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 --------------------------------------------------------------------------------
