This is a multi-part MIME message sent by reportbug.


Source: ghmm
Version: 0.9~rc3-4
Severity: serious
Tags: patch pending
Justification: library ABI skew on upgrade
User: debian-arm@lists.debian.org
Usertags: time-t

Dear maintainer,

As part of the 64-bit time_t transition required to support 32-bit architectures in 2038 and beyond (https://wiki.debian.org/ReleaseGoals/64bit-time), we have identified
ghmm as a source package shipping runtime libraries whose ABI
either is affected by the change in size of time_t, or could not be
analyzed via abi-compliance-checker (and therefore to be on the safe
side we assume is affected).

To ensure that inconsistent combinations of libraries with their reverse-dependencies are never installed together, it is necessary to
have a library transition, which is most easily done by renaming the
runtime library package.

Since turning on 64-bit time_t is being handled centrally through a change
to the default dpkg-buildflags (https://bugs.debian.org/1037136), it is important that libraries affected by this ABI change all be uploaded close together in time. Therefore I have prepared a 0-day NMU for ghmm
which will initially be uploaded to experimental if possible, then to
unstable after packages have cleared binary NEW.

Please find the patch for this NMU attached.

If you have any concerns about this patch, please reach out ASAP. Although this package will be uploaded to experimental immediately, there will be a period of several days before we begin uploads to unstable; so if information becomes available that your package should not be included in the transition, there is time for us to amend the planned uploads.



-- System Information:
Debian Release: trixie/sid
APT prefers unstable
APT policy: (500, 'unstable')
Architecture: amd64 (x86_64)

Kernel: Linux 6.5.0-14-generic (SMP w/8 CPU threads; PREEMPT)
Kernel taint flags: TAINT_PROPRIETARY_MODULE, TAINT_OOT_MODULE
Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8), LANGUAGE not set
Shell: /bin/sh linked to /usr/bin/dash
Init: systemd (via /run/systemd/system)

ZGlmZiAtTnJ1IGdobW0tMC45fnJjMy9kZWJpYW4vY2hhbmdlbG9nIGdobW0tMC45fnJjMy9kZWJp YW4vY2hhbmdlbG9nCi0tLSBnaG1tLTAuOX5yYzMvZGViaWFuL2NoYW5nZWxvZwkyMDIxLTAxLTI0 IDE5OjI3OjI4LjAwMDAwMDAwMCArMDAwMAorKysgZ2htbS0wLjl+cmMzL2RlYmlhbi9jaGFuZ2Vs b2cJMjAyNC0wMi0wMSAxMDoxMDoxNy4wMDAwMDAwMDAgKzAwMDAKQEAgLTEsMyArMSwxMSBAQAor Z2htbSAoMC45fnJjMy00LjEpIGV4cGVyaW1lbnRhbDsgdXJnZW5jeT1tZWRpdW0KKworICAqIE5v bi1tYWludGFpbmVyIHVwbG9hZC4KKyAgKiBSZW5hbWUgbGlicmFyaWVzIGZvciA2NC1iaXQgdGlt ZV90IHRyYW5zaXRpb24uCisgICogQnVtcCBidWlsZC1kZXBlbmRlbmN5IG9uIGQtc2hsaWJzIGZv ciAtLXQ2NCBzdXBwb3J0LgorCisgLS0gTHVrYXMgTcOkcmRpYW4gPHNseW9uQGRlYmlhbi5vcmc+ ICBUaHUsIDAxIEZlYiAyMDI0IDEwOjEwOjE3ICswMDAwCisKIGdobW0gKDAuOX5yYzMtNCkgdW5z dGFibGU7IHVyZ2VuY3k9bWVkaXVtCiAKICAgKiBUZWFtIHVwbG9hZC4KZGlmZiAtTnJ1IGdobW0t MC45fnJjMy9kZWJpYW4vY29udHJvbCBnaG1tLTAuOX5yYzMvZGViaWFuL2NvbnRyb2wKLS0tIGdo bW0tMC45fnJjMy9kZWJpYW4vY29udHJvbAkyMDIxLTAxLTI0IDE5OjI3OjI4LjAwMDAwMDAwMCAr MDAwMAorKysgZ2htbS0wLjl+cmMzL2RlYmlhbi9jb250cm9sCTIwMjQtMDItMDEgMTA6MTA6MTcu MDAwMDAwMDAwICswMDAwCkBAIC00LDcgKzQsNyBAQAogU2VjdGlvbjogc2NpZW5jZQogUHJpb3Jp dHk6IG9wdGlvbmFsCiBCdWlsZC1EZXBlbmRzOiBkZWJoZWxwZXItY29tcGF0ICg9IDEzKSwKLSAg ICAgICAgICAgICAgIGQtc2hsaWJzLAorICAgICAgICAgICAgICAgZC1zaGxpYnMgKD49IDAuMTA2 KSwKICAgICAgICAgICAgICAgIHB5dGhvbjMtZGV2LAogICAgICAgICAgICAgICAgcGtnLWNvbmZp ZywKICAgICAgICAgICAgICAgIGxpYnhtbDItZGV2LApAQCAtMjQsNyArMjQsNyBAQAogRGVwZW5k czogJHtzaGxpYnM6RGVwZW5kc30sCiAgICAgICAgICAke21pc2M6RGVwZW5kc30sCiAgICAgICAg ICBweXRob24zLAotICAgICAgICAgbGliZ2htbTEKKyAgICAgICAgIGxpYmdobW0xdDY0CiBEZXNj cmlwdGlvbjogR2VuZXJhbCBIaWRkZW4tTWFya292LU1vZGVsIGxpYnJhcnkgLSB0b29scwogIFRo ZSBHZW5lcmFsIEhpZGRlbiBNYXJrb3YgTW9kZWwgTGlicmFyeSAoR0hNTSkgaXMgYSBDIGxpYnJh cnkgd2l0aAogIGFkZGl0aW9uYWwgUHl0aG9uMyBiaW5kaW5ncyBpbXBsZW1lbnRpbmcgYSB3aWRl IHJhbmdlIG9mIHR5cGVzIG9mCkBAIC0zOCw4ICszOCw4IEBACiBTZWN0aW9uOiBsaWJkZXZlbAog RGVwZW5kczogJHtzaGxpYnM6RGVwZW5kc30sCiAgICAgICAgICAke21pc2M6RGVwZW5kc30sCi0g ICAgICAgICBsaWJnaG1tMSAoPj0gJHtzb3VyY2U6VXBzdHJlYW0tVmVyc2lvbn0pLAotICAgICAg ICAgbGliZ2htbTEgKDw8ICR7c291cmNlOlVwc3RyZWFtLVZlcnNpb259KzEpCisgICAgICAgICBs aWJnaG1tMXQ2NCAoPj0gJHtzb3VyY2U6VXBzdHJlYW0tVmVyc2lvbn0pLAorICAgICAgICAgbGli Z2htbTF0NjQgKDw8ICR7c291cmNlOlVwc3RyZWFtLVZlcnNpb259KzEpCiBEZXNjcmlwdGlvbjog R2VuZXJhbCBIaWRkZW4tTWFya292LU1vZGVsIGxpYnJhcnkgLSBoZWFkZXIgZmlsZXMKICBUaGUg R2VuZXJhbCBIaWRkZW4gTWFya292IE1vZGVsIExpYnJhcnkgKEdITU0pIGlzIGEgQyBsaWJyYXJ5 IHdpdGgKICBhZGRpdGlvbmFsIFB5dGhvbjMgYmluZGluZ3MgaW1wbGVtZW50aW5nIGEgd2lkZSBy YW5nZSBvZiB0eXBlcyBvZgpAQCAtNDgsNyArNDgsMTAgQEAKICAuCiAgSGVhZGVyIGZpbGVzIGFu ZCBzdGF0aWMgbGlicmFyeSB0byBjb21waWxlIGFnYWluc3QgdGhlIGxpYnJhcnkuCiAKLVBhY2th Z2U6IGxpYmdobW0xCitQYWNrYWdlOiBsaWJnaG1tMXQ2NAorUHJvdmlkZXM6ICR7dDY0OlByb3Zp ZGVzfQorUmVwbGFjZXM6IGxpYmdobW0xCitCcmVha3M6IGxpYmdobW0xICg8PCAke3NvdXJjZTpW ZXJzaW9ufSkKIEFyY2hpdGVjdHVyZTogYW55CiBTZWN0aW9uOiBsaWJzCiBEZXBlbmRzOiAke3No bGliczpEZXBlbmRzfSwKZGlmZiAtTnJ1IGdobW0tMC45fnJjMy9kZWJpYW4vbGliZ2htbTF0NjQu bGludGlhbi1vdmVycmlkZXMgZ2htbS0wLjl+cmMzL2RlYmlhbi9saWJnaG1tMXQ2NC5saW50aWFu LW92ZXJyaWRlcwotLS0gZ2htbS0wLjl+cmMzL2RlYmlhbi9saWJnaG1tMXQ2NC5saW50aWFuLW92 ZXJyaWRlcwkxOTcwLTAxLTAxIDAwOjAwOjAwLjAwMDAwMDAwMCArMDAwMAorKysgZ2htbS0wLjl+ cmMzL2RlYmlhbi9saWJnaG1tMXQ2NC5saW50aWFuLW92ZXJyaWRlcwkyMDI0LTAyLTAxIDEwOjA5 OjQyLjAwMDAwMDAwMCArMDAwMApAQCAtMCwwICsxIEBACitsaWJnaG1tMXQ2NDogcGFja2FnZS1u YW1lLWRvZXNudC1tYXRjaC1zb25hbWVzIGxpYmdobW0xCmRpZmYgLU5ydSBnaG1tLTAuOX5yYzMv ZGViaWFuL3J1bGVzIGdobW0tMC45fnJjMy9kZWJpYW4vcnVsZXMKLS0tIGdobW0tMC45fnJjMy9k ZWJpYW4vcnVsZXMJMjAyMS0wMS0yNCAxOToyNzoyOC4wMDAwMDAwMDAgKzAwMDAKKysrIGdobW0t MC45fnJjMy9kZWJpYW4vcnVsZXMJMjAyNC0wMi0wMSAxMDoxMDoxNy4wMDAwMDAwMDAgKzAwMDAK QEAgLTE1LDYgKzE1LDcgQEAKIAlkaF9pbnN0YWxsCiAJZmluZCAkKENVUkRJUikvZGViaWFuL3Rt cCAtbmFtZSAiKi5weWMiIC1kZWxldGUKIAlkLXNobGlibW92ZSAtLWNvbW1pdCBcCisJCSAgICAt LXQ2NCBcCiAJCSAgICAtLW11bHRpYXJjaCBcCiAJCSAgICAtLWRldnVudmVyc2lvbmVkIFwKIAkJ ICAgIC0tZXhjbHVkZS1sYSBcCg==

--- SoupGate-Win32 v1.05
* Origin: fsxNet Usenet Gateway (21:1/5)

Dear maintainer,

please note that ghmm seems to FTBFS for a reason unrelated to this NMU:

dh_install
dh_install: warning: Cannot find (any matches for) "usr/lib/python3*/site-packages/*" (tried in ., debian/tmp)

dh_install: warning: ghmm missing files: usr/lib/python3*/site-packages/* dh_install: error: missing files, aborting
make[1]: *** [debian/rules:15: override_dh_install] Error 255
make[1]: Leaving directory '/home/slyon/time_t/ghmm-0.9~rc3'
make: *** [debian/rules:9: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2


The python files seem to be generated in wrong directory (see tree below).

Cheers,
Lukas


slyon@sid-time-t:~/time_t/ghmm-0.9~rc3$ tree debian/tmp/
debian/tmp/
└── usr
├── bin
│   ├── cluster
│   ├── ghmm-config
│   ├── probdist
│   ├── scluster
│   └── smix_hmm
├── include
│   └── ghmm
│   ├── cfbgibbs.h
│   ├── cluster.h
│   ├── discrime.h
│   ├── fbgibbs.h
│   ├── foba.h
│   ├── ghmmconfig.h
│   ├── ghmm.h
│   ├── gradescent.h
│   ├── kbest.h
│   ├── model.h
│   ├── obsolete.h
│   ├── pmodel.h
│   ├── psequence.h
│   ├── pviterbi.h
│   ├── pviterbi_propagate.h
│   ├── reestimate.h
│   ├── rng.h
│   ├── scanner.h
│   ├── scluster.h
│   ├── sdfoba.h
│   ├── sdmodel.h
│   ├── sequence.h
│   ├── sfoba.h
│   ├── sgenerate.h
│   ├── smap_classify.h
│   ├── smixturehmm.h
│   ├── smodel.h
│   ├── sreestimate.h
│   ├── sviterbi.h
│   ├── unsupported.h
│   ├── viterbi.h
│   ├── xmlreader.h
│   └── xmlwriter.h
├── lib
│   └── x86_64-linux-gnu
│   ├── libghmm.a
│   ├── libghmm.la
│   ├── libghmm.so -> libghmm.so.1.0.0
│   ├── libghmm.so.1 -> libghmm.so.1.0.0
│   └── libghmm.so.1.0.0
├── local
│   ├── bin
│   │   └── HMMEd
│   └── lib
│   └── python3.11
│   └── dist-packages
│   ├── ghmmwrapper-0.8-py3.11-linux-x86_64.egg
│   │   ├── class_change.py
│   │   ├── EGG-INFO
│   │   │   ├── dependency_links.txt
│   │   │   ├── native_libs.txt
│   │   │   ├── not-zip-safe
│   │   │   ├── PKG-INFO
│   │   │   ├── SOURCES.txt
│   │   │   └── top_level.txt
│   │   ├── ghmmhelper.py
│   │   ├── ghmm.py
│   │   ├── _ghmmwrapper.cpython-311-x86_64-linux-gnu.so
│   │   ├── _ghmmwrapper.py
│   │   ├── ghmmwrapper.py
│   │   ├── modhmmer.py
│   │   └── __pycache__
│   │   ├── class_change.cpython-311.pyc
│   │   ├── ghmm.cpython-311.pyc
│   │   ├── ghmmhelper.cpython-311.pyc
│   │   ├── _ghmmwrapper.cpython-311.pyc
│   │   ├── ghmmwrapper.cpython-311.pyc
│   │   └── modhmmer.cpython-311.pyc
│   └── HMMEd-0.8-py3.11.egg
└── share
└── ghmm
└── ghmm.dtd.1.0

17 directories, 65 files


-----BEGIN PGP SIGNATURE-----

iQIzBAABCgAdFiEE496GmCL5m2y8NfJ5v322IrMDrIsFAmW7chwACgkQv322IrMD rIu4Ag/+MF3kNsl7p8hcDdqY/a0V2p4ChlOxVNqeLldcO2QHlF2vnDZvmYfsz7Sb JLtjix937z3Hk/TsDouk1E1h104+ifKChdTVx1K5qlMg05m/SIcFo3Z+9q+Cdm0X MYf00jcnfcYSTpo1TmcciLug0c3lRrdPxVAL5nhNcOFZxyNPM7BmhMD6SxXjV1E9 Wght9UFVmJBHkE1Fp1qfB34A/mK0a5QHYmX366JCXf1N1rHx68JSuk2ktwl1g3wl 2WkMor9xbJzv5/8olxP5AckrKtpwRMWeEXZ+sni7LDlhs8yw+3LoVX90RUewPVgw vc2tYFCeMigQkmoQrgrtN/A5/chvtR7sG+++0Txa2SU3WeSJjqe3FLuxu7hxTB83 33PjjO5h7UKsi6wzHY5XaeGkeyRue8Hf+o5XYzV2d7vbj1tRQeCaf/vt4uPb9Dqw 03YkZ8rqZUZ3awac4eBlHhP6E6uRE8vNAS1Qn6vnATvJ/8eJW+SxfsFUiMNzh3Yl eUhBgBJ5oRxLpim6ZYB56h/PV7O8QBwKTE1NmM8cVOHhelTfXBjcvXOsHEVzLbDN dCyRhu+c1yL+6xmtrCE2xJiHo+Sap6DWpccYzR5BzJSCal7XPETVwrGb0XNEylkz clJhPFs8VwuDW6d2L7L4DRN4KmrINhyxgHGp+F2umkDTdquORsY=
=TSee
-----END PGP SIGNATURE-----

--- SoupGate-Win32 v1.05
* Origin: fsxNet Usenet Gateway (21:1/5)

Hi Lukas,

Am Thu, Feb 01, 2024 at 11:27:43AM +0100 schrieb Lukas Märdian:

please note that ghmm seems to FTBFS for a reason unrelated to this NMU:

dh_install
dh_install: warning: Cannot find (any matches for) "usr/lib/python3*/site-packages/*" (tried in ., debian/tmp)

dh_install: warning: ghmm missing files: usr/lib/python3*/site-packages/* dh_install: error: missing files, aborting
make[1]: *** [debian/rules:15: override_dh_install] Error 255
make[1]: Leaving directory '/home/slyon/time_t/ghmm-0.9~rc3'
make: *** [debian/rules:9: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2

The python files seem to be generated in wrong directory (see tree below).

The uploaded package was lagging quite behind packaging in Git. Since I
was able to upload a fixed package to unstable today I applied all your
changes in another upload to experimental which I "sponsored" for you as ghmm_0.9~rc3-5.1~exp.

Hope this contributes a bit to all your huge work for the time_t
transition.

Kind regards and thanks a lot for your work
Andreas.

PS: In case you notice in tracker.debian.org that
"version in VCS is newer than in repository, is it time to upload?"
is set it might be useful to contact the maintainers of the package.

--
http://fam-tille.de

--- SoupGate-Win32 v1.05
* Origin: fsxNet Usenet Gateway (21:1/5)