Bug#1120217: marked as done (macs: FTBFS: NameError: name 'long' is not defined)

Sat, 13 Dec 2025 09:55:32 -0800 

Your message dated Sat, 13 Dec 2025 17:52:44 +0000
with message-id <[email protected]>
and subject line Bug#1120217: fixed in openmpi 5.0.9-2
has caused the Debian Bug report #1120217,
regarding macs: FTBFS: NameError: name 'long' is not defined
to be marked as done.

This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.

(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact [email protected]
immediately.)


-- 
1120217: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1120217
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message --- 
Package: src:macs
Version: 3.0.2-1
Severity: serious
Tags: ftbfs forky sid

Dear maintainer:

During a rebuild of all packages in unstable, this package failed to build.

Below you will find the last part of the build log (probably the most
relevant part, but not necessarily). If required, the full build log
is available here:

https://people.debian.org/~sanvila/build-logs/202511/

About the archive rebuild: The build was made on virtual machines from AWS,
using sbuild and a reduced chroot with only build-essential packages.

If you cannot reproduce the bug please contact me privately, as I
am willing to provide ssh access to a virtual machine where the bug is
fully reproducible.

If this is really a bug in one of the build-depends, please use
reassign and add an affects on src:macs, so that this is still
visible in the BTS web page for this package.

Thanks.

--------------------------------------------------------------------------------
[...]
 debian/rules clean
dh clean --buildsystem=pybuild
   debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
rm -Rf test/macs3.0.2-1* test/speedtest*
rm -f debian/*.1 debian/*-man-include
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   dh_autoreconf_clean -O--buildsystem=pybuild
   dh_clean -O--buildsystem=pybuild
 debian/rules binary
dh binary --buildsystem=pybuild
   dh_update_autotools_config -O--buildsystem=pybuild
   dh_autoreconf -O--buildsystem=pybuild
   dh_auto_configure -O--buildsystem=pybuild
   debian/rules override_dh_auto_build

[... snipped ...]

 ... clear!
 checking 
../temp/macs3.0.2-1-3.13_run_callpeak_pe_narrow/run_callpeak_bedpe_narrow.log...
 ... clear!
 checking 
../temp/macs3.0.2-1-3.13_run_callpeak_pe_narrow/run_callpeak_pe_narrow_onlychip.log...
 ... clear!
 checking ../temp/macs3.0.2-1-3.13_run_callvar/run_callvar_PE.log...
 ... clear!
 checking ../temp/macs3.0.2-1-3.13_run_cmbreps/run_cmbreps_fisher.log...
 ... clear!
 checking ../temp/macs3.0.2-1-3.13_run_cmbreps/run_cmbreps_max.log...
 ... clear!
 checking ../temp/macs3.0.2-1-3.13_run_cmbreps/run_cmbreps_mean.log...
 ... clear!
 checking ../temp/macs3.0.2-1-3.13_run_filterdup/run_filterdup.log...
 ... clear!
 checking ../temp/macs3.0.2-1-3.13_run_filterdup/run_filterdup_d.log...
 ... clear!
 checking ../temp/macs3.0.2-1-3.13_run_filterdup/run_filterdup_pe.log...
 ... clear!
 checking ../temp/macs3.0.2-1-3.13_run_filterdup/run_filterdup_pe_d.log...
 ... clear!
 checking ../temp/macs3.0.2-1-3.13_run_hmmratac/run_hmmratac.log...
NameError: name 'long' is not defined
 ... error/warning found!
the log file:
INFO  @ 06 Nov 2025 10:17:21: [119 MB] 
# Command line: hmmratac -i yeast_500k_SRR1822137.bam --hmm-type gaussian -n 
hmmratac_yeast500k --save-training-data --outdir 
../temp/macs3.0.2-1-3.13_run_hmmratac
# Random seed selected as: 10151
# Use --hmm-type to select a Gaussian ('gaussian') or Poisson ('poisson') model 
for the hidden markov model in HMMRATAC. Default: 'gaussian'. 
 
INFO  @ 06 Nov 2025 10:17:21: [119 MB] #1 Read fragments from BAMPE file... 
INFO  @ 06 Nov 2025 10:17:22: [151 MB] 467908 fragments have been read. 
INFO  @ 06 Nov 2025 10:17:22: [151 MB] #2 Use EM algorithm to estimate means 
and stddevs of fragment lengths 
INFO  @ 06 Nov 2025 10:17:22: [151 MB] #  for mono-, di-, and tri-nucleosomal 
signals... 
INFO  @ 06 Nov 2025 10:17:22: [151 MB] # A random seed 10151 has been used in 
the sampling function 
INFO  @ 06 Nov 2025 10:17:22: [151 MB] # Downsampled 24874 fragments will be 
used for EM training... 
Traceback (most recent call last):
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_MACS3/scripts/macs3", line 983, 
in <module>
    main()
    ~~~~^^
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_MACS3/scripts/macs3", line 97, 
in main
    run( args )
    ~~~^^^^^^^^
  File 
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_MACS3/build/MACS3/Commands/hmmratac_cmd.py",
 line 136, in run
    em_trainer = HMMR_EM( petrack, options.em_means[1:4], 
options.em_stddevs[1:4], seed = options.hmm_randomSeed )
  File "MACS3/Signal/HMMR_EM.pyx", line 165, in 
MACS3.Signal.HMMR_EM.HMMR_EM.__init__
  File "MACS3/Signal/HMMR_EM.pyx", line 191, in 
MACS3.Signal.HMMR_EM.HMMR_EM._HMMR_EM__learn
  File "MACS3/Signal/HMMR_EM.pyx", line 227, in 
MACS3.Signal.HMMR_EM.HMMR_EM._HMMR_EM__iterate
NameError: name 'long' is not defined
 checking ../temp/macs3.0.2-1-3.13_run_hmmratac/run_hmmratac_bedpe.log...
NameError: name 'long' is not defined
 ... error/warning found!
the log file:
INFO  @ 06 Nov 2025 10:17:24: [120 MB] 
# Command line: hmmratac -i yeast_500k_SRR1822137.bedpe.gz -n 
hmmratac_yeast500k_bedpe -f BEDPE --outdir ../temp/macs3.0.2-1-3.13_run_hmmratac
# Random seed selected as: 10151
# Use --hmm-type to select a Gaussian ('gaussian') or Poisson ('poisson') model 
for the hidden markov model in HMMRATAC. Default: 'gaussian'. 
 
INFO  @ 06 Nov 2025 10:17:24: [120 MB] #1 Read fragments from BEDPE file... 
INFO  @ 06 Nov 2025 10:17:25: [174 MB] #2 Use EM algorithm to estimate means 
and stddevs of fragment lengths 
INFO  @ 06 Nov 2025 10:17:25: [174 MB] #  for mono-, di-, and tri-nucleosomal 
signals... 
INFO  @ 06 Nov 2025 10:17:25: [174 MB] # A random seed 10151 has been used in 
the sampling function 
INFO  @ 06 Nov 2025 10:17:25: [174 MB] # Downsampled 24874 fragments will be 
used for EM training... 
Traceback (most recent call last):
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_MACS3/scripts/macs3", line 983, 
in <module>
    main()
    ~~~~^^
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_MACS3/scripts/macs3", line 97, 
in main
    run( args )
    ~~~^^^^^^^^
  File 
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_MACS3/build/MACS3/Commands/hmmratac_cmd.py",
 line 136, in run
    em_trainer = HMMR_EM( petrack, options.em_means[1:4], 
options.em_stddevs[1:4], seed = options.hmm_randomSeed )
  File "MACS3/Signal/HMMR_EM.pyx", line 165, in 
MACS3.Signal.HMMR_EM.HMMR_EM.__init__
  File "MACS3/Signal/HMMR_EM.pyx", line 191, in 
MACS3.Signal.HMMR_EM.HMMR_EM._HMMR_EM__learn
  File "MACS3/Signal/HMMR_EM.pyx", line 227, in 
MACS3.Signal.HMMR_EM.HMMR_EM._HMMR_EM__iterate
NameError: name 'long' is not defined
 checking 
../temp/macs3.0.2-1-3.13_run_hmmratac/run_hmmratac_bedpe_poisson.log...
NameError: name 'long' is not defined
 ... error/warning found!
the log file:
INFO  @ 06 Nov 2025 10:17:26: [119 MB] 
# Command line: hmmratac -i yeast_500k_SRR1822137.bedpe.gz --hmm-type poisson 
-n hmmratac_yeast500k_bedpe_poisson -f BEDPE --outdir 
../temp/macs3.0.2-1-3.13_run_hmmratac
# Random seed selected as: 10151
# Use --hmm-type to select a Gaussian ('gaussian') or Poisson ('poisson') model 
for the hidden markov model in HMMRATAC. Default: 'gaussian'. 
 
INFO  @ 06 Nov 2025 10:17:26: [119 MB] #1 Read fragments from BEDPE file... 
INFO  @ 06 Nov 2025 10:17:26: [174 MB] #2 Use EM algorithm to estimate means 
and stddevs of fragment lengths 
INFO  @ 06 Nov 2025 10:17:26: [174 MB] #  for mono-, di-, and tri-nucleosomal 
signals... 
INFO  @ 06 Nov 2025 10:17:26: [174 MB] # A random seed 10151 has been used in 
the sampling function 
INFO  @ 06 Nov 2025 10:17:26: [174 MB] # Downsampled 24874 fragments will be 
used for EM training... 
Traceback (most recent call last):
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_MACS3/scripts/macs3", line 983, 
in <module>
    main()
    ~~~~^^
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_MACS3/scripts/macs3", line 97, 
in main
    run( args )
    ~~~^^^^^^^^
  File 
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_MACS3/build/MACS3/Commands/hmmratac_cmd.py",
 line 136, in run
    em_trainer = HMMR_EM( petrack, options.em_means[1:4], 
options.em_stddevs[1:4], seed = options.hmm_randomSeed )
  File "MACS3/Signal/HMMR_EM.pyx", line 165, in 
MACS3.Signal.HMMR_EM.HMMR_EM.__init__
  File "MACS3/Signal/HMMR_EM.pyx", line 191, in 
MACS3.Signal.HMMR_EM.HMMR_EM._HMMR_EM__learn
  File "MACS3/Signal/HMMR_EM.pyx", line 227, in 
MACS3.Signal.HMMR_EM.HMMR_EM._HMMR_EM__iterate
NameError: name 'long' is not defined
 checking 
../temp/macs3.0.2-1-3.13_run_hmmratac/run_hmmratac_load_hmm_model.log...
NameError: name 'long' is not defined
 ... error/warning found!
the log file:
INFO  @ 06 Nov 2025 10:17:30: [119 MB] 
# Command line: hmmratac -i yeast_500k_SRR1822137.bam -n 
hmmratac_yeast500k_load_hmm_model --model 
../temp/macs3.0.2-1-3.13_run_hmmratac/hmmratac_yeast500k_model.json --outdir 
../temp/macs3.0.2-1-3.13_run_hmmratac
# Random seed selected as: 10151
# Use --hmm-type to select a Gaussian ('gaussian') or Poisson ('poisson') model 
for the hidden markov model in HMMRATAC. Default: 'gaussian'. 
 
INFO  @ 06 Nov 2025 10:17:30: [119 MB] #1 Read fragments from BAMPE file... 
INFO  @ 06 Nov 2025 10:17:31: [153 MB] 467908 fragments have been read. 
INFO  @ 06 Nov 2025 10:17:32: [153 MB] #2 Use EM algorithm to estimate means 
and stddevs of fragment lengths 
INFO  @ 06 Nov 2025 10:17:32: [153 MB] #  for mono-, di-, and tri-nucleosomal 
signals... 
INFO  @ 06 Nov 2025 10:17:32: [153 MB] # A random seed 10151 has been used in 
the sampling function 
INFO  @ 06 Nov 2025 10:17:32: [153 MB] # Downsampled 24874 fragments will be 
used for EM training... 
Traceback (most recent call last):
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_MACS3/scripts/macs3", line 983, 
in <module>
    main()
    ~~~~^^
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_MACS3/scripts/macs3", line 97, 
in main
    run( args )
    ~~~^^^^^^^^
  File 
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_MACS3/build/MACS3/Commands/hmmratac_cmd.py",
 line 136, in run
    em_trainer = HMMR_EM( petrack, options.em_means[1:4], 
options.em_stddevs[1:4], seed = options.hmm_randomSeed )
  File "MACS3/Signal/HMMR_EM.pyx", line 165, in 
MACS3.Signal.HMMR_EM.HMMR_EM.__init__
  File "MACS3/Signal/HMMR_EM.pyx", line 191, in 
MACS3.Signal.HMMR_EM.HMMR_EM._HMMR_EM__learn
  File "MACS3/Signal/HMMR_EM.pyx", line 227, in 
MACS3.Signal.HMMR_EM.HMMR_EM._HMMR_EM__iterate
NameError: name 'long' is not defined
 checking 
../temp/macs3.0.2-1-3.13_run_hmmratac/run_hmmratac_load_hmm_model_poisson.log...
NameError: name 'long' is not defined
 ... error/warning found!
the log file:
INFO  @ 06 Nov 2025 10:17:32: [120 MB] 
# Command line: hmmratac -i yeast_500k_SRR1822137.bam --hmm-type poisson -n 
hmmratac_yeast500k_poisson_load_hmm_model --model 
../temp/macs3.0.2-1-3.13_run_hmmratac/hmmratac_yeast500k_poisson_model.json 
--outdir ../temp/macs3.0.2-1-3.13_run_hmmratac
# Random seed selected as: 10151
# Use --hmm-type to select a Gaussian ('gaussian') or Poisson ('poisson') model 
for the hidden markov model in HMMRATAC. Default: 'gaussian'. 
 
INFO  @ 06 Nov 2025 10:17:32: [120 MB] #1 Read fragments from BAMPE file... 
INFO  @ 06 Nov 2025 10:17:33: [153 MB] 467908 fragments have been read. 
INFO  @ 06 Nov 2025 10:17:33: [153 MB] #2 Use EM algorithm to estimate means 
and stddevs of fragment lengths 
INFO  @ 06 Nov 2025 10:17:33: [153 MB] #  for mono-, di-, and tri-nucleosomal 
signals... 
INFO  @ 06 Nov 2025 10:17:33: [153 MB] # A random seed 10151 has been used in 
the sampling function 
INFO  @ 06 Nov 2025 10:17:33: [153 MB] # Downsampled 24874 fragments will be 
used for EM training... 
Traceback (most recent call last):
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_MACS3/scripts/macs3", line 983, 
in <module>
    main()
    ~~~~^^
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_MACS3/scripts/macs3", line 97, 
in main
    run( args )
    ~~~^^^^^^^^
  File 
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_MACS3/build/MACS3/Commands/hmmratac_cmd.py",
 line 136, in run
    em_trainer = HMMR_EM( petrack, options.em_means[1:4], 
options.em_stddevs[1:4], seed = options.hmm_randomSeed )
  File "MACS3/Signal/HMMR_EM.pyx", line 165, in 
MACS3.Signal.HMMR_EM.HMMR_EM.__init__
  File "MACS3/Signal/HMMR_EM.pyx", line 191, in 
MACS3.Signal.HMMR_EM.HMMR_EM._HMMR_EM__learn
  File "MACS3/Signal/HMMR_EM.pyx", line 227, in 
MACS3.Signal.HMMR_EM.HMMR_EM._HMMR_EM__iterate
NameError: name 'long' is not defined
 checking 
../temp/macs3.0.2-1-3.13_run_hmmratac/run_hmmratac_load_training_regions.log...
NameError: name 'long' is not defined
 ... error/warning found!
the log file:
INFO  @ 06 Nov 2025 10:17:27: [119 MB] 
# Command line: hmmratac -i yeast_500k_SRR1822137.bam -n 
hmmratac_yeast500k_load_training_regions -t 
../temp/macs3.0.2-1-3.13_run_hmmratac/hmmratac_yeast500k_training_regions.bed 
--outdir ../temp/macs3.0.2-1-3.13_run_hmmratac
# Using -t, --training input to train HMM instead of using fold change settings 
to select. 
# Random seed selected as: 10151
# Use --hmm-type to select a Gaussian ('gaussian') or Poisson ('poisson') model 
for the hidden markov model in HMMRATAC. Default: 'gaussian'. 
 
INFO  @ 06 Nov 2025 10:17:27: [119 MB] #1 Read fragments from BAMPE file... 
INFO  @ 06 Nov 2025 10:17:28: [151 MB] 467908 fragments have been read. 
INFO  @ 06 Nov 2025 10:17:28: [151 MB] #2 Use EM algorithm to estimate means 
and stddevs of fragment lengths 
INFO  @ 06 Nov 2025 10:17:28: [151 MB] #  for mono-, di-, and tri-nucleosomal 
signals... 
INFO  @ 06 Nov 2025 10:17:28: [151 MB] # A random seed 10151 has been used in 
the sampling function 
INFO  @ 06 Nov 2025 10:17:28: [151 MB] # Downsampled 24874 fragments will be 
used for EM training... 
Traceback (most recent call last):
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_MACS3/scripts/macs3", line 983, 
in <module>
    main()
    ~~~~^^
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_MACS3/scripts/macs3", line 97, 
in main
    run( args )
    ~~~^^^^^^^^
  File 
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_MACS3/build/MACS3/Commands/hmmratac_cmd.py",
 line 136, in run
    em_trainer = HMMR_EM( petrack, options.em_means[1:4], 
options.em_stddevs[1:4], seed = options.hmm_randomSeed )
  File "MACS3/Signal/HMMR_EM.pyx", line 165, in 
MACS3.Signal.HMMR_EM.HMMR_EM.__init__
  File "MACS3/Signal/HMMR_EM.pyx", line 191, in 
MACS3.Signal.HMMR_EM.HMMR_EM._HMMR_EM__learn
  File "MACS3/Signal/HMMR_EM.pyx", line 227, in 
MACS3.Signal.HMMR_EM.HMMR_EM._HMMR_EM__iterate
NameError: name 'long' is not defined
 checking 
../temp/macs3.0.2-1-3.13_run_hmmratac/run_hmmratac_load_training_regions_poisson.log...
NameError: name 'long' is not defined
 ... error/warning found!
the log file:
INFO  @ 06 Nov 2025 10:17:28: [119 MB] 
# Command line: hmmratac -i yeast_500k_SRR1822137.bam --hmm-type poisson -n 
hmmratac_yeast500k_poisson_load_training_regions -t 
../temp/macs3.0.2-1-3.13_run_hmmratac/hmmratac_yeast500k_poisson_training_regions.bed
 --outdir ../temp/macs3.0.2-1-3.13_run_hmmratac
# Using -t, --training input to train HMM instead of using fold change settings 
to select. 
# Random seed selected as: 10151
# Use --hmm-type to select a Gaussian ('gaussian') or Poisson ('poisson') model 
for the hidden markov model in HMMRATAC. Default: 'gaussian'. 
 
INFO  @ 06 Nov 2025 10:17:28: [119 MB] #1 Read fragments from BAMPE file... 
INFO  @ 06 Nov 2025 10:17:29: [152 MB] 467908 fragments have been read. 
INFO  @ 06 Nov 2025 10:17:30: [152 MB] #2 Use EM algorithm to estimate means 
and stddevs of fragment lengths 
INFO  @ 06 Nov 2025 10:17:30: [152 MB] #  for mono-, di-, and tri-nucleosomal 
signals... 
INFO  @ 06 Nov 2025 10:17:30: [152 MB] # A random seed 10151 has been used in 
the sampling function 
INFO  @ 06 Nov 2025 10:17:30: [152 MB] # Downsampled 24874 fragments will be 
used for EM training... 
Traceback (most recent call last):
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_MACS3/scripts/macs3", line 983, 
in <module>
    main()
    ~~~~^^
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_MACS3/scripts/macs3", line 97, 
in main
    run( args )
    ~~~^^^^^^^^
  File 
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_MACS3/build/MACS3/Commands/hmmratac_cmd.py",
 line 136, in run
    em_trainer = HMMR_EM( petrack, options.em_means[1:4], 
options.em_stddevs[1:4], seed = options.hmm_randomSeed )
  File "MACS3/Signal/HMMR_EM.pyx", line 165, in 
MACS3.Signal.HMMR_EM.HMMR_EM.__init__
  File "MACS3/Signal/HMMR_EM.pyx", line 191, in 
MACS3.Signal.HMMR_EM.HMMR_EM._HMMR_EM__learn
  File "MACS3/Signal/HMMR_EM.pyx", line 227, in 
MACS3.Signal.HMMR_EM.HMMR_EM._HMMR_EM__iterate
NameError: name 'long' is not defined
 checking ../temp/macs3.0.2-1-3.13_run_hmmratac/run_hmmratac_poisson.log...
NameError: name 'long' is not defined
 ... error/warning found!
the log file:
INFO  @ 06 Nov 2025 10:17:23: [119 MB] 
# Command line: hmmratac -i yeast_500k_SRR1822137.bam --hmm-type poisson -n 
hmmratac_yeast500k_poisson --save-training-data --outdir 
../temp/macs3.0.2-1-3.13_run_hmmratac
# Random seed selected as: 10151
# Use --hmm-type to select a Gaussian ('gaussian') or Poisson ('poisson') model 
for the hidden markov model in HMMRATAC. Default: 'gaussian'. 
 
INFO  @ 06 Nov 2025 10:17:23: [119 MB] #1 Read fragments from BAMPE file... 
INFO  @ 06 Nov 2025 10:17:24: [152 MB] 467908 fragments have been read. 
INFO  @ 06 Nov 2025 10:17:24: [152 MB] #2 Use EM algorithm to estimate means 
and stddevs of fragment lengths 
INFO  @ 06 Nov 2025 10:17:24: [152 MB] #  for mono-, di-, and tri-nucleosomal 
signals... 
INFO  @ 06 Nov 2025 10:17:24: [152 MB] # A random seed 10151 has been used in 
the sampling function 
INFO  @ 06 Nov 2025 10:17:24: [152 MB] # Downsampled 24874 fragments will be 
used for EM training... 
Traceback (most recent call last):
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_MACS3/scripts/macs3", line 983, 
in <module>
    main()
    ~~~~^^
  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_MACS3/scripts/macs3", line 97, 
in main
    run( args )
    ~~~^^^^^^^^
  File 
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_MACS3/build/MACS3/Commands/hmmratac_cmd.py",
 line 136, in run
    em_trainer = HMMR_EM( petrack, options.em_means[1:4], 
options.em_stddevs[1:4], seed = options.hmm_randomSeed )
  File "MACS3/Signal/HMMR_EM.pyx", line 165, in 
MACS3.Signal.HMMR_EM.HMMR_EM.__init__
  File "MACS3/Signal/HMMR_EM.pyx", line 191, in 
MACS3.Signal.HMMR_EM.HMMR_EM._HMMR_EM__learn
  File "MACS3/Signal/HMMR_EM.pyx", line 227, in 
MACS3.Signal.HMMR_EM.HMMR_EM._HMMR_EM__iterate
NameError: name 'long' is not defined
 checking ../temp/macs3.0.2-1-3.13_run_pileup/run_pileup_CTRL.bed.log...
 ... clear!
 checking ../temp/macs3.0.2-1-3.13_run_pileup/run_pileup_CTRLPE.bampe.log...
 ... clear!
 checking ../temp/macs3.0.2-1-3.13_run_pileup/run_pileup_CTRLPE.bedpe.log...
 ... clear!
 checking ../temp/macs3.0.2-1-3.13_run_pileup/run_pileup_ChIP.bed.log...
 ... clear!
 checking ../temp/macs3.0.2-1-3.13_run_pileup/run_pileup_ChIPPE.bampe.log...
 ... clear!
 checking ../temp/macs3.0.2-1-3.13_run_pileup/run_pileup_ChIPPE.bedpe.log...
 ... clear!
 checking ../temp/macs3.0.2-1-3.13_run_predictd/run_predictd.log...
 ... clear!
 checking ../temp/macs3.0.2-1-3.13_run_predictd/run_predictd_bampe.log...
 ... clear!
 checking ../temp/macs3.0.2-1-3.13_run_predictd/run_predictd_bedpe.log...
 ... clear!
 checking ../temp/macs3.0.2-1-3.13_run_randsample/run_randsample.log...
 ... clear!
 checking ../temp/macs3.0.2-1-3.13_run_randsample/run_randsample_bampe.log...
 ... clear!
 checking ../temp/macs3.0.2-1-3.13_run_randsample/run_randsample_bedpe.log...
 ... clear!
 checking ../temp/macs3.0.2-1-3.13_run_refinepeak/run_refinepeak_w_ofile.log...
 ... clear!
 checking ../temp/macs3.0.2-1-3.13_run_refinepeak/run_refinepeak_w_prefix.log...
 ... clear!
 Error or Warning can be found! Quit the test!
make[1]: *** [debian/rules:43: override_dh_auto_test] Error 1
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:18: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--------------------------------------------------------------------------------

--- End Message ---
--- Begin Message --- 
Source: openmpi
Source-Version: 5.0.9-2
Done: Alastair McKinstry <[email protected]>

We believe that the bug you reported is fixed in the latest version of
openmpi, which is due to be installed in the Debian FTP archive.

A summary of the changes between this version and the previous one is
attached.

Thank you for reporting the bug, which will now be closed.  If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Alastair McKinstry <[email protected]> (supplier of updated openmpi package)

(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])


-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512

Format: 1.8
Date: Sat, 13 Dec 2025 14:49:55 +0000
Source: openmpi
Binary: libopenmpi-dev libopenmpi40 libopenmpi40-dbgsym openmpi-bin 
openmpi-bin-dbgsym openmpi-common openmpi-doc
Architecture: source arm64 all
Version: 5.0.9-2
Distribution: experimental
Urgency: medium
Maintainer: Debian Science Maintainers 
<[email protected]>
Changed-By: Alastair McKinstry <[email protected]>
Description:
 libopenmpi-dev - high performance message passing library -- header files
 libopenmpi40 - high performance message passing library -- shared library
 openmpi-bin - high performance message passing library -- binaries
 openmpi-common - high performance message passing library -- common files
 openmpi-doc - high performance message passing library -- man pages
Closes: 910251 983600 1094805 1101509 1118105 1120217
Changes:
 openmpi (5.0.9-2) experimental; urgency=medium
 .
   * Drop MA:foreign from openmpi-bin (#1057727)
   * Ditto dropping MA: same from libopenmpi-dev. Closes: #983600
   * Drop obsolete breaks/replaces/conflicts
   * Drop Spurious build-dep on libpsm-infinipath1-dev. Closes: #1101509
   * Add salsa-ci.yml to enable CI automatically
   * Close previously fixed bug: Closes: #910251
   * Updated build_hurd patch from Drew Parsons. Closes: #1120217
   * B-D on sphinx-common for dh_sphinxdoc
   * d/watch now at version 4
   * Re-enable UCX by default in openmpi-mca-params.conf.
     Closes: #1094805
   * openmpi-bin.postinst/prerm: delete obsolete conffiles
   * Enable ucx for loong64. Closes: #1118105
   * openmpi-doc: dep on node-mathjax-full for tex-mml-chtml.js
   * privacy-mathjax.patch: Use local files not web
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--- End Message ---

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