Bug 1548824

Summary: scipy: Some Python extension modules are linked without BIND_NOW
Product: [Fedora] Fedora Reporter: Florian Weimer <fweimer>
Component: scipyAssignee: Thomas Spura <tomspur>
Status: CLOSED EOL QA Contact: Fedora Extras Quality Assurance <extras-qa>
Severity: unspecified Docs Contact:
Priority: unspecified    
Version: 29CC: cstratak, igor.raits, mhroncok, tomspur
Target Milestone: ---   
Target Release: ---   
Hardware: Unspecified   
OS: Unspecified   
Whiteboard:
Fixed In Version: Doc Type: If docs needed, set a value
Doc Text:
Story Points: ---
Clone Of: Environment:
Last Closed: 2019-11-27 19:02:43 UTC Type: Bug
Regression: --- Mount Type: ---
Documentation: --- CRM:
Verified Versions: Category: ---
oVirt Team: --- RHEL 7.3 requirements from Atomic Host:
Cloudforms Team: --- Target Upstream Version:
Embargoed:
Bug Depends On:    
Bug Blocks: 1539083    

Description Florian Weimer 2018-02-25 10:22:20 UTC
In scipy-1.0.0-7.fc28, this affects:

/usr/lib64/python2.7/site-packages/scipy/fftpack/_fftpack.so
/usr/lib64/python2.7/site-packages/scipy/fftpack/convolve.so
/usr/lib64/python2.7/site-packages/scipy/integrate/_dop.so
/usr/lib64/python2.7/site-packages/scipy/integrate/_odepack.so
/usr/lib64/python2.7/site-packages/scipy/integrate/_quadpack.so
/usr/lib64/python2.7/site-packages/scipy/integrate/_test_odeint_banded.so
/usr/lib64/python2.7/site-packages/scipy/integrate/lsoda.so
/usr/lib64/python2.7/site-packages/scipy/integrate/vode.so
/usr/lib64/python2.7/site-packages/scipy/interpolate/_bspl.so
/usr/lib64/python2.7/site-packages/scipy/interpolate/_fitpack.so
/usr/lib64/python2.7/site-packages/scipy/interpolate/dfitpack.so
/usr/lib64/python2.7/site-packages/scipy/io/_test_fortran.so
/usr/lib64/python2.7/site-packages/scipy/linalg/_fblas.so
/usr/lib64/python2.7/site-packages/scipy/linalg/_flapack.so
/usr/lib64/python2.7/site-packages/scipy/linalg/_flinalg.so
/usr/lib64/python2.7/site-packages/scipy/linalg/_interpolative.so
/usr/lib64/python2.7/site-packages/scipy/linalg/cython_blas.so
/usr/lib64/python2.7/site-packages/scipy/linalg/cython_lapack.so
/usr/lib64/python2.7/site-packages/scipy/odr/__odrpack.so
/usr/lib64/python2.7/site-packages/scipy/optimize/_cobyla.so
/usr/lib64/python2.7/site-packages/scipy/optimize/_lbfgsb.so
/usr/lib64/python2.7/site-packages/scipy/optimize/_minpack.so
/usr/lib64/python2.7/site-packages/scipy/optimize/_nnls.so
/usr/lib64/python2.7/site-packages/scipy/optimize/_slsqp.so
/usr/lib64/python2.7/site-packages/scipy/optimize/minpack2.so
/usr/lib64/python2.7/site-packages/scipy/sparse/linalg/eigen/arpack/_arpack.so
/usr/lib64/python2.7/site-packages/scipy/sparse/linalg/isolve/_iterative.so
/usr/lib64/python2.7/site-packages/scipy/special/_ufuncs.so
/usr/lib64/python2.7/site-packages/scipy/special/cython_special.so
/usr/lib64/python2.7/site-packages/scipy/special/specfun.so
/usr/lib64/python2.7/site-packages/scipy/stats/mvn.so
/usr/lib64/python2.7/site-packages/scipy/stats/statlib.so
/usr/lib64/python3.6/site-packages/scipy/fftpack/_fftpack.cpython-36m-x86_64-linux-gnu.so
/usr/lib64/python3.6/site-packages/scipy/fftpack/convolve.cpython-36m-x86_64-linux-gnu.so
/usr/lib64/python3.6/site-packages/scipy/integrate/_dop.cpython-36m-x86_64-linux-gnu.so
/usr/lib64/python3.6/site-packages/scipy/integrate/_odepack.cpython-36m-x86_64-linux-gnu.so
/usr/lib64/python3.6/site-packages/scipy/integrate/_quadpack.cpython-36m-x86_64-linux-gnu.so
/usr/lib64/python3.6/site-packages/scipy/integrate/_test_odeint_banded.cpython-36m-x86_64-linux-gnu.so
/usr/lib64/python3.6/site-packages/scipy/integrate/lsoda.cpython-36m-x86_64-linux-gnu.so
/usr/lib64/python3.6/site-packages/scipy/integrate/vode.cpython-36m-x86_64-linux-gnu.so
/usr/lib64/python3.6/site-packages/scipy/interpolate/_bspl.cpython-36m-x86_64-linux-gnu.so
/usr/lib64/python3.6/site-packages/scipy/interpolate/_fitpack.cpython-36m-x86_64-linux-gnu.so
/usr/lib64/python3.6/site-packages/scipy/interpolate/dfitpack.cpython-36m-x86_64-linux-gnu.so
/usr/lib64/python3.6/site-packages/scipy/io/_test_fortran.cpython-36m-x86_64-linux-gnu.so
/usr/lib64/python3.6/site-packages/scipy/linalg/_fblas.cpython-36m-x86_64-linux-gnu.so
/usr/lib64/python3.6/site-packages/scipy/linalg/_flapack.cpython-36m-x86_64-linux-gnu.so
/usr/lib64/python3.6/site-packages/scipy/linalg/_flinalg.cpython-36m-x86_64-linux-gnu.so
/usr/lib64/python3.6/site-packages/scipy/linalg/_interpolative.cpython-36m-x86_64-linux-gnu.so
/usr/lib64/python3.6/site-packages/scipy/linalg/cython_blas.cpython-36m-x86_64-linux-gnu.so
/usr/lib64/python3.6/site-packages/scipy/linalg/cython_lapack.cpython-36m-x86_64-linux-gnu.so
/usr/lib64/python3.6/site-packages/scipy/odr/__odrpack.cpython-36m-x86_64-linux-gnu.so
/usr/lib64/python3.6/site-packages/scipy/optimize/_cobyla.cpython-36m-x86_64-linux-gnu.so
/usr/lib64/python3.6/site-packages/scipy/optimize/_lbfgsb.cpython-36m-x86_64-linux-gnu.so
/usr/lib64/python3.6/site-packages/scipy/optimize/_minpack.cpython-36m-x86_64-linux-gnu.so
/usr/lib64/python3.6/site-packages/scipy/optimize/_nnls.cpython-36m-x86_64-linux-gnu.so
/usr/lib64/python3.6/site-packages/scipy/optimize/_slsqp.cpython-36m-x86_64-linux-gnu.so
/usr/lib64/python3.6/site-packages/scipy/optimize/minpack2.cpython-36m-x86_64-linux-gnu.so
/usr/lib64/python3.6/site-packages/scipy/sparse/linalg/eigen/arpack/_arpack.cpython-36m-x86_64-linux-gnu.so
/usr/lib64/python3.6/site-packages/scipy/sparse/linalg/isolve/_iterative.cpython-36m-x86_64-linux-gnu.so
/usr/lib64/python3.6/site-packages/scipy/special/_ufuncs.cpython-36m-x86_64-linux-gnu.so
/usr/lib64/python3.6/site-packages/scipy/special/cython_special.cpython-36m-x86_64-linux-gnu.so
/usr/lib64/python3.6/site-packages/scipy/special/specfun.cpython-36m-x86_64-linux-gnu.so
/usr/lib64/python3.6/site-packages/scipy/stats/mvn.cpython-36m-x86_64-linux-gnu.so
/usr/lib64/python3.6/site-packages/scipy/stats/statlib.cpython-36m-x86_64-linux-gnu.so

I don't see a pattern for the DSOs which use BIND_NOW and those which do not.  These files, next to the others, do use BIND_NOW, for example:

/usr/lib64/python2.7/site-packages/scipy/stats/_stats.so
/usr/lib64/python3.6/site-packages/scipy/linalg/_decomp_update.cpython-36m-x86_64-linux-gnu.so

Comment 1 Miro Hrončok 2018-06-22 20:37:29 UTC
I'm updating scipy to 1.1.0. How do I recheck this?

Comment 2 Florian Weimer 2018-06-23 04:46:25 UTC
(In reply to Miro Hrončok from comment #1)
> I'm updating scipy to 1.1.0. How do I recheck this?

You could run checksec on individual files, or annocheck (from annobin) on the whole RPM.  annocheck is still under heavy development, but its report about BIND_NOW will be accurate at least.

Comment 3 Miro Hrončok 2018-06-23 07:12:06 UTC
Note that I've tried to add LDFLAGS="$RPM_LD_FLAGS" to the build but it failed with ld error (undefined reference to main).

https://koji.fedoraproject.org/koji/taskinfo?taskID=27792463

------


(In reply to Florian Weimer from comment #2)
> You could run checksec on individual files, or annocheck (from annobin) on
> the whole RPM.  annocheck is still under heavy development, but its report
> about BIND_NOW will be accurate at least.

Sorry for dump questions, but you have an exact command and rpm I need?

Nothing provides /usr/bin/checkspec or /usr/bin/annocheck on F28.

Comment 4 Igor Raits 2018-07-21 07:37:38 UTC
any news here?

Comment 5 Jan Kurik 2018-08-14 10:13:49 UTC
This bug appears to have been reported against 'rawhide' during the Fedora 29 development cycle.
Changing version to '29'.

Comment 6 Ben Cotton 2019-10-31 20:52:56 UTC
This message is a reminder that Fedora 29 is nearing its end of life.
Fedora will stop maintaining and issuing updates for Fedora 29 on 2019-11-26.
It is Fedora's policy to close all bug reports from releases that are no longer
maintained. At that time this bug will be closed as EOL if it remains open with a
Fedora 'version' of '29'.

Package Maintainer: If you wish for this bug to remain open because you
plan to fix it in a currently maintained version, simply change the 'version' 
to a later Fedora version.

Thank you for reporting this issue and we are sorry that we were not 
able to fix it before Fedora 29 is end of life. If you would still like 
to see this bug fixed and are able to reproduce it against a later version 
of Fedora, you are encouraged  change the 'version' to a later Fedora 
version prior this bug is closed as described in the policy above.

Although we aim to fix as many bugs as possible during every release's 
lifetime, sometimes those efforts are overtaken by events. Often a 
more recent Fedora release includes newer upstream software that fixes 
bugs or makes them obsolete.

Comment 7 Ben Cotton 2019-11-27 19:02:43 UTC
Fedora 29 changed to end-of-life (EOL) status on 2019-11-26. Fedora 29 is
no longer maintained, which means that it will not receive any further
security or bug fix updates. As a result we are closing this bug.

If you can reproduce this bug against a currently maintained version of
Fedora please feel free to reopen this bug against that version. If you
are unable to reopen this bug, please file a new report against the
current release. If you experience problems, please add a comment to this
bug.

Thank you for reporting this bug and we are sorry it could not be fixed.

Comment 8 Thomas Spura 2020-03-01 21:06:38 UTC
On FC29 there is at least not an error about BIND_NOW, so assuming this is not an issue in recent versions anymore.

Instead there are these failings with annocheck (duplicates were skipped in the output):
$ annocheck /usr/lib64/python3.7/site-packages/scipy/fftpack/_fftpack.cpython-37m-x86_64-linux-gnu.so 
Hardened: _fftpack.cpython-37m-x86_64-linux-gnu.so: fail: (addr range: 0xda40..0xdd75): Insufficient value for -D_FORTIFY_SOURCE: 0.
Hardened: _fftpack.cpython-37m-x86_64-linux-gnu.so: fail: (addr range: 0xda40..0xdd75): Compiled without -D_GLIBCXX_ASSERTIONS.
Hardened: _fftpack.cpython-37m-x86_64-linux-gnu.so: FAIL: Parts of the binary were compiled without -D_FORTIFY_SOURCE=2.
Hardened: _fftpack.cpython-37m-x86_64-linux-gnu.so: FAIL: Parts of the binary were compiled without -D_GLIBCXX_ASSRTIONS.