amzn1.x86_64 (installed)
     libdb-4.7.so()(64bit)
    Obsoleted By: libdb4-4.8.30-13.el7.x86_64 (epel)
    ~libdb-4.8.so()(64bit)

Error: Package: python27-libs-2.7.12-2.120.amzn1.x86_64 (amzn-updates)
    Requires: libdb-4.7.so()(64bit)
    Removing: db4-4.7.25-18.11.amzn1.x86_64 (installed)
     libdb-4.7.so()(64bit)
    Obsoleted By: libdb4-4.8.30-13.el7.x86_64 (epel)
    ~libdb-4.8.so()(64bit)

Error: libdb4 conflicts with filesystem-2.4.30-3.8.amzn1.x86_64

Error: Package: rpm-build-libs-4.11.2-2.73.amzn1.x86_64 (installed)
    Requires: libdb-4.7.so()(64bit)
    Removing: db4-4.7.25-18.11.amzn1.x86_64 (installed)
     libdb-4.7.so()(64bit)
    Obsoleted By: libdb4-4.8.30-13.el7.x86_64 (epel)
    ~libdb-4.8.so()(64bit)

Error: Package: sendmail-8.14.4-8.12.amzn1.x86_64 (installed)
    Requires: libdb-4.7.so()(64bit)
    Removing: db4-4.7.25-18.11.amzn1.x86_64 (installed)
     libdb-4.7.so()(64bit)
    Obsoleted By: libdb4-4.8.30-13.el7.x86_64 (epel)
    ~libdb-4.8.so()(64bit)

Error: Package: cyrus-sasl-lib-2.1.23-13.16.amzn1.x86_64 (installed)
    Requires: libdb-4.7.so()(64bit)
    Removing: db4-4.7.25-18.11.amzn1.x86_64 (installed)
     libdb-4.7.so()(64bit)
    Obsoleted By: libdb4-4.8.30-13.el7.x86_64 (epel)
    ~libdb-4.8.so()(64bit)

Error: Package: pam-1.1.8-12.33.amzn1.x86_64 (installed)
    Requires: libdb-4.7.so()(64bit)
    Removing: db4-4.7.25-18.11.amzn1.x86_64 (installed)
     libdb-4.7.so()(64bit)
    Obsoleted By: libdb4-4.8.30-13.el7.x86_64 (epel)
    ~libdb-4.8.so()(64bit)

Error: Package: subversion-1.9.4-2.55.amzn1.x86_64 (@amzn-updates)
    Requires: libdb-4.7.so()(64bit)
    Removing: db4-4.7.25-18.11.amzn1.x86_64 (installed)
     libdb-4.7.so()(64bit)
    Obsoleted By: libdb4-4.8.30-13.el7.x86_64 (epel)
    ~libdb-4.8.so()(64bit)

Error: Package: apr-util-1.4.1-4.17.amzn1.x86_64 (@amzn-main)
    Requires: libdb-4.7.so()(64bit)
    Removing: db4-4.7.25-18.11.amzn1.x86_64 (installed)
     libdb-4.7.so()(64bit)
    Obsoleted By: libdb4-4.8.30-13.el7.x86_64 (epel)
    ~libdb-4.8.so()(64bit)

Error: Package: rpm-libs-4.11.2-2.73.amzn1.x86_64 (installed)
    Requires: libdb-4.7.so()(64bit)
    Removing: db4-4.7.25-18.11.amzn1.x86_64 (installed)
     libdb-4.7.so()(64bit)
    Obsoleted By: libdb4-4.8.30-13.el7.x86_64 (epel)
    ~libdb-4.8.so()(64bit)

Error: Package: pam_ccreds-10-4.9.amzn1.x86_64 (installed)
    Requires: libdb-4.7.so()(64bit)
    Removing: db4-4.7.25-18.11.amzn1.x86_64 (installed)
     libdb-4.7.so()(64bit)
    Obsoleted By: libdb4-4.8.30-13.el7.x86_64 (epel)
    ~libdb-4.8.so()(64bit)

Error: Package: subversion-libs-1.9.4-2.55.amzn1.x86_64 (@amzn-updates)
    Requires: libdb-4.7.so()(64bit)
    Removing: db4-4.7.25-18.11.amzn1.x86_64 (installed)
     libdb-4.7.so()(64bit)
    Obsoleted By: libdb4-4.8.30-13.el7.x86_64 (epel)
    ~libdb-4.8.so()(64bit)

Error: Package: cyrus-sasl-2.1.23-13.16.amzn1.x86_64 (installed)
    Requires: libdb-4.7.so()(64bit)
    Removing: db4-4.7.25-18.11.amzn1.x86_64 (installed)
     libdb-4.7.so()(64bit)
    Obsoleted By: libdb4-4.8.30-13.el7.x86_64 (epel)
    ~libdb-4.8.so()(64bit)

Error: Package: libserf-1.3.7-1.7.amzn1.x86_64 (@amzn-main)
    Requires: libdb-4.7.so()(64bit)
    Removing: db4-4.7.25-18.11.amzn1.x86_64 (installed)
     libdb-4.7.so()(64bit)
    Obsoleted By: libdb4-4.8.30-13.el7.x86_64 (epel)
    ~libdb-4.8.so()(64bit)

Error: Package: rpm-4.11.2-2.73.amzn1.x86_64 (installed)
    Requires: libdb-4.7.so()(64bit)
    Removing: db4-4.7.25-18.11.amzn1.x86_64 (installed)
     libdb-4.7.so()(64bit)
    Obsoleted By: libdb4-4.8.30-13.el7.x86_64 (epel)
    ~libdb-4.8.so()(64bit)

You could try using --skip-broken to work around the problem
You could try running: rpm -Va --nofiles --nodigest

[ec2-user@ip-172-31-16-247 ~]$

Answer 1

There is a conflict between epel and ami packages. The thing to do (since you are on AMI) is to disable other repositories first, run clean + update, then renable them (for one-off install/upgrades on a per-package basis).

yum-config-manager --disable epel
yum clean all
yum update
yum-config-manager --enable epel

Answer 2

For me, the solution was to exclude libdb from the epel repository by updating /etc/yum.repos.d/epel.repo like so:

[epel]
name=Extra Packages for Enterprise Linux 7 - $basearch
#baseurl=http://download.fedoraproject.org/pub/epel/7/$basearch
metalink=https://mirrors.fedoraproject.org/metalink?repo=epel-7&arch=$basearch
failovermethod=priority
enabled=1
gpgcheck=1
gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-EPEL-7
exclude=libdb*