• Updates to PETSc-3.10.4
  • Update to petsc4py-3.10.1
  • Update to sundials-4.1.0
  • Update to bionetgen-2.5.0 (bundled cvode)
  • New package Sundials2

This update has been submitted for testing by sagitter.

2 years ago

This update test gating status has been changed to 'waiting'.

2 years ago

This update test gating status has been changed to 'ignored'.

2 years ago

This update has been pushed to testing.

2 years ago
User Icon tis commented & provided feedback 2 years ago
karma

sundials-openmpi-4.1.0-3.el7.x86_64 has dependency:

devtoolset-8-gcc-gfortran(x86-64)

That is not allowed on epel7.

Bodhi is disabling automatic push to stable due to negative karma. The maintainer may push manually if they determine that the issue is not severe.

2 years ago

I ment with this: runtime dependency on devltoolset is not allowed.

sagitter edited this update.

New build(s):

  • sundials-4.1.0-4.el7

Removed build(s):

  • sundials-4.1.0-3.el7

Karma has been reset.

2 years ago

This update has been submitted for testing by sagitter.

2 years ago

I found some other issues:

package: bionetgen-2.4.0-2.el7.x86_64

unresolved deps:

 libsundials_cvode.so.2()(64bit)
 libsundials_nvecserial.so.2()(64bit)

package: python2-assimulo-2.9-15.el7.x86_64

unresolved deps:

 libsundials_cvodes.so.2()(64bit)
 libsundials_idas.so.1()(64bit)
 libsundials_kinsol.so.2()(64bit)
 libsundials_nvecserial.so.2()(64bit)

I guess both bionetgen and python-assimulo should be added to this update.

This update has been pushed to testing.

2 years ago

sagitter edited this update.

New build(s):

  • bionetgen-2.5.0-4.el7

Karma has been reset.

2 years ago

This update has been submitted for testing by sagitter.

2 years ago

python-assimulo is an orphaned package...

This update has been pushed to testing.

2 years ago

This also breaks octave 5 from copr and more generally is a abi change.

http://linuxsoft.cern.ch/mirror/copr-be.cloud.fedoraproject.org/results/%2540scitech/octave5.1/epel-7-x86_64/00866411-octave/octave-5.1.0-1.el7.x86_64.rpm

rpm -q --requires octave | grep sundial

libsundials_ida.so.2()(64bit) libsundials_nvecserial.so.2()(64bit)

maybe a compat package can be made also.

karma

@stevetraylen

Octave5 is even built against sundials-4.1.0 on Fedora Rawhide.

This is binary abi change in epel7 which as mentioned above is not really meant to happen.

One way to do this is to add a sundials2 package is a good idea. This can be generated from the same .spec file. Example of building an old existing tar ball in addition to the new one being added here. You build the old one first and delete the files that would normally be in the -devel package so you have a runtime only of sundials2. https://src.fedoraproject.org/rpms/activemq-cpp/blob/epel7/f/activemq-cpp.spec#_15

This update has reached 14 days in testing and can be pushed to stable now if the maintainer wishes

2 years ago

This update has been unpushed.

I'm working to get a sundials2 package on EPEL7

sagitter - thanks a lock, I checked if you needed a review but I see already done - thanks again.

sagitter edited this update.

New build(s):

  • petsc4py-3.10.1-2.el7
  • sundials-4.1.0-5.el7
  • sundials2-2.7.0-1.el7
  • petsc-3.10.4-3.el7
  • bionetgen-2.5.0-5.el7

Removed build(s):

  • bionetgen-2.5.0-4.el7
  • petsc-3.10.4-1.el7
  • petsc4py-3.10.1-1.el7
  • sundials-4.1.0-4.el7

Karma has been reset.

a year ago

This update has been submitted for testing by sagitter.

a year ago

This update has been pushed to testing.

a year ago
User Icon orion commented & provided feedback a year ago
karma

Still broken because sundials2 provides names like 'libsundials2_nvecserial.so.2()(64bit)' instead of 'libsundials_nvecserial.so.2()(64bit)'.

Error: Package: 6:octave-4.4.1-1.el7.x86_64 (@group_scitech-octave4.4)
           Requires: libsundials_nvecserial.so.2()(64bit)
           Removing: sundials-2.7.0-10.el7.x86_64 (@epel)
               libsundials_nvecserial.so.2()(64bit)
           Obsoleted By: sundials2-2.7.0-1.el7.x86_64 (epel-testing)
              ~libsundials2_nvecserial.so.2()(64bit)
Error: Package: 6:octave-4.4.1-1.el7.x86_64 (@group_scitech-octave4.4)
           Requires: libsundials_ida.so.2()(64bit)
           Removing: sundials-2.7.0-10.el7.x86_64 (@epel)
               libsundials_ida.so.2()(64bit)
           Obsoleted By: sundials2-2.7.0-1.el7.x86_64 (epel-testing)
              ~libsundials2_ida.so.2()(64bit)

```

Bodhi is disabling automatic push to stable due to negative karma. The maintainer may push manually if they determine that the issue is not severe.

a year ago

Still broken because sundials2 provides names like 'libsundials2_nvecserial.so.2()(64bit)' instead of 'libsundials_nvecserial.so.2()(64bit)'.

Unversioned libraries conflict without renaming libraries in libsundials2-*

Could we modify Octave to point to libsundials2-*?

It's fine to have the -devel packages with the unversioned .so files conflict (which they should be explicit about). You're removing an existing soname from EL7 which should be avoided if possible, which it is.

It's fine to have the -devel packages with the unversioned .so files conflict (which they should be explicit about). You're removing an existing soname from EL7 which should be avoided if possible, which it is.

Unversioned files are the same in sundials2 and in newer sundials-4.1.0

They cannot be co-installed without changing the library name.

sagitter edited this update.

New build(s):

  • sundials2-2.7.0-2.el7

Removed build(s):

  • sundials2-2.7.0-1.el7

Karma has been reset.

a year ago

This update has been submitted for testing by sagitter.

a year ago

This update has been pushed to testing.

a year ago

Thanks for fixing the sonames. However I don't really have a way of testing much else.

This update can be pushed to stable now if the maintainer wishes

a year ago

This update has been submitted for stable by bodhi.

a year ago

This update has been pushed to stable.

a year ago

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Metadata
Type
enhancement
Severity
low
Karma
0
Signed
Content Type
RPM
Test Gating
Settings
Unstable by Karma
-3
Stable by Karma
3
Stable by Time
14 days
Dates
submitted
2 years ago
in testing
a year ago
in stable
a year ago
modified
a year ago

Automated Test Results